Abstracts From the 40th Human Genetics Society of Australasia Annual Scientific Meeting Hobart, Tasmania: August 6–9, 2016

Plenary 1
INTEGRATING HIGH THROUGHPUT GENOMIC DIAGNOSTICS WITH HEALTH CARE: GENOMICS ENGLAND

Mark Caulfield

Plenary 2
INTEGRATING GENOMICS INTO CLINICAL PRACTICE: THE AUSTRALIAN GENOMICS HEALTH ALLIANCE

Kathryn North AM ^1,2,3

¹Murdoch Children's Research Institute, Melbourne, VIC, Australia
² Victorian Clinical Genetics Service, Melbourne, VIC, Australia
³ University of Melbourne, Melbourne, VIC, Australia

Next-gen sequencing is already transforming the diagnosis and management of genetic disorders. However, effective integration of this ‘disruptive technology’ into everyday clinical practice will require a whole-of-system approach that builds on existing expertise. In Australia, we also need to overcome the ‘state/federal divide’ in the funding of genetic testing to develop a cohesive national approach that is cost effective and provides equitable access. The Australian Genomics Health Alliance (AGHA) is an NHMRC-funded national network committed to implementing genomic medicine within Australia and providing evidence to inform policy and practice. AGHA comprises 47 partner organisations including the diagnostic pathology and clinical genetics services of all Australian States and Territories, along with the major research and academic institutions and peak professional bodies. By approaching clinical genomics at a national rather than state-based level, we increase our critical mass and offer a single point of contact for government and for national and international consortia. Our approach — starting with the patient and developing a system that is focused on improving patient care and outcomes — provides us with a unique opportunity to lead internationally in the integration of genomics into healthcare.

Plenary 3
INTEGRATING THE GENOME AND THE PHENOME: A NEW PLATFORM FOR HEALTHCARE

Marcel E. Dinger ^1,2

¹Garvan Institute of Medical Research, Sydney, NSW, Australia
² St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia

The use of massively parallel sequencing for accurately diagnosing disease is becoming increasingly routine in clinical practice. As the cost of sequencing continues to decrease, larger numbers of genes are examined as part of a single test. Indeed, it appears inevitable that sequencing costs will reach a point where sequencing the entire genome will be more practical than sequencing subsets of it. Apart from the capability to diagnose greater numbers of diseases in a single test, one of the other repercussions of this trend is that increasing amounts of information become available for understanding the basis of disease for which there is no clear diagnosis. Although this data can be collected at almost no cost, the value of this information can only be fully realized with associated phenotype data. Existing medical information systems are not structured in a manner to allow integration of genomic and phenomic data, and as a result there is currently no means by which to derive new associations between genotype and phenotype from clinical data. In this presentation, I will describe the clinical framework that we are implementing as a pilot at the Kinghorn Centre for Clinical Genomics, which aims to mutually benefit both individual practitioners, through increased diagnostic yields, and researchers, through integrated access to genomic and phenomic information. We propose that this model, the utility of which grows with increasing participation, could be extended into other clinical genetic settings and ultimately become part of a standard platform for healthcare.

Plenary 4
EXPERIENCE FROM 10,000 DIAGNOSTIC EXOMES

Han G. Brunner ^1,2

¹Radboud UMC, Department of Human Genetics, The Netherlands, and Maastricht University Medical Center, Department of Clinical Genetics, the Netherlands
² Han.Brunner@RadboudUMC.nl

We are using exome sequencing in clinical diagnosis for a broad range of diseases. For the year 2016, we expect to run 8,000 diagnostic exome tests. We have reviewed our experience of the first 10,000 exome tests, and find that this has now become an integrated part of modern medical care for patients with rare diseases. After 5 years of experience with exomes in a clinical setting, the following conclusions are drawn:

• • Exomes do better than doctors most of the time.

• • Exomes do not generate large numbers of incidental findings.

• • Incidental findings can be managed by a combination of careful informed consent, targeted analysis where possible, and informed genetic counseling.

• • Genomes do better than exomes, but not much at this point.

• • We do not understand enough of non-coding DNA to allow easy detection of variants that impact disease.

• • We find similar mutations for seemingly distinct neurodevelopmental disorders, suggesting broad clinical heterogeneity, and fueling nosological debate.

• • De novo mutations are an important cause of severe genetic disease in non-consaguineous populations.

Plenary 5
PEDIATRIC GENOMES — TECHNOLOGY, SCIENCE AND EMOTION

Sarah Bowdin

Hospital for Sick Children, Toronto, Canada

The ability to sequence and interpret an individual genome is a technological and scientific breakthrough of massive proportions. Physicians are now introducing this transformative technology to clinical care, which brings huge responsibilities both to our patients and to the healthcare systems within which we operate. In order to pilot the implementation of pediatric genomic medicine, we developed the SickKids Genome Clinic, a multidisciplinary research project that conducts whole genome sequencing (WGS) for children who are undergoing genetic evaluations. WGS was chosen given the potential to capture all classes of genetic variation in one experiment. The Genome Clinic team is composed of clinical geneticists, genetic counselors, molecular and cytogeneticists, ethicists and health economists, with design input from computational medicine and bioinformatics. The clinic allows us to study outcomes beyond the diagnostic rate of WGS, including the impact of actively searching for predictive secondary variants in the pediatric population, healthcare utilization following WGS, and the new work flows demanded by this technology. We have approached 321 families to date, with 54% agreeing to participate. With parents’ permission, we systematically search children's genomes for diagnostic variants that explain the patient's known phenotype and predictive secondary variants (PSVs) associated with occult or future disease. WGS identified genetic variants meeting clinical diagnostic criteria in 34 of the first 100 cases, including four subjects with two distinct genetic diagnoses. Each facet of this study has provided new insights into how WGS can be safely and effectively integrated into clinical medicine, and this talk will highlight the team's most important learning experiences to date.

Plenary 6
RETURN OF RESULTS FOR MYOCILIN GLN368TER

David Mackey

University of Western Australia, Perth, WA, Australia

Aim: Population-based genetic screening for glaucoma is not yet recommended. Screening for glaucoma mutations from array and sequencing data might be viable. Myocilin has been known as a genetic cause of primary open angle glaucoma for nearly 20 years. Cascade genetic screening of other family members is standard of care in families with myocilin glaucoma. The most commonly found mutation in Europeans is Gln368Ter, present in approximately 1/500 people of European ancestry and shows a strong founder effect. We identified a SNP haplotype that could impute the mutation with high sensitivity and specificity. Method: We reviewed the frequency of the founder haplotype in different human populations and the Australian and New Zealand Registry of Advanced Glaucoma (ANZRAG). Results: The haplotype associated with Gln368Ter is common and at similar frequencies across most European populations. Thus imputing Gln368Ter from arrays of European derived cohorts would be viable.Gln368Ter accounts for 25 of 1200 (2%) of advanced glaucoma cases from ANZRAG. Discussion: Myocilin mutations can be identified from whole exome sequencing data and accurately imputed from most GWAS studies. Consideration that these results should be returned to participants is required. The treatable nature of glaucoma and the implications for other family members make this an important consideration if we are to attempt to reduce glaucoma blindness. Given the ‘lack of consent’ in screening clinically for glaucoma, there would appear to be no difference in feeding back this genetic risk to patients who have had a genetic test for any eye disease.

Sutherland Lecture
MEDICINE IN THE TIME OF GENOMICS: FROM DIAGNOSIS TO TREATMENT

Ravi Savarirayan

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, and Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia

Quantum advances have occurred in human genetics since Watson and Crick proposed a structure for the salt of deoxyribose nucleic acid (DNA). These culminated in the human genome project, which opened myriad possibilities, including individualized genetic medicine; medical advice, management, and therapy tailored to a specific genetic constitution. Advances in genetic diagnostic capabilities have been rapid, and the genome can now be sequenced for several thousand dollars. The enhanced ability to molecularly confirm a suspected genetic diagnosis is having profound impacts on clinical medicine for single gene and complex disorders alike. It has allowed further insights into pathogenesis of genetic disease and, crucially, the identification of precision intervention targets. If we are to move swiftly to an era of ‘bespoke’ medicine, it is vital that effective, quick, and robust pathways are established leading from identification of key clinical, biochemical, and molecular hallmarks of a genetic condition to biologically plausible intervention points. This will require effective liaison between clinicians, basic scientists, consumers, funding bodies and industry, and employ animal and cellular models as proof-of-principle with well-designed human clinical trials that include appropriate functional endpoints. This 12th Sutherland lecture will use inherited disorders of cartilage and bone (skeletal dysplasias) as a rare genetic disease template to illustrate the journey from accurate diagnosis and natural history delineation to pathogenesis-based therapies based on animal models, and delivered via human clinical trials. It will also outline research aimed at enabling equitable access to these new disease-modifying and life-changing treatments in all populations, including Indigenous Australians.

Plenary 7
THE RETURN OF MEDICALLY ACTIONABLE SECONDARY FINDINGS IN THE UNITED STATES: WHO GETS TO CHOOSE FOR THE FAMILY?

Allison Werner-Lin ^1,2

¹School of Social Policy and Practice, University of Pennsylvania, Philadelphia, PA, USA
² Acknowledgments: Victoria Miller, PhD, Sarah Walser; Barbara Bernhardt, MS, CGC; Translational Medicine and Medical Genetics, Hospital of the University of Pennsylvania, Philadelphia, PA, USA

For biomedical research involving minors, parental permission replaces consent as the primary way to protect children from potential harm. Adolescent participation via assent, though, is critical to the ethical conduct of biomedical research. Pediatric genomic sequencing challenges classic notions of autonomy and assent because findings may have significant health implications for the teen's family members. Consequently, conventional approaches to achieving consent for health research may be insufficient to the risks, benefits, and possibilities offered by genomic sequencing. This research focused on describing the content of informed consent interactions to discover how best to encourage, support, and nurture adolescent participation in genomic sequencing. Our team offered whole exome sequencing to patients from five pediatric disease cohorts at an urban teaching and research hospital in the United States. Twenty-five adolescents aged 12–19 and their parents completed informed consent sessions with study clinicians. Researchers used grounded theory techniques to analyze session content and processes. Adolescent participants were briefly vocal when asked direct questions. Otherwise, they mostly stayed quiet. Parents functioned as protectors and information-holders, particularly when adolescents felt unprepared to make decisions. Clinicians used proscriptive language to direct families to consider adolescents’ expressed preferences, to balance the interests of multiple caregivers, and to give families time to consider their options before making decisions. In two cases of significant family disagreement, providers maintained a non-directive stance towards all parties, and then excused themselves from intense discussion by deferring decisions to a later date. Adolescents with ongoing health conditions may have complex caregiving relationships with caregivers and clinicians that support dependency during a developmental period marked by an increasing drive towards interdependence. Rather than target adolescent autonomy, enhancing the agency of adolescents in decision making may more appropriately address their needs so that all stakeholders provide input and are respected throughout the informed consent process.

Plenary 8
IMPLEMENTING GENOMICS IN THE CLINIC: A COLLABORATIVE APPROACH

Clara Gaff ^1,2

¹The University of Melbourne, Melbourne, VIC, Australia
² Melbourne Genomics Health Alliance, Melbourne, VIC, Australia

Implementing genomics into healthcare practice requires change across the healthcare system. The Melbourne Genomics Health Alliance is addressing this challenge by taking a collaborative approach across 10 independent healthcare, research and academic organisations and ‘starting with the patient and working backwards’ to embed change. In order to build genomic capability, evaluate the impact of genomic sequencing and identify how it can best be delivered, a 2-year demonstration project was conducted. More than 300 patients were offered whole exome sequencing (WES) in parallel with standard care by clinicians. Patients had one of five clinical indications, enabling condition-specific and common approaches to be identified. Clinicians from six disciplines and genetic counselors provided pre- and post-test counseling. Common systems, tools and policies were developed and applied across the participating hospitals and laboratories. Evaluation data were collected through clinical records, participant surveys and interviews with 32 clinicians and 14 other stakeholders. Impact evaluation included the rate of detection and resulting change in patient management. The evaluation of processes encompassed data sharing, patient selection, consent, genetic counseling and clinical interpretation. The impact of involvement on clinicians was also explored. The results of this comprehensive evaluation are informing implementation of systems locally that meet the needs of both the workforce and patients. Crucial insights will be provided into the aspects of clinical practice which will need to alter to progress the introduction of genomic medicine.

Plenary 9
INTEGRATING GENETICS SERVICES INTO PAEDIATRIC CANCER CARE. WHAT DOES THE FUTURE HOLD?

Claire E. Wakefield ^1,2*, B. C. McGill^1,2, E. J. Doolan^1,2, G. Georgiou^1,2, J. E. Fardell^1,2, C. Signorelli^1,2, K. Tucker^3,4, A. F. Patenaude⁵, R. J. Cohn^1,2

¹Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
² Discipline of Paediatrics, School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Sydney, NSW, Australia
³ Department of Medical Oncology, Prince of Wales Hospital, Sydney, NSW, Australia
⁴ Prince of Wales Clinical School, University of NSW, Sydney, NSW, Australia
⁵ Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Department of Psychiatry, Harvard Medical School, Boston, MA, USA

Background: Little is known about genetic testing, genetics-related beliefs, and acceptability of genetics services in childhood cancer survivors and their parents. This presentation will describe the largest series of genetics services studies undertaken in pediatric oncology in Australia and New Zealand. Method: 1,215 individuals participated (385 survivors, 190 parents, 429 age/rurality-matched young-person controls, 211 parent controls). Participants completed questionnaires and optional interviews. Quantitative data were analysed with SPSS20. Qualitative data were analysed with NVivo11. Results: 7.2% of survivors had been offered cancer-related genetic testing (80% consented). In survivors and their parents, ‘bad luck/chance’ was the most commonly endorsed belief regarding the cause of childhood cancer (71.8%), followed by environmental (30.3%) and then genetic (15.8%) attributions. Controls were more likely to endorse genetic causes (p < .01). Despite endorsing access to genetic services and information as ‘important/very important’, many reported unmet genetics information needs (survivors: 40.3%; parents: 43.1%). Survivors and parents described positive attitudes towards two new genetics technologies (genetic testing to determine survivors’ risk of developing late side effects and using patient-derived xenografts to test potential treatments for newly diagnosed children). Perceived benefits outweighed negatives, and most participants reported that they were willing to pay, and wait, for these services. Conclusion: Childhood cancer survivors and their parents have substantial unmet needs regarding genetics information/services. Though clinical efficacy is yet to be clearly demonstrated, they describe positive interest in new genetics services. Individuals in the general community appear more cautious, possibly because they have not personally experienced the impact of childhood cancer.

Plenary 10
BACK TO THE FUTURE — A PERSONAL REFLECTION OF THE DEVELOPING PROFESSION OF GENETIC COUNSELING IN AUSTRALIA

Margaret Sahhar ^1,2,3

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Murdoch Childrens Research Institute, Melbourne, VIC, Australia
³ Victoria Department of Paediatrics, RCH, Melbourne, VIC, Australia

This presentation is a personal reflection of the experience of developing the profession of genetic counseling in Australia, and subsequently establishing student education at a masters level. Genetic counseling is a relatively new profession first established in the United States in the 1940s. In Australia, the first discussions occurred at HGSA meetings in the 1980s. Several professional groups had an interest in this process, including clinical geneticists, scientists, social workers, and nurses in existing roles in genetic services. The first official meeting occurred in 1989, with the author appointed as ‘a person with counseling expertise’. Official guidelines and certification were developed in 1990. These original guiding principles remain as the key competencies of the profession. From these beginnings, training programs were established — some in house (at the Victorian Clinical Genetics Service), with the first Graduate Diploma of Genetic Counseling established at Newcastle University in 1995. This was followed by the University of Melbourne program, in 1996.The development of this program into a 2-year masters-level program is discussed, with reference to the ongoing challenges of developing curriculum, modes of teaching, and the overall philosophy guiding student education. A glimpse into the future of genetic counseling will be offered.

Plenary 11
NOVEL THERAPIES IN CONGENITAL DISORDERS OF GLYCOSYLATION

Eva Morava ^1,2

¹Tulane University Medical Center, Hayward Genetics Center, New Orleans, LA, USA
² University Hospitals Leuven, Department of Pediatrics, Leuven, Belgium

Although the number of subtypes are exponentially growing, curative treatment is still not available in most types of congenital disorders of glycosylation (CDGs). Oral monosaccharide therapy has been shown to be clinically efficient in different types of this intriguing inborn error of metabolism, including MPI-CDG and SLC35A2-CDG. We evaluated the possible efficiency of monosaccharide therapy using galactose treatment in 16 patients with different types of CDGs evaluating their fibroblasts by glycomics, ICAM1 immunohistochemistry and Western blot analysis. The patients also underwent a dietary protocol of incremental increase of oral galactose treatment with increase of the dosage from 0.5g/kg/day to 1.5g/kg/day every 6 weeks to a maximum dose of 50g/day, followed by clinical and laboratory investigations. Glycane analysis, immunohistochemistry and protein expression of ICAM1 in defective cells confirmed the severe glycosylation defect. Galactose supplementation added to the cell culture led to significant improvement of N-linked glycosylation in 5 days. Galactose concentration between 0.75mEq and 2mEq were the most effective. Higher dose galactose concentrations (5-10 mEq) inhibited glycosylation. The monosugar supplementary therapies affected both ER and Golgi function and increased mannosylation, galactosylation and sialylation in patients both in vitro and in vivo. Laboratory evaluations on oral galactose supplementation showed improving endocrine liver and coagulation parameters during the clinical trial. Galactose was well tolerated, without side effects.

Plenary 12
NOVEL GENOME ENGINEERING TOOLS BASED ON CRISPR-CAS SYSTEM AND THEIR APPLICATION AND INTERSECTION WITH GENOMICS ANALYSIS

Le Cong

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA

Advances in genome sequencing and related technology have led to unprecedented pace at which we can identify genomic and epigenomic changes associated with human health and disease. Nonetheless, due to the vast number of variants under investigation, validating their biological functions and exploring them as potential drug targets remain extremely time and cost consuming. The ability to quickly and accurately assess these candidate variants is essential to the goal of precision medicine. For this purpose, genome editing tools adapted from CRISPR-Cas system can be employed for modifying DNA sequences at genome scale with minimal expenses. I discuss here how genome engineering technology can be deployed as versatile discovery tool. I will focus on the power and precision of novel technology development and describing its potential therapeutic application. In addition, I will highlight the emerging trend on how computational analysis could be integrated with new generation of molecular tools to transform our ability to connect genotype with phenotype for treating human diseases.

Plenary 13
NANOPARTICLE-MEDIATED TRANSFER FOR THE TREATMENT OF MUCOPOLYSACCHARIDOSES

M. Scarpa^1,4,7, M. Salvalaio^1,2, L. Rigon¹, D. Belletti³, F. D'Avanzo^1,4, F. Pederzoli^3,2, B. Ruozi³, O. Marin^5,6, M. A. Vandelli³, F. Forni³, R. Tomanin¹, C. Lampe^4,7, G. Tosi³

¹ Department of Women's and Children's Health, University of Padova, Padova, Italy
² Pediatric Research Institute ‘Città della Speranza’, Padova, Italy
³ Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
⁴ Brains for Brain Foundation-Onlus, Padova, Italy
⁵ Department of Biomedical Sciences, University of Padova, Padova, Italy
⁶ CRIBI Biotechnology Center, University of Padova, Padova, Italy
⁷ Center for Rare Diseases, Helios dr. Horst Schmidt Kliniken, Wiesbaden, Germany

Nanotechnology has represented in the last year a very promising approach for the delivery of therapeutic molecules across the blood-brain barriers. For this reason, we have investigated whether they may be used to contrast the progression of the CNS alterations typical of the neuronopathic phenotype present in patients affected by lysosomal diseases (LSDs). LSDs are a group of metabolic syndromes, each one due to the deficit of one lysosomal enzyme. Many LSDs affect most of the organ systems and overall about 75% of the patients present neurological impairment. Enzyme replacement therapy, although determining some systemic clinical improvements, is ineffective on the CNS disease, due to enzymes’ inability to cross the blood-brain barrier (BBB). With the aim to deliver the therapeutic enzymes across the BBB, we here assayed biodegradable and biocompatible PLGA-nanoparticles (NPs) in two murine models for LSDs, Mucopolysaccharidosis type I and II (MPS I and MPS II). PLGA-NPs were modified with a 7-aminoacid glycopeptide (g7), yet demonstrated to be able to deliver low molecular weight (MW) molecules across the BBB in rodents. We specifically investigated, for the first time, the g7-NPs ability to transfer a model drug (FITC-albumin) with a high MW, comparable to the enzymes to be delivered for LSDs brain therapy. In vivo experiments, conducted on wild-type mice and knockout mouse models for MPS I and II, also included a whole series of control injections to obtain a broad preliminary view of the procedure efficiency. Results clearly showed efficient BBB crossing of albumin in all injected mice, underlying the ability of NPs to deliver high MW molecules to the brain. These results encourage successful experiments with enzyme-loaded g7-NPs to deliver sufficient amounts of the drug to the brain district on LSDs, where exerting a corrective effect on the pathological phenotype.

Plenary 14
LIVER-TARGETED GENE TEHRAPY FOR UREA CYCLE DISORDERS

Ian E. Alexander ¹, S. C. Cunningham¹, N. Sasaki¹, J. Baruteau², P. Gissen³

¹Gene Therapy Research Unit, The Children's Hospital at Westmead and Children's Medical Research Institute, Sydney, NSW, Australia
² Department of Maternal & Fetal Medicine
³ MRC Laboratory of Molecular Cell Biology, University College London, London, UK

Exciting developments in AAV vector technology and success in the treatment of neonatal lethal urea cycle defects in mice (OTC and ASS deficiency) by gene therapy, bode well for human translation. As with all gene therapy trials, potential success is fundamentally dependent upon accurately approximating the reach of the chosen gene transfer technology with the demands imposed by the pathophysiology of the target disease and biology of the target organ. Experimental studies of liver-targeted gene therapy in urea cycle deficient mice, mathematical modeling and lessons from nature provide insight into the gene transfer efficiencies required, and suggest that the hepatocyte transduction levels needed for therapeutic benefit in severe OTC deficiency could be in the order of 20%. This target is plausibly achievable with emerging AAV vector technology, but will require careful vector optimization, including selection of the most human tropic capsid available. In the developing liver, loss of episomal vector genomes over time, as a consequence of hepatocellular proliferation, will also need to be considered in configuring an early phase trial. While potentially subject to debate, a ‘bridge- to-transplant’ trial for infants and children with severe disease ffers a realistic prospect of therapeutic benefit while accommodating possible risks.

Plenary 15
DEVELOPMENT OF NOVEL GENETIC THERAPIES FOR HAEMOGLOBIN DISORDERS

Jim Vadolas ^1,2, Astrid Glaser^1,2, Bradley McColl^1,2

¹Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia

The β-thalassemias, sickle cell disease (SCD) and hemoglobin E (HbE) disease represent the most important hemoglobinopathies from a clinical point of view, causing severe morbidity and mortality worldwide. Current standard of care involves life-long regular blood transfusions and iron chelation therapy to reduce iron toxicity. The transfer of gene-corrected autologous hematopoietic stem cells (HSCs) could provide a therapeutic alternative, as recent lentiviral gene therapy trials have demonstrated. The greatest caveat in the use of integrating lentiviral vectors lies in the inability to control the site of integration, which can potentially cause genotoxicity. This issue has driven the search for safer gene therapy approaches. One possible solution is to target the integration of a therapeutic gene into a genomic ‘safe harbour’ site that supports long-term transgene expression. Alternatively, genome editing could be used to correct patient HSCs ex vivo. Ideally, correction of the β-globin gene in HSCs could be achieved through homology-directed repair (HDR), resulting in the production of healthy erythrocytes. Several studies including work from our group have shown that the human β-globin locus is amenable to genome editing. However, technical limitations and safety concerns need to be overcome for this novel approach to become clinically feasible. Here, we highlight recent developments and important new directions in β-thalassemia and SCD gene therapy.

HGSA Oration
LINKS AND SECOND CHANCES

Agnes Bankier

Royal Childrens Hospital Human Research Ethics Committee, Royal Children's Hospital, Melbourne, VIC, Australia

This year we celebrate 40 years of the HGSA. I have been privileged to share 35 of those years, in many leadership roles. This period has seen exciting advances in human genetics. Parallel with these has been the development of clinical and diagnostic genetic services, emergence of clinical geneticists and genetic counselors as recognised professions, and a broad range of ethical and translational challenges from scientific discovery to clinical practice. The growth and maturity of the HGSA, its special interest groups, accreditation bodies and advisory groups have paralleled this development. As Honorary Archivist to the HGSA, it has been a joy to review the original documents and see how much we achieved. The Oration has been an opportunity to also reflect on my genetic journey and my time as Director of the VCGS. Victoria, through the vision of the late David M. Danks and development of clinical services by John G. Rogers and others, led the way, training the first clinical geneticists in Australia. This year we celebrated 40 years of newborn screening. We could also celebrate the advances in our diagnostic services and Possum. Possum has been a great project. Developed in 1984 as an aid for the diagnosis of children with patterns of birth defects, it was the first to combine computerized information linked to images on a videodisc. Its early development was very exciting. Over the past 30 years Possum has undergone several technological transformations. Now web-based, Possum is known and valued internationally. And second chances? That is about opportunity and gratitude . . . to be elaborated.

Plenary 16
APPLICATION OF DISEASE REGISTRIES IN CLINICAL PRACTICE AND RARE DISEASE RESEARCH

John McNeil

Monash University, School of Public Health and Preventive Medicine, Melbourne, VIC, Australia

Clinical registries have been established across a range of diseases in order to monitor quality of care, establish the safety of drugs devices and new interventions, and to support research. In the case of rare diseases registries are particularly valuable because they provide information about the epidemiology of a condition, and to facilitate various forms of clinical research. The essential feature of a clinical registry is the collection of an identical dataset from patients at each site where they are treated. Typically, the enduring data is kept to a minimum but additional information is added when necessary, typically for a limited time or from a minority of specialist hospitals. Another common feature is the systematic collection of outcome data at identical times after treatment using standard definitions. The data is sent to a central custodian responsible for amalgamating and interpreting the information. Registries are increasingly focusing on the collection of biomarkers at the time of registration. These samples are important for the identification of new markers of prognosis or of response to treatment. They are also being seen as a potential infrastructure for clinical trials. In this way registries are starting to provide a ‘missing link’ that will enable more rapid evaluation and approval of new drugs and other treatments. Despite the obvious value of registries for facilitating clinical research, the success of new registries depends particularly on matters such as governance and funding models. In this presentations, these issues will be discussed in detail, accompanied by an update on progress with rare disease registries in the United States, United Kingdom, and Europe.

Plenary 17
INTERNATIONAL PEDIATRIC SURVEILLANCE UNITS CONTRIBUTING TO RARE DISEASE REGISTRIES

Yvonne Zurynski

Australian Paediatric Surveillance Unit and the Discipline of Paediatric and Adolescent Medicine, The University of Sydney, Sydney, NSW, Australia

There are 11 pediatric surveillance units across the world, dedicated to collecting population-based data about children with rare diseases. Together, they form the International Network of Paediatric Surveillance Units (INoPSU). Each national unit collects cases diagnosed according to standardised criteria and protocols including diagnostic features, complications, treatments and outcomes. We estimate that a total of 12,000 pediatricians and child health specialists across the 11 units by responding to monthly surveillance report cards that list selected rare childhood diseases. This surveillance methodology has been adapted in some countries to include a patient consent process to support disease registries; for example, Australian Rett Syndrome Registry (Aussie-Rett), British Paediatric Orphan Lung Diseases (BPOLD) registry, Australian Registry Network for Orphan Lung Diseases (ARNOLD), the Portuguese Cerebral Palsy Register. The Australian Paediatric Surveillance Unit is currently working towards establishing a registry for fetal alcohol spectrum disorders. Detailed registry data including demographics, diagnostic features and tests, treatment and outcomes are collected for each case via a secure online portal. Cases are reported prospectively, by specialist clinicians, according to standardized case definitions, to ensure high level of data quality, timeliness and completeness. There is potential for data sharing and comparisons internationally, and the registry platforms, once established, can support basic research, clinical research, longitudinal studies and clinical trials. There is also potential for data linkage with other data collections to assess educational outcomes, economic impact and social inclusion.

Plenary 18
REGISTRIES FOR RARE RESPIRATORY DISEASES

Adam Jaffe ¹

¹School of Women's and Children's Health, Faculty of Medicine, UNSW Medicine, Sydney, NSW, Australia

In Australasia, there is limited capacity to measure the impact heath care makes on the outcomes of patients with rare respiratory diseases in line with best evidence. Clinical registries for patients with rare respiratory diseases enable a systematic approach to serve a scientific, clinical or policy purpose. There is a growing interest in the use of clinical quality registries for rare respiratory diseases in Australasia. These registries may be single disease focused — for example, the Australian Cystic Fibrosis Data Registry (ACFDR), the Australian Idiopathic Pulmonary Fibrosis Registry and the Australian Bronchiectasis Registry — or focused on gathering prevalence data on multiple rare respiratory diseases — for example, the Australasian Registry Network for Orphan Lung Disease (Casamento et al., 2016 Journal of Rare Diseases, 11:42). Single disease registries, such as the ACFDR, allow detailed analysis of health outcomes of patients with CF in Australia and are published annually. Recently, the health outcomes of each CF center have been published transparently, thus allowing intercenter comparisons, as well as international benchmarking (Martin et al, 2012, Pediatrics 129: e348-345). This transparent benchmarking has resulted in quality improvement projects that have significantly improved the health outcomes of people with CF. Furthermore, these registries enable national research studies. Like all registries, barriers such as gaining ethical consent across multiple jurisdictions need to be streamlined as well as overcoming IT barriers through the development of user-friendly interfaces and ensuring that databases are relational and linked. The harmonization of data in international registries will allow international comparisons and collaborative research opportunities that will benefit our patients.

Plenary 19
THE AUSTRALIAN CONTRIBUTION TO THE EU FRAMEWORK 7 PROJECT RD-CONNECT: REGISTRIES, BIOBANKS AND CLINICAL BIOINFORMATICS

Matthew Bellgard ^1,2

¹Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia
² Western Australian Neuroscience Research Institute, Perth, WA, Australia

RD-Connect is a global infrastructure initiative linking up databases, registries, biobanks and clinical bioinformatics data used in rare disease for researchers worldwide. RD-Connect is a 6-year initiative, funded through the European Union, connecting researchers across the world, with the aim of developing an integrated research platform in which complete clinical profiles are combined with omics data and sample availability for rare disease research; in particular, research funded under the International Rare Diseases Research Consortium (IRDiRC). In this talk, I will provide an overview of the work undertaken by the Australian consortium for the EU RD Connect project, funded through the NH&MRC. This work spans patient registries, phenotypying, linking biobanks, a bioinformatics workflow to enable integrative omics analysis, as well as 3D facial analysis.

Plenary 20
DISEASE REGISTRIES AND THE HUMAN VARIOME

Ingrid Winship ^1,2

¹Melbourne Health, Melbourne, VIC, Australia
²University of Melbourne, Office for Research, Royal Melbourne Hospital, Melbourne, VIC, Australia

Convergence of the contributions of engineers, mathematicians, ethicists, lawyers, informaticians, scientists and medical researchers with the community stakeholders will help to frame the research questions and find the answers. Registries are a significant resource to facilitate research and provide options for participation. An example of this is the registry for hereditary hemorrhagic telangiectasia (HHT), where health and clinical information from patients diagnosed with HHT are provided by participants to create economies of scale. This platform enables consideration of the needs of the HHT population, and facilitates international clinical trials. Multiple high penetrance gene mutations in adult onset genetic disorders have proven clinical validity and utility. The identification of mutations in disease causing or predisposing genes may be used in a preventive role, where at-risk unaffected family members can be tested for a pathogenic family specific mutation, thus personalising risk assessment and risk management. Accurate assignment of pathogenicity of variants is essential for clinical use. International collaborations such as The Human Variome Project and the Global Alliance for Genomic Health, in conjunction with substantial international databases, LOVD and Clinvar, have created the platform for sharing on a global scale and thus determination of genetic variation across many disease related genes and most populations. In the Australian context, where the population is increasingly heterogeneous, this knowledge will serve to realize the full potential of genomics in enhancing healthcare services for our communities.

Plenary 21
HUMAN VARIOME PROJECT — AUSTRALIA — ROAD MAP TO 2020

Vincent Harley

Human Variome Project Australian node (HVPA) Hudson Institute of Medical Research, Melbourne, VIC, Australia

Rates of variant annotation are falling well behind rates of variant discovery. Some 85% of variants are rare with no listed effect and limited validation. For the phenotype observed in an individual, there is often insufficient evidence for association with the variants found. Sharing of variants from unsolved cases is therefore an essential endeavor. With NGS moving into a service setting, most human genetic variants will be detected in a diagnostic context. Genetic variants will become part of a patient's medical record, and annotating variation in the human genome gives hope for complex disorders, cancer predispositions, and so on. The HVP goal is to increase information about clinically validated and classified genomic variants available in open curated databases, through effective partnering and data sharing globally. HVP has over 1,200 consortium members and 60 data provider members. The aim of the HVP-A is to capture human genome variant data from Australian clinical genetics diagnostics laboratories primarily and researchers. HVPA provides a national data sharing facility for improving clinical genetic testing services and supporting medical research. Data that has been recorded in a pathology report is submitted by diagnostic laboratories via software provided by HVPA. This allows users to check whether the same variants or patients with related phenotypes have been seen previously by other laboratories. HVPA seeks to build capacity. Variant annotation and interpretation continues to be a challenge; examples from the NHMRC program on Disorders of Sex development will be given. Established linkages to existing resources such as ClinVar and LOVD will be discussed.

Concurrent Session 1: Australasian Society of Genetic Counsellors

ASGC Oral 1
REFLECTIONS ON THE INTRODUCTION OF A GENETIC STEWARDSHIP GATEKEEPING PROGRAM

Lucinda Freeman ¹, Yemima Berman¹, Vivienne Schiavone¹, Sondy Ghedia¹

¹Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia

While genetic tests are not new, their complexity has grown over the past decade with the advent of technologies such as NGS and WGS. This has opened up genetic testing to a wide range of disciplines within the hospital as clinicians from non-genetic fields wish to use genetic testing to diagnose and manage their patients. With the significant and increasing cost implications of specialized genetic testing, it has proven necessary to implement some fiscal responsibility within the Northern Sydney Local Health District. In this study, we describe the effectiveness of a gatekeeping process for specialised genetic testing. This process involves all overseas genetic tests and multigene panels ordered by clinicians outside the Genetics Department. The aim of the process is to provide education for clinicians and increase clinical benefit for patients. The process of overseeing the ordering of genetic tests across all disciplines within the area of health service also allows for reflection on clinical utility of each test ordered. By analyzing the referral indications and requests by clinicians, we will describe a shift in clinician knowledge reflected in their test requisitions. We also show a change in clinician behavior coming into line with NSW Health policy on prioritization of genetic testing. The audit has also allowed for the elucidation of clinical scenarios highlighting the clinical utility of this process.

ASGC Oral 2
AN EXPLORATION OF AUSTRALASIAN GENETIC COUNSELORS’ ATTITUDES TOWARDS COMPASSION FATIGUE, MINDFULNESS AND GENETIC COUNSELING

Matthew Burgess ¹, Geneieve Tai², Nathalie Martinek², Melody Menezes^2,3, Martin Delatycki^1,2

¹Austin Hospital, Melbourne, VIC, Australia
² Murdoch Childrens' Research Institute, Melbourne, VIC, Australia,
³ Monash Ultrasound for Women, Monash IVF, Melbourne, VIC, Australia

Aim: To collect information about the experiences of Australasian genetic counselors in relation to compassion fatigue and mindfulness. Method: An online questionnaire open to Australasian genetic counselors. The first part collected demographic information. The second part was the Professional Quality of Life Scale, Compassion Satisfaction and Fatigue Subscales — Revision IV. The final part was the Mindful Attention Awareness Scale. Both scales are validated. Results: 99 genetic counselors completed the survey. There was a significant positive correlation between genetic counselors having a high level of compassion satisfaction and a high level of mindfulness (r = .40, p < .01). There was a significant negative correlation between genetic counselors having high levels of compassion fatigue and low levels of mindfulness (r = -.52, p < .01). There is a significant positive correlation between genetic counselors feeling high levels of burnout and compassion fatigue (r = .58, p < .01). Individuals working in adult, prenatal and cardiac clinics have higher compassion fatigue (CF) and burnout (BO) scores than the other genetic counselors who answered the survey working in other areas of clinical genetics. (adult, CF, p = .049, BO, p = .044; prenatal, CF, p = .01, BO, p < .01; cardiac, CF, p = .04, BO, p < .01). Individuals that are currently experiencing compassion fatigue have higher compassion fatigue (p = .03) and burnout (p = .01) scores compared to those that do not. Conclusion: The results may have implications for the training of genetic counselors. There may also be implications for how genetic counselors work in various clinics thus helping reduce levels of compassion fatigue. Mindful awareness training may help reduce levels of compassion fatigue and burnout.

ASGC Oral 3
FOETAL SEX CHROMOSOME DETECTION DURING EARLY PREGNANCY VIA NON INVASIVE PRENATAL TESTING (NIPT)

Justine Elliott ¹, Alison Archibald^1,2,3, Katrina Scarff¹, Nicola Flowers¹, David Amor^1,2,3,4, Mark Pertile^1,2

¹Victorian Clinical Genetics Services (VCGS), Melbourne, VIC, Australia
² Murdoch Childrens Research Institute, Melbourne, VIC, Australia
³ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁴ Royal Children's Hospital, Melbourne, VIC, Australia

Sex chromosome detection via non-invasive prenatal testing (NIPT) raises a number of genetic counseling issues, including the ethics of reporting fetal sex in early pregnancy, detection of unexpected maternal mosaicism, reporting of high risk results where there is a high false positive rate and detection of mild conditions where there may be minimal clinical effect. In April 2015, Victorian Clinical Genetics Services launched percept™, an Australian-based NIPT service that reports fetal sex and sex chromosome aneuploidies (SCAs) in addition to common trisomies. An audit of the first 5,000 percept™ samples revealed that 44 of 128 (34%) high risk results involved SCAs. Of these, 28 were high risk for monosomy X, of which 5/19 (26%) were confirmed following diagnostic testing, including 2 cases of true foetal mosaicism for cell lines involving normal or structurally abnormal Y chromosomes. There were 14 false positive results, 2 of which were associated with confined placental mosaicism. Incidental findings of maternal 45,X mosaicism were recorded in 4 cases. Diagnostic confirmation was unavailable for 5 pregnancies. Cytogenetic confirmation rates were higher for 16 remaining SCAs with 7/9 cases diagnosed (2/3 XXX; 2/3 XXY and 3/3 XYY). The false positive XXY was confirmed as a maternal Y chromosome CNV in a female foetus. Diagnostic testing was either declined or unavailable for 7 patients. These results highlight the importance of pre- and post-test genetic counseling and have prompted the development of educational resources for health professionals and patients to help facilitate understanding of high risk NIPT results.

ASGC Oral 4
SHOULD NON-INVASIVE PRENATAL TESTING FOR SEX CHROMOSOME ANEUPLOIDIES (SCA) BE OPTIONAL? A CLINICAL AUDIT OF 5,409 MIXED-RISK PREGNANCIES

Melody Menezes ^1,2, Samantha Ayres ¹

¹Monash Ultrasound for Women, Epworth Centre, Melbourne, VIC, Australia
² Murdoch Childrens Research Institute, Melbourne, VIC, Australia

Non-invasive prenatal testing (NIPT) technologies allow couples to screen for sex chromosome aneuploidies (SCA) from as early as 10 weeks gestation. However, detection rates associated with SCA screening remain unknown. Monash Ultrasound for Women has offered NIPT since March 2013. All women have pre-test genetic counseling where SCA screening is discussed with the use of a counseling aid developed in house. SCA screening is offered as an optional panel to all patients. The objective of this study was to analyze the uptake of SCA screening among women who had HarmonyTM NIPT and determine the performance of NIPT for SCA in our sample population. Statistical analysis was performed using descriptive statistics and chi-square analysis. Data from 5409 mixed-risk women who had NIPT between March 2013 and December 2015 was performed. 17% of women overall declined SCA screening following genetic counseling. Of those who had SCA screening, 33 received a high-risk assessment: 3/33 true positives, 10/33 false positives, 20/33 declined further testing with the view to test the fetus at birth. The false positive rate for the SCA panel was significantly higher than the false positive rates for the autosomal aneuploidies. We will present the findings of this audit in detail, and discuss our experience of offering SCA screening as optional aspect of NIPT. Given the high rate of women declining SCA screening and the low number of true positive results observed on our sample, we conclude that SCA screening should continue to be offered as an optional aspect of NIPT.

ASGC Oral 5
DEVELOPMENT OF A SHARED CLINICAL EXOME SEQUENCING CONSENT FORM ACROSS MULTIPLE ORGANISATIONS

Ivan Macciocca ^1,2,3, Zornitza Stark^1,3, Damien Bruno^1,3, Jessica Taylor⁴, SW White^1,3,5, TY Tan^1,3,5, GR Brett^1,2,3, Emma Creed^2,4, Elly Lynch², Community Advisory Group², Alon Januszewicz⁶, Clara Gaff^2,5,7

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
³ Murdoch Childrens Research Institute, Melbourne, VIC, Australia
⁴ Royal Melbourne Hospital, Melbourne, VIC, Australia
⁵ University of Melbourne, Melbourne, VIC, Australia
⁶ Health Legal, Melbourne, VIC, Australia
⁷ Walter and Eliza Hall Institute, Melbourne, VIC, Australia

Introduction: Informed consent for exome sequencing poses new challenges due to the complexity of the test and the many opportunities for data sharing post-test. As part of the Melbourne Genomics Health Alliance (www.melbournegenomics.org.au), a shared clinical exome sequencing consent form was developed for clinical services and testing laboratories embedded within the 10 partner organisations of the Alliance. Method: A working group of representatives from laboratory genetics, medical genetics and genetic counseling from partner organizations was convened to develop the consent form. Consensus was reached on key elements of the form, following review of literature and selected local and international clinical consent forms for exome sequencing. Early consumer input was achieved through the Melbourne Genomics Community Advisory Group. The documents were refined over 10 months and subjected to independent legal review. Outcomes and conclusion: The outcome was a single page consent form for singleton or trio analyses supported by a series of information sheets describing genomic sequencing and providing an explanation of the points that patients agree to in the consent form. To date, the consent form has been adopted by two Alliance laboratories and one clinical department and will be used to consent more than 500 patients from five hospitals over the next 2 years. Up-skilling of health professionals on the use of the consent form is ongoing. A collaborative approach to the development of an exome sequencing consent form is achievable, enabling a standardized approach to consent across multiple organizations, and facilitating data sharing in an ethically acceptable manner.

ASGC Oral 6
PERCEPTIONS OF AUTHENTICITY AND TRUST: INFORMATION-SEEKING ABOUT PERSONAL GENOMICS BY THE AUSTRALIAN PUBLIC

Chriselle Hickerton ^1,2, Jacqueline Savard³, Bronwyn Terrill⁴, Erin Turbitt^1,2, Ainsley Newson³, Clara Gaff^2,5, Kathleen Gray², Anna Middleton⁶, Brenda Wilson⁷, Sylvia Metcalfe^1,2

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² The University of Melbourne, Melbourne, VIC, Australia
³ The University of Sydney, Sydney, NSW, Australia
⁴ Garvan Institute of Medical Research, Melbourne, VIC, Australia
⁵ The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
⁶ Wellcome Trust Sanger Institute, United Kingdom
⁷ University of Ottawa, Ontario Canada

Background: Personal genomics provides the public with access to diverse personal genomic tests, often online. Personal genomic testing provides healthy individuals with access to their own genetic makeup for purposes that include ancestry, paternity, sporting ability and health. These tests are increasingly becoming accessible to all Australians but little is known about their perspectives. Aim: To explore Australians’ awareness of personal genomic testing. Methods: Stage 1 of a multi-staged project involved seven focus groups with 56 members of the public who were allocated into three age groups: 18–25, 26–49 and ≥50 years. Three researchers coded transcripts independently and themes were generated. Results: Here we present themes focusing on awareness of personal genomic testing, information seeking, and trust in the companies offering these tests. Most were not familiar with the term ‘personal genomic testing’, but could deduce what ‘personal genomics’ might entail. Participants in the focus groups identified similar modes of information-seeking behavior, including online resources, talking to health professionals, or consulting friends whom they believe are knowledgeable. Their perceptions of reliable sources of information about personal genomic testing included observing repeated occurrences of same/similar information, irrespective of authenticity of source, and valuing promotion by ‘celebrities/experts’. However, most were unclear how they could verify the authenticity of the information they received and/or found. Conclusion: Findings highlighted ways in which participants seek information regarding personal genomics, including challenges they face when seeking accurate, reliable and trustworthy information. This has implications for clinical practice, lifestyle choices and education if people trust misinformed sources.

Concurrent Session 2: Australasian Society for Inborn Errors of Metabolism

ASIEM Oral 1
THE USE OF TANDEM MASS SPECTROMETRY IN NEWBORN SCREENING

Veronica Wiley ¹, Tiffany Wotton¹, WonTae Kim¹, Rosie Junek¹

¹NSW Newborn Screening Programme, Sydney, NSW, Australia

Electrospray ionisation tandem mass spectrometry, which has been used in NSW since 1998, has now been incorporated in many newborn-screening programs worldwide. There have been many changes in methodology to prospectively screen newborns for inborn errors of amino acids, fatty acid oxidation and organic acidurias. However despite many attempts to harmonise its introduction, it remains the responsibility of each program to determine which disorders are screened, what sample to use, and what is acceptable performance. For each analyte tested there is sample, analytical and interpretative considerations. Sample aspects include the optimal time of collection after birth, the effect of feed status and gestational age. Analytical considerations include the instrumentation, sample preparation, establishing action limits, normal percentiles and expected results for proven positives as well as appropriate quality assurance protocols. The follow-up algorithms for diagnosis, which may include ratios of analytes or second tier testing on the initial sample as well as additional samples of urine and blood, need to optimize the performance metrics of resample rate, sensitivity, specificity and positive predictive value. Using various MSMS protocols since 1998, we have screened samples collected at 48–72 hours of age from 1.8 million babies, request further samples from 0.15%, and detect a disorder in 1:2691 babies with a sensitivity, specificity and positive predictive value which are currently 99%, 99.9% and 25% respectively. The use of tandem mass spectrometry in newborn screening is expanding to include many other disorders. The challenge remains whether disorders should be included because it is possible.

ASIEM Oral 2
THE NATURAL HISTORY OF ELEVATED TETRADECENOYL-L-CARNITINE DETECTED BY NEWBORN SCREENING IN NEW ZEALAND: IMPLICATIONS FOR VERY LONG CHAIN ACYL-COA DEHYDROGENASE DEFICIENCY SCREENING AND TREATMENT

Callum Wilson ¹, Emma Glamuzina^1,2, Bryony Ryder¹, Detlef Knoll¹, Donald Love³, Phillip Shepherd⁴, Jennifer Love³, Peter Reed⁵, Mark de Hora², Dianne Webster²

¹National Metabolic Service, Starship Children's Hospital, Auckland, New Zealand
² Newborn Metabolic Screening Unit, Auckland City Hospital, New Zealand
³ Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
⁴ Auckland Uniservices Ltd, Grafton, Auckland, Aucklad, New Zealand,
⁵ Children's Research Centre, Starship Children's Health, Auckland, New Zealand

Very long chain acyl-CoA dehydrogenase deficiency (VLCADD, OMIM #201475) has been increasingly diagnosed since the advent of expanded newborn screening (NBS). Elevated levels of tetradecenoyl-L- carnitine (C14:1) in newborn screening blood spot samples are particularly common in New Zealand; however, this has not translated into increased VLCADD clinical presentations. A high proportion of screen-positive cases in NZ are of Maori or Pacific ethnicity and positive for the c.1226C>T (p.Thr409Met) ACADVL gene variant. We performed a retrospective, blinded, case-control study of 255 cases, born between 2006 and 2013, with elevated NBS C14:1 levels between 0.9 and 2.4 μmol/L, below the NZ C14:1 notification cut-off of 2.5 μmol/L. Coded healthcare records were audited for cases and age- and ethnicity-matched controls. The clinical records of those with possible VLCADD-related symptoms were reviewed. The follow-up period was 6 months to 7 years. Two of 247 cases (0.8%) had possible VLCADD-like symptoms while four of 247 controls (2%) had VLCADD-like symptoms (p = .81). Maori were overrepresented (68% of the cohort vs. 15% of population). Targeted analysis of the c.1226 locus revealed the local increase in screening C14:1 levels is associated with the c.1226C>T variant (97/152 alleles tested), found predominantly in Maori and Pacific people. There was no increase in clinically significant childhood disease, irrespective of ethnicity. The study suggests that children with elevated C14:1, between 0.9-2.4 μmol/L, on NBS are at very low risk of clinically significant childhood disease. A minimally interventional approach to managing these patients is indicated, at least in the New Zealand population.

ASIEM Oral 3
ARGININE AS AN ANTI-AGGREGATION AGENT AND A POTENTIAL THERAPEUTIC FOR TREATMENT PHENYLKETONURIA ASSOCIATED WITH AGGREGATED MUTANT PAH PROTEIN

Minal Menezes ^1,2, John Christodoulou^2,3

¹The Children's Hospital Westmead, Sydney, NSW, Australia
² Discipline of Paediatrics & Child Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
³ Neurodevelopmental Genomics Research Group, Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia

Background: Phenylketonuria (PKU), an autosomal recessive inborn error of phenylalanine metabolism, is predominantly caused by mutations in the PAH gene, and shows marked genetic heterogeneity. A subset of these missense mutations, specifically those in the N-terminal region are known to cause aggregation of the PAH protein, hypothesised to be a result of misfolding of the mutant polypeptide. In some genetic disorders such misfolding and aggregation lead to a greater rate of targeted degradation. Arginine is a protein stabilizer, proposed to exert an anti-aggregation effect by increasing the activation energy of protein aggregation. This study aims to test whether arginine supplementation has an anti-aggregation effect and might improve expression and activity of selected PAH mutants. Methods: Three missense mutations at the N-terminus of the PAH polypeptide (p.Phe39Leu, p.Leu48Ser and p.Ile65Thr), known to form highly insoluble protein aggregates in the cell were expressed in a COS-7 cell line. Cells were treated with varying concentration of arginine, followed by subsequent analyses including immunofluorescence, SDS-PAGE and enzymatic assays to test for improved expression and catalytic activity. Results: The three missense mutations all showed high levels of punctate staining in untreated cells. We found that cells supplemented with arginine showed significant reduction in the number of aggregates in the cells. Conclusion: Preliminary results reveal that arginine shows beneficial anti-aggregation effect, leading us to hypothesize that it might constitute a promising therapeutic agent in specific cases of PKU. Further investigations are in progress to assess the effect of arginine on PAH protein levels and catalytic activity.

ASIEM Oral 4
LEIGH-LIKE SYNDROME DUE TO HOMOPLASMIC M.8993T>G VARIANT WITH HYPOCITRULLINEMIA AND UNUSUAL BIOCHEMICAL FEATURES SUGGESTIVE OF MULTIPLE CARBOXYLASE DEFICIENCY (MCD)

Shanti Balasubramaniam ^1,2,3, Minna Koo³, Barry Lewis⁴, Andre Mattman⁵, Clara van Karneebek⁶, Richard Rodenburg⁷, John Christodoulou^8,9

¹Metabolic Unit, Dept of Rheumatology and Metabolic Medicine, Princess Margaret Hospital, Perth, Australia
² School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
³ Western Sydney Genetics Programme, Sydney, NSW, Australia
⁴ PathWest Lab Med WA, Princess Margaret Hospital, Perth, Australia
⁵ Adult Metabolic Disease Clinic, Division of Endocrinology & Metabolics, Vancouver General Hospital, University of British Columbia, Vancouver, Canada
⁶ Dept of Pediatrics, University of British Columbia, Vancouver, Canada
⁷ Nijmegen Center for Mitochondrial Disorders, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
⁸ Neurodevelopmental Genomics Research Group, Murdoch Children's Research Institute and Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, Australia
⁹ Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia

Background: Leigh-like syndrome is considered in individuals who do not fulfil the diagnostic criteria but have features of Leigh syndrome, a relentlessly progressive neurodegenerative disorder of early childhood. Case: A unique presentation of Leigh-like syndrome is described in a 2-year-old boy with elevated 3-hydroxyisovalerylcarnitine (C5-OH) on NBS. Subsequent persistent plasma elevations of C5-OH and propionylcarnitine (C3), and fluctuating urinary markers suggested MCD. Clinical features at 13 months of age comprised psychomotor delay, central hypotonia, myopathy, failure to thrive, hypocitrullinemia, recurrent decompensations with lactic acidosis and an episode of hyperammonemia. Biotin treatment was associated with increased activity levels, alertness, and attainment of new developmental milestones, despite lack of significant correlation with biochemical improvements. Results: Normal enzymology and mutational analysis excluded MCD. Biotin uptake studies were normal. Complex IV activity was mildly reduced in skeletal muscle. Apart from a small lactate doublet on spectroscopy, brain MRI was normal. Whole exome sequencing analysis failed to identify any other variants which could likely contribute to the observed phenotype, apart from the homoplasmic (100%) m.8993T>G variant initially detected by mtDNA sequencing. Discussion: Hypocitrullinemia has been reported in patients with m.8993T>G mutation and other mitochondrial disorders. Persistent elevations of C3 and C5-OH have previously only been reported in one other patient with this mutation. We suggest considering the m.8993T>G variant early in the diagnostic evaluation of MCD-like biochemical disturbances, particularly when associated with hypocitrullinemia on NBS and subsequent confirmatory tests. An oral biotin trial is also warranted.

ASIEM Oral 5
CHARACTERIZING BIOCHEMICAL EFFECTS OF COMPLEX I DEFICIENCY IN HUMAN EMBRYONIC KIDNEY 293 (HEK293T) CELLS

Sophia-Louise Frentz ^1,2, Bi-Xia Ke^1,2, Ann Frazier^1,2, David Thorburn^1,2

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia

Mitochondrial disorders are the most common inborn error of metabolism, affecting 1 in 5,000 live births; the most common being complex I (CI) deficiency. Deleterious mutations in CI subunits are varied in pathological presentations; NDUFS4 mutations are typically associated with progressive neurodegeneration, whereas mutations in NDUFS6 are associated with acidosis and early mortality. Current treatments are inadequate, emphasizing the need for effective and accurate experimental systems. We characterized HEK293T knockouts for NDUFS4 and NDUFS6, due to their association with disease and different severities. The ability to compare with isogenic controls increased experimental sensitivity. Cells were investigated using the Seahorse XF24-3, which can measure oxygen consumption in live cells, and by assays for mitochondrial membrane potential, ATP synthesis, and respiratory chain enzyme activity. CI activity and ATP synthesis were decreased in both knockouts to a comparable degree. The Seahorse XF24-3 and membrane potential assays showed differences in severity between the cell lines. Maximal respiration was reduced to 30% of controls in NDUFS6 knockouts (n=5, p=0.0001) and 50% in NDUFS4 knockouts (n=5, p=0.0010). Broadly, a CI defect was detected in both knockouts; however, the Seahorse XF24-3 and mitochondrial membrane potential assays were more sensitive, likely due to their measuring function in the more physiological situation of intact cells. These results are consistent with both mouse knockouts and human presentations. The data support the use of this model system to further understand mitochondrial disorders and to test novel treatments, particularly important given the paucity of effective therapies and clinical variation in these disorders.

ASIEM Oral 6
OUT OF HOURS TELEPHONE SUPPORT PREVENTS HOSPITAL PRESENTATIONS AND ADMISSIONS IN CHILDREN WITH GENETIC METABOLIC DISORDERS

Troy Dalkeith ^1,2, Andrew Biggin², Yvonne Zurynski^2,3, John Christodoulou^2,4,5

¹Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Sydney, NSW, Australia
² Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW, Australia
³ Australian Paediatric Surveillance Unit, University of Sydney, Sydney, NSW, Australia
⁴ Discipline of Genetic Medicine, Sydney Medical School, Sydney, NSW, Australia
⁵ Neurodevelopmental Genomics Research Group, Murdoch Childrens Research Institute, Melbourne, VIC, Australia

Introduction: The Genetic Metabolic Disorders Service at the Children's Hospital at Westmead provides 24- hour on-call support to 600+ patients, of who 20% are at high risk of metabolic decompensation. Service requirements have previously been neither quantified nor qualified. In determining demand, a data collection tool was developed to simplify collection. Methods: A database, the Metabolic Occasion of Service Electronic Record (MOOSER) was developed enabling data entry using an iOS interface. After proof of concept testing and enhancements, MOOSER was released in May 2014. To enhance usability, auto-entry of pertinent patient details was incorporated, including support for generation of overnight clinical handover. Demand data for on-call services was collected over an initial 45-day period. Entries were clinically categorized, identifying preventable hospital admissions. An analysis of a subset of out-of-hours interactions was performed. Results: Thirty-eight children accounted for 84 telephone interactions, totalling 700 minutes, with 15% of activity occurring between midnight and 8:30 am. Seven children were asked to present to hospital; four were admitted to wards and three were managed in short-stay/emergency department. Hospital admission was prevented in 19% of interactions, where significant clinical metabolic advice was given to change the patient- specific treatment regimen to stabilise the patient. Conclusion: On-call services also provide direct clinical advice to patients and families and prevent admissions. Ongoing data collection will further validate the usefulness of telephone support both during and outside of standard working hours. A cost-benefit analysis is needed to determine the monetary value of telephone support services.

Concurrent Session 3: Australasian Society of Diagnostic Genomics

ASDG Oral 1
HIGH READ DEPTH NIPT ENABLES TRISOMY DETECTION AT LOW FETAL FRACTION WITH HIGH SENSITIVITY AND SPECIFICITY AND VERY LOW FAILURE RATE

Mark Pertile ^1,2, Nicola Flowers¹, Katrina Scarff¹, Alison Archibald¹, Justine Elliott¹, Grace Shi¹, Sara Cronin¹, Ralph Oertel¹, Fiona Norris¹, David Francis¹, David Amor^1,2, Damien Bruno¹

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia

Non-invasive prenatal testing (NIPT) can achieve high sensitivity and specificity with very low failure rates by analyzing cell-free DNA from maternal plasma at high sequencing read depths. To investigate this we reviewed 5,172 consecutive referrals from high- and average-risk pregnancies referred to Victorian Clinical Genetics Services and processed using percept™ NIPT. Percept uses whole-genome massively parallel sequencing of cell-free DNA from maternal plasma to identify pregnancies at increased risk for autosomal trisomies (13,18,21) and sex chromosome aneuploidies. The test has been validated to detect trisomy from as little as 2.5% fetal fraction, with an observed ‘no call’ rate of 0.2% (10/5172). Cytogenetic outcome data were obtained in 84/85 (99%) cases with increased risk results for standard trisomies. High-risk results were confirmed in 46/46 (100%) T21, 5/5 (100%) T18 and 9/15 (60%) T13. One case of double-aneuploidy was also confirmed. Confined placental mosaicism for T13 was responsible for 2/2 false-positive results where placental material was available for analysis. Of 7 ‘intermediate (borderline) risk’ results for all trisomies, 1/7 (14%) was confirmed with T21. Finally, 8/84 (10%) pregnancies miscarried without opportunity for cytogenetic confirmation. Overall confirmation rate for all trisomies with cytogenetic outcome data was 62/74 (84%). No known false-negative outcomes have been reported from approximately 4,000 births. These data provide evidence for the clinical utility of high read depth NIPT utilizing normalized chromosome values (NCV), which places low emphasis on the requirement for fetal fraction above 4%. Further evidence is provided in support of this claim.

ASDG Oral 2
NONINVASIVE PRENATAL TESTING (NIPT) FOR SCREENING PREGNANCIES OF BALANCED RECIPROCAL TRANSLOCATION CARRIERS

Nicola Flowers ¹, Grace Shi¹, Olivia Giouzeppos¹, Clare Love¹, Damien Bruno¹, Mark Pertile^1,2

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia

Background: Carriers of balanced reciprocal translocations are at increased risk of producing embryos that carry an unbalanced form of the parental rearrangement. Current testing available to translocation carrier couples includes Pre-implantation Genetic Diagnosis (PGD) or invasive testing using CVS or amniocentesis. A new approach is to use whole genome sequencing data obtained from NIPT to screen for segmental copy number imbalances associated with the translocation. Aim: We sought to investigate the utility of NIPT to screen pregnancies of balanced reciprocal translocation carriers and to determine guidelines for the screening of pregnancies by NIPT in our laboratory where we offer percept™.Methods: Normalized chromosome coverage data were examined in 11 cases referred for NIPT and translocation screening. Cases underwent additional assessment for segmental imbalances using WISECONDOR(1) and Cartagenia OneSight Software(2).

Results: To date, 11 pregnancies have been screened for chromosomal imbalances associated with the known carriers of balanced reciprocal translocations. Of these, 4 showed an abnormal NIPT result that was confirmed in the fetus by invasive testing. Segmental chromosomal imbalances ranged in size from 10–67 Mb. Invasive testing in 3 pregnancies with normal results confirmed the normal/balanced NIPT results obtained. The remaining 4 pregnancies with normal NIPT results are ongoing. Discussion: These data demonstrate the clinical utility of NIPT for screening pregnancies of reciprocal translocation carriers. In translocations meeting the determined guidelines (size of translocated segments, ascertainment, gestation), NIPT can offer another option for these couples, at high sensitivity.

ASDG Oral 3
ACCREDITING AUSTRALASIA'S FIRST CLINICAL WHOLE GENOME SEQUENCING (WGS) SERVICE

Aga Borcz^1,2, Michael Buckley^1,2,3, Peter Budd^1,2, Leslie Burnett ^1,2,3,4, Liviu Constantinescu^1,2, Joe Copty^1,2, Mark Cowley^1,2, Marcel Dinger^1,2, Lisa Ewans^1,2,5, Maria Gonzalez^1,2, Tudor Groza^1,2, Warren Kaplan^1,2, Maria Lubka-Pathak^1,2, Ben Lundie^1,2, John Mattick¹, Scott Mead^1,2,3,5, David Miller⁶, Paula Morris^1,2, Mark Pinese^1,2, Tony Roscioli^1,2,5, Dahlia Saroufim^1,2, Aaron Statham^1,2, Justin Stockmyer^1,2, Kevin Ying^1,2

¹Garvan Institute of Medical Research, Sydney, NSW, Australia
² Kinghorn Centre for Clinical Genomics, Sydney, NSW, Australia
³ SEALS Genetics, NSW Health Pathology, Sydney, NSW, Australia
⁴ Sydney Medical School, Sydney, NSW, Australia
⁵ St. Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
⁶ Illumina Inc., La Jolla, San Diego, CA, USA

Background: Garvan's KCCG operates the Illumina HiSeq X Ten whole genome sequencing (WGS) system. This enables a minimum 30x coverage of the human genome. Application of WGS to clinical practice requires accreditation. Worldwide, very few WGS facilities have gained accreditation and, to our knowledge, none have achieved the international standard of ISO 15189. Aims: To describe the process for NATA/RCPA accreditation for human clinical WGS, including certification to ISO 15189. Methods: Following WGS facility commissioning, a 12-month plan progressively upgraded infrastructure and processes to accreditation requirements. Key accreditation developments included a Quality Management System to control procedures and documents, introducing audit and corrective action programs and a clinical Code of Conduct for all staff. Innovations included wikis and job ticketing systems facilitating rapid communication between expert teams. WGS-specific issues included design and execution of validation plans to meet NPAAC Requirements for in-house IVDs and RCPA Guidelines for massively parallel sequencing; online web requesting; information systems capable of integrating phenotype ontologies with genotypes; informatics meeting NPAAC Requirements for information communication; optimisation of filtering pipelines; and structured clinical reports compliant with ACMG Guidelines. Results: NATA accreditation was achieved at first submission. Discussion: The initial WGS IVD detects SNVs and indels <20nt in bioinformatically defined panels. While it can diagnose individuals, it is optimized for familial trios. Although our IVD outperformed Sanger sequencing during validation, we will routinely orthogonally confirm medically significant findings in the short term. The second version of our WGS IVD will include CNV detection at resolutions comparable to current microarray technologies.

ASDG Oral 4
NEXT GENERATION SCREENING: TRUSIGHT ONE ‘CLINICAL EXOME’ FOR PRECONCEPTION SCREENING IN CONSANGUINEOUS COUPLES

Edwin Kirk ¹, Kristine Barlow-Stewart⁴, Arthavan Selvanathan⁵, Sarah Josephi-Taylor⁶, Lisa Worgan⁵, Sulekha Rajagopalan⁵, Madhura Bakshi⁵, Alan Bittles⁷, Leslie Burnett³, Michael Buckley³, Alison Colley⁵, Tony Roscioli⁸

¹Sydney Children's Hospital, Sydney, NSW, Australia
² School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
³ South Eastern Area Laboratory Service, Sydney, NSW, Australia
⁴ University of Sydney, Sydney, NSW, Australia
⁵ Liverpool Hospital, Sydney, NSW, Australia
⁶ Royal North Shore Hospital, Sydney, NSW, Australia
⁷ Murdoch University, Perth, WA, Australia
⁸ The Garvan Institute, Sydney, NSW, Australia

Background: Autosomal recessive (AR) disorders are a major cause of morbidity and mortality. Consanguineous couples are at increased risk for having a child with these disorders but to date, risk assessment based on family history and/or ethnicity often added little to that based on empiric observational data. Therefore, exome (and in the future, whole genome) sequencing offers the prospect of ‘the screen for everything’, providing information that can inform reproductive choice in this at-risk group. More broadly, it may provide a paradigm for assessment of the practicability and effectiveness of this screening approach in the general population. Study design: We used the TruSight One ‘clinical exome’, which includes 4,813 genes linked to human disease, to pilot screen 15 consanguineous couples who were planning a pregnancy for AR and X-linked disorders. Results: Three couples were found to be at risk of having children affected by AR disorders: severe neurological conditions (n = 2), and a metabolic disorder which is relatively straightforward to treat but can be difficult to diagnose and can have severe consequences for an untreated child (n = 1). Interviews conducted with the couples pre-test identified an intention to utilize any positive findings in their future pregnancy planning. Conclusion: Variant interpretation remains a considerable challenge, which will limit the sensitivity of this approach. Nonetheless, our results indicate that the benefits of screening are likely to be considerable and a major advance over a targeted approach.

ASDG Oral 5
GENOMIC APPROACHES AND NEW DIAGNOSES IN OCULAR ANTERIOR SEGMENT DISORDERS

Alan Ma ^1,4, Saira Yousoof¹, John Grigg^1,3, Anson Cheng^1,3, Bruce Bennetts^2,4, Robyn Jamieson^1,3,4

¹Eye Genetics Research Group, Sydney Children's Hospital Network, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
² Sydney Genome Diagnostics, Sydney Children's Hospital Network, Westmead, Sydney, NSW, Australia
³ Save Sight Institute, University of Sydney, Sydney, NSW, Australia
⁴ Discipline of Genetic Medicine, CHW Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, Australia

Introduction: Disorders of the ocular anterior segment, such as Axenfeld-Rieger syndrome, Peters anomaly and sclerocornea, occur due to abnormalities in several developmental pathways in eye embryogenesis contributing to their marked clinical and genetic heterogeneity. We seek to determine the utility of genomic approaches to genetic diagnosis in these conditions. Methods: We performed NGS in 29 probands with ocular anterior segment abnormalities, where copy number variants were excluded by CGH microarray. A panel targeted at over 4,000 known disease genes was used in 10 patients (Illumina TruSight One, HiSeq 2500), while whole exome sequencing was used in the remaining 19 (Agilent SureSelect, Illumina HiSeq 4000).We examined known anterior segment abnormality genes, syndromic and non-syndromic, and genes contributing to overlapping genetic eye disorders such as cataracts and microphthalmia. A customized alignment and variant calling pipeline was utilized, and variants of interest were confirmed with Sanger sequencing and segregation studies. Results: In our cohort of 29, likely causative mutations were found in 41% (12/29) of patients. Mutations were found in the known anterior segment abnormality genes FOXC1/PITX2 in 4/29 patients, and also in the more rarely reported genes COL4A1 and PXDN. Novel phenotypes were found associated with the anophthalmia gene SOX2, and in two patients with GJA8 mutations. Mutations were also found in the syndromal gene ADAMTS17. Discussion: This study demonstrates a significant yield of mutations in a cohort of patients with ocular anterior segment abnormalities, providing new diagnostic and management information in all cases.

ASDG Oral 6
A PANEL APPROACH USING MASSIVELY PARALLEL SEQUENCING TO DIAGNOSE GENETIC LEUKODYSTROPHIES: FIRST RESULTS FROM THE CHW LABORATORY

Katherine Holman ², Karen Wong², Bruce Bennetts², Michel Tchan ¹

¹Westmead Hospital, Sydney, NSW, Australia
² The Children's Hospital at Westmead, Sydney, NSW, Australia

Background: There are many molecular causes for a clinical diagnosis of leukodystrophy. Genetic testing for individual genes may be a time consuming and expensive process, hence designing a panel using massively parallel sequencing to analyze multiple genes concurrently is an attractive approach. Aim: To present the first six patients tested using a multi-gene panel approach. Methods: Six adult patients with undiagnosed leukodystrophy were consented. These patients had already undergone multiple unrevealing investigations prior to utilising the leukodystrophy panel. Massively parallel sequencing using the Trusight One clinical exome was performed, and the sequences of 79 genes known to cause leukodystrophy analyzed. Results: Disease causing mutations were found in 3 out of 6 patients, with the following diagnoses being made: CARASIL, 4H syndrome, and progressive leukoencephalopoathy with ovarian failure. One patient had pseudo-deficiency variants for metachromatic leukodystrophy confirmed (previously known). The remaining two patients did not have pathogenic variants detected. Discussion/Conclusion: The leukodystrophy panel was successful in making a diagnosis in 50% of patients in this initial cohort of adult patients.

Concurrent Session 4: Australasian Association of Clinical Geneticists

AACG Oral 1
THE CLINICAL UTILITY OF WHOLE EXOME SEQUENCING IN A DIVERSE NEW ZEALAND COHORT OF CLINICAL CONUNDRUMS

Colina McKeown ¹, Samantha Connors², Tim Morgan², Ian Hayes¹, Katherine Neas¹, Joanne Dixon¹, Kate Gibson¹, David M. Markie², Stephen P. Robertson^1,2

¹Genetic Health Service, New Zealand
² Dunedin School of Medicine, University of Otago, New Zealand

Aim: To determine the clinical utility of whole exome sequencing (WES) for a series of patients referred to Genetic Health Service New Zealand. Method: WES using a trio design was performed on 42 individuals from 12 families. All probands had prior expert clinical review and appropriate investigations yet a molecular diagnosis remained elusive. Clinical diagnoses included multiple congenital anomalies (4), developmental delay (4), myopathy (1), pancreatic failure (1), cardiomyopathy (1) and skeletal dysplasia (1). Exome sequencing was provided by NZGL with Nextera 37Mb exome capture and paired-end sequencing on an Illumina platform. Data were processed for alignment, variants called according to the current best practice guidelines using the GATK (Broad Institute) and candidates validated using Sanger sequencing. Results: A likely or definite molecular diagnosis was made in 7/12 families, an overall diagnostic yield of 58%. Seven families had a child with a presumed sporadic condition, four had sibling recurrences and one had an X-linked inheritance pattern. The highest diagnostic yield was in those with sibling recurrences, with 4/4 solved. Of the seven diagnoses made, four were previously recognized pathogenic mutations, one was a novel mutation in a known gene and two were in genes yet to be associated with a human disease phenotype. Conclusion: WES using a trio design was a useful tool to obtain a molecular diagnosis in this cohort of patients, particularly for families with sibling recurrence. The high diagnostic yield is likely attributable to the distinctive phenotypes studied and the depth of work-up undertaken prior to WES.

AACG Oral 2
IMPACT OF EXOME SEQUENCING ON THE DIAGNOSTIC TRAJECTORY AND HEALTHCARE COSTS OF OLDER SEQUENCING-NAÏVE CHILDREN WITH SUSPECTED MONOGENIC CONDITIONS

Tiong Yang Tan ¹, Oliver Dillon³, Zornitza Stark^1,2, Belinda Chong^1,2, Dean Phelan^1,2, Gemma Brett^1,2, Emma Creed^1,2, Patrick Yap^1,2, Maie Walsh^1,2, Lilian Downie^1,2, David Amor^1,2,3, Ravi Savarirayan^1,2,3, George McGillivray^1,2, Alison Yeung^1,2, Heidi Peters^2,4, Susan Robertson⁴, Aaron Robinson⁴, Ivan Macciocca^1,2, Simon Sadedin², Katrina Bell², Alicia Oshlack^2,3, Natalie Thorne⁵, Deborah Schofield^2,6,7, Khurshid Alam^2,3,6, Clara Gaff^3,5,8, Susan White^1,2,3

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Murdoch Children's Research Institute, Melbourne, VIC, Australia
³ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁴ The Royal Children's Hospital, Melbourne, VIC, Australia
⁵ Walter and Eliza Hall Institute, Melbourne, VIC, Australia
⁶ University of Sydney, Sydney, NSW, Australia
⁷ Garvan Institute of Medical Research, Sydney, NSW, Australia
⁸ Melbourne Genomics Health Alliance, Melbourne, VIC, Australia

Background: Exome sequencing has been shown to have diagnostic and clinical utility in different disease subgroups, including our previous study involving infants with monogenic disorders. Most published cohorts recruited children at the end of their diagnostic trajectory, having had prior sequencing. Objective: We sought to investigate the impact of exome sequencing in sequencing-naïve children suspected of having a monogenic disorder and evaluate hypothetical changes in their diagnostic trajectory and healthcare costs had exome sequencing been available at an earlier age. Methods: Children aged >2 years suspected of having a monogenic disorder were prospectively recruited from outpatient clinics of The Royal Children's Hospital and Victorian Clinical Genetics Services. All children had non-diagnostic microarrays and no prior single-gene or panel sequencing. We undertook exome sequencing with targeted phenotype-driven analysis and examined the clinical utility of a molecular diagnosis. We also evaluated hypothetical diagnostic trajectories depending on timing of exome sequencing to determine the impact on healthcare costs. Results: We recruited 42 children aged from 2 years 11 months to 18 years and achieved a diagnosis in 19 (45%) by exome sequencing. The average duration of diagnostic trajectory was 6 years, with each child having an average of 19 tests for diagnostic purposes, 4 clinical genetics and 4 non-genetics specialist consultations. We report health economic analyses of exome sequencing offered at the start of the diagnostic trajectory versus standard care. Conclusion: Exome sequencing in outpatient children with suspected monogenic conditions is clinically indicated and should be offered at the start of their diagnostic trajectory.

AACG Oral 3
MOLECULAR DIAGNOSIS OF GENETIC MUSCLE DISORDERS IN NEW ZEALAND

Gemma Poke ¹, Miriam Rodrigues², Richard Roxburgh³, Susannah Bawden¹, Stephanie Oates¹, Katrina Rufino⁴, Kimberley Flintoff⁴, Don Love⁵, Elsa Parker⁶, Alice Theadom⁷

¹Genetic Health Service New Zealand, Wellington, New Zealand
² NZ Neuromuscular Disease Registry, Auckland, New Zealand
³ Auckland Hospital, Auckland, New Zealand
⁴ Wellington Regional Genetics Laboratory, Wellington, New Zealand
⁵ LabPlus, Auckland, New Zealand
⁶ Canterbury Health Laboratories, Christchurch, New Zealand
⁷ Auckland University of Technology, Auckland, New Zealand

The MD-Prev study is a national population-based study that is working to determine prevalence of inherited muscle disorders in New Zealand. The study's census date was 1 April 2015, with approximately 900 affected individuals ascertained to date. Early study findings will be presented, with a focus on the individuals who have had their diagnosis confirmed molecularly. The proportion of individuals with a molecular diagnosis varies according to several factors, the main one being subtype of muscle disorder. The advantages and limitations of molecular genetic testing for muscle disorders will be discussed, with specific case examples. Special subgroups will also be discussed, such as individuals who have had a diagnosis made pre-symptomatically or prenatally.

AACG Oral 4
INHERITED PERIPHERAL NEUROPATHY: GENE PANEL OR WHOLE EXOME?

Maie Walsh ¹, Katrina Bell¹, Belinda Chong¹, Gemma Brett¹, Emma Creed², Kate Pope¹, Jessica Taylor², Adrienne Sexton², Natalie P. Thorne^1,3,4, Alicia Oshlack^1,3, Simon Sadedin¹, Peter Georgeson³, Eppie M. Yu⁵, Timothy Day², Lynette Kiers², Michael Fahey^2,6, Elsdon Storey^2,6, Ivan Macciocca¹, Clara Gaff ^3,4, Paul A. James², Zornitza Stark¹, Monique Ryan^1,3,5

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Royal Melbourne Hospital, Melbourne, VIC, Australia
³ University of Melbourne, Melbourne, VIC, Australia
⁴ Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
⁵ Royal Childrens Hospital, Melbourne, VIC, Australia
⁶ Alfred Hospital, Melbourne, VIC, Australia

Purpose: To compare the diagnostic yield of a virtual gene panel and of whole exome sequencing (WES) in patients with presumed genetic peripheral neuropathy. Methods: Singleton WES was performed in a cohort of patients recruited though the Royal Children's and Royal Melbourne hospitals between February 2014 and August 2015. Initial analysis was restricted to an evidence-based gene list of 55 genes associated with peripheral neuropathies and related disorders. Patients with uninformative results underwent analysis of the remainder of the WES data. Results: 50 patients with chronic peripheral neuropathy were recruited (age range 3–70 years, average 30 years). Of these, 11 had additional features suggestive of a complex phenotype. 12 out of 50 patients received a molecular diagnosis through the initial targeted analysis of 55 neuropathy genes (24%). A further 9 patients received a diagnosis following the analysis of untargeted exome data, increasing the overall diagnostic yield to 42%. The additional diagnoses were due to mutations in genes newly associated with neuropathies, or genes that cause complex phenotypes that have neuropathy as a feature. Another two patients received a diagnosis through SNP microarray identifying pathogenic copy number variants. Conclusions: This study provides evidence that WES is superior to a targeted gene panel in patients presenting with a presumed genetic peripheral neuropathy. It also outlines an approach to the reanalysis of data from patients in whom a diagnosis is not reached following initial analysis, and reinforces the importance of microarray as a first-tier test in this cohort of patients.

AACG Oral 5
IDENTIFICATION AND ANALYSIS OF TWO NOVEL ENHANCERS OF HUMAN SOX9: IMPLICATIONS FOR DISORDERS OF SEX DEVELOPMENT

Andrew Sinclair ¹, Thomas Ohnesorg¹, Jo Bowles², Peter Koopman²

¹Murdoch Children's Research Institute, Melbourne, VIC, Australia
² Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia

Disorders of Sex Development (DSDs) encompass a wide spectrum of conditions and often manifest with atypical gonads or genitalia. The cause is often a flaw in the network of gene regulation responsible for development of testes or ovaries. The majority of DSD patients cannot be given an accurate diagnosis, which severely compromizes their clinical management. While mutations in coding regions of gonad genes have been important in understanding the etiology of DSD, little attention has focused on the regulatory regions of gonad genes. Recent reports of 46,XX testicular DSD patients with duplications and 46,XY gonadal dysgenesis patients carrying deletions ~500-600kb upstream of SOX9 suggest the presence of a gonad enhancer of SOX9. Using a comprehensive tiling luciferase approach, we identified two novel putative enhancers within this region. The enhancer showing the strongest activity in vitro was further analyzed and used to generate transgenic reporter mice. We show that this enhancer mediates SOX9 auto-regulation in vitro and leads to strong reporter gene expression in embryonic gonads at the time of sex determination and gonad differentiation. Our results strongly suggest that deletions or duplications (CNVs) of this enhancer lead to DSD. While this enhancer appears to be responsible for the maintenance of SOX9 expression, we have identified an additional enhancer close to human SOX9, which may be responsible for SRY-dependent up-regulation of SOX9 and subsequent testis development.

AACG Oral 6
SUCCESSES AND CHALLENGES IN THE CARDIAC GENETICS CLINIC

Julie McGaughran ^1,2

¹Genetic Health Queensland, Brisbane, QLD, Australia
² School of Medicine, University of Queensland, Brisbane, QLD, Australia

Background: Over recent years, there has been a significant increase in referrals to cardiac genetics clinics with an increase in the availability of genetic testing. Results: As of February 2016, 814 patients had undergone diagnostic genetic testing and 208 predictive testing in the Queensland Cardiac Genetics clinic. Discussion: In some areas, such as sudden unexpected death in the young, this has enabled family members to not only have a diagnosis but to also be able to access genetic testing. Over time, it has become clear that cardiac genetics is a complex area of clinical genetics as there can be great inter- and intra-familial variability in clinical presentation. In addition, the increased use of large gene panels has demonstrated that mutations in particular genes can cause different cardiac conditions in different families or apparent mutations are found in genes that do not match the phenotype. Interpretation of genetic variants is also complex. A number of these clinical examples will be presented to illustrate these challenges.

Concurrent Session 5: Australasian Society of Genetic Counsellors

ASGC Oral 7
BROADENING THE DEFINITION OF GENETIC COUNSELOR ROLES

Gemma Brett ^1,2, Ella Wilkins¹, Justine Elliott¹, Alison Archibald^1,2, Chloe Hanna³, Natalie McLean^2,4, Kate Pope^1,2, Ivan Macciocca¹

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Murdoch Childrens Research Institute, Melbourne, VIC, Australia
³ Royal Children's Hospital, Melbourne, VIC, Australia
⁴ Children's Tumour Foundation of Australia, Sydney, NSW, Australia

As the genetic counseling profession continues to evolve in Australasia, it is important to recognise existing and emerging roles. The unique skill set and perspective of genetic counselors is becoming acknowledged as an invaluable asset in a variety of settings. This presentation describes and compares genetic counselor roles across the Melbourne Children's Campus, both within the clinical genetics service and other departments. These roles involve varying degrees of ‘traditional’ genetic counseling, with genetic counseling skills also applied to multidisciplinary clinic development and maintenance, laboratory liaison, program development and evaluation, research, education, coordination of care across multiple hospitals, support services and development of consumer and professional information resources. For example, while genetic counselors have worked in clinic coordination roles within clinical genetics services for many years, an expansion of genetic counselor roles in recent years has occurred as individual hospital departments establish designated clinics for genetic conditions. These clinics increasingly employ genetic counselors to provide clinic coordination and case management, in place of nurse coordinators. Additionally, genetic counselors are increasingly involved in facilitating the implementation of new genetic and genomic technologies. Such roles involve working collaboratively with clinical and laboratory teams to facilitate appropriate implementation of the technologies. The expertise of genetic counselors in genetics knowledge and communicating complex concepts in lay language are fundamental to their value in these roles and many others. As genetic counselors apply their skills to increasingly varied roles, it is important the emerging roles are recognised as valuable applications of genetic counseling training.

ASGC Oral 8
THE MOVE INTO PRIVATE PRACTICE FOR GENETIC COUNSELORS

Sarah Collis ¹, Clara Gaff^1,3, Samantha Wake^4,5,6, Alison McEwen²

¹University Of Melbourne, Melbourne, VIC, Australia
² Genetic Health Service NZ, Wellington, New Zealand,
³ Walter and Eliza Hall Institute, Melbourne, VIC, Australia
⁴ Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
⁵ Victorian Clinical Genetics Services, Melbourne, VIC, Australia
⁶ Murdoch Childrens Research Institute, Melbourne, VIC, Australia

A small but increasing number of genetic counselors in Australasia are moving into private practice. This qualitative research study aims to understand the scope of the role of genetic counselors who are working in private practice and to identify ways in which these genetic counselors can be supported. In the first phase of the project, content analysis was performed on documents produced from the meetings of a private practice working party established in 2015 by the Australasian Society of Genetic Counselors (ASGC). The aim of this working party was to develop a professional guideline for genetic counseling in the private practice setting. Themes identified within the working party documents included: demand for services, business considerations, professional development requirements, role promotion considerations, unique professional issues and support systems desired. These themes and their subcategories informed the interview schedule used in the second phase of the project. They also formed the coding frame used to analyze interview data. In phase two, semi-structured interviews were conducted to explore the experiences of genetic counselors who have worked in private practice. Study participants were recruited from the ASGC private practice working party and the ASGC general membership. Early results from interview data will be presented. This research study will offer recommendations for training, certification and workplace. The findings can contribute to the ongoing evolution of the genetic counseling profession and the scope of practice for genetics counselors in Australasia.

ASGC Oral 9
PROVIDING OPTIONS TO CLIENTS ABOUT HOW THEY RECEIVE PREDICTIVE GENETIC TEST RESULTS: A CHANGE IN PRACTICE

Gemma Correnti ¹, Vanessa Huntley¹, Jacqui Armstrong¹, Alisha McLauchlan¹, Sally Russell¹, Debra Trott¹

¹South Australian Clinical Genetics Service, Adelaide, SA, Australia

In September 2014, the Adult Genetics Unit (South Australian Clinical Genetics Service) began offering most clients the option to receive their predictive genetic test result by letter, telephone or appointment. Prior to this, results were routinely given at an appointment. This change in practice was made in an effort to promote flexibility and client autonomy. We audited 305 files from clients seen for predictive testing for a range of conditions (predominantly cancer, cardiac and neurological disorders) by six genetic counselors in the year 2015. Counselors felt comfortable allowing the majority of clients (287 / 94%) a choice: 158 (55%) chose to receive their result by letter, 113 (39%) chose telephone, and only 16 (6%) chose appointment; 18 (6%) were not given a choice and had an appointment made for them. The 112 clients who received an abnormal result by letter or telephone were given the opportunity to have a second appointment and only 16 (14%) accepted. Informal counselor interviews highlighted overall satisfaction with the new process. Counselors noted a positive effect on their workload. A preference emerged for sending results by letter due to difficulties associated with ‘chasing’ people by telephone and phoning at inappropriate times. Our experience supports offering clients a choice for how they receive their predictive test result. We intend to continue this process and may refine some aspects based on counselor feedback. We also intend to seek feedback from clients about this process in the future.

ASGC Oral 10
USING GENEALOGY IN CASCADE TESTING — THE VALUE IN CONCATENATION

Briony Patterson ¹, Jo Burke¹, David Amor², Paul A James³

¹Tasmanian Clinical Genetics Service, Hobart, TAS, Australia
² Victorian Clinical Genetics Services, Melbourne, VIC, Australia
³ Peter MacCallum Familial Cancer Services, Melbourne, VIC, Australia

The breast and ovarian cancer predisposition genes, BRCA1 and BRCA2, have a low rate of new mutations and there is a high chance that two individuals that carry an identical mutation share a common ancestor at some time in the past. The Tasmanian Clinical Genetics Service has investigated the frequency of recurrently identified BRCA1/2 mutations in Tasmanians undergoing clinical testing. Out of the 52 mutations identified to date, 11 mutations have been detected between 2 and 5 times. Identifying the same mutation provides an opportunity to concatenate (link) previously independent pedigrees. Concatenation can significantly enlarge pedigrees, provide valuable penetrance data for a particular mutation, maximize the number of at-risk relatives to whom predictive testing can be offered, as well as identify relatives who are not at risk, all of which maximize the benefit of the initial mutation detection result. In some cases, concatenation can occur through the records of a genetic service; however, the TCGS is ideally situated to make use of external genealogical records to concatenate branches of distantly related pedigrees where the same mutation has been identified. To date, three extended pedigrees have been created through genealogical concatenation of seven families. The average number of predictive tests in these seven families is 21.1 and in all other BRCA1/2 families it is 6.4. Genealogical concatenation requires significant resources and currently cannot be applied routinely, but given the benefits we have been exploring novel opportunities for expanding this work including a process for engaging the expertise of volunteer genealogists.

ASGC Oral 11
BREAST CANCER GENETIC TESTING AT AUSTIN HEALTH – A CLINICAL AUDIT OF CLINICAL INDICATIONS FOR TESTING AND OUTCOMES

Megan Cotter ¹, Elly Lynch¹, Anna Leaver¹, Stephanie Kearton¹, Giulia Valente¹, Mathew Wallis¹, Martin Delatycki^1,2

¹Austin Health Clinical Genetics Service, Melbourne, VIC, Australia
² Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Centre, Melbourne, VIC, Australia

Background: Genetic testing of BRCA1 and BRCA2 is currently recommended for individuals with a greater than 10% chance of identifying a mutation as determined by the genetic testing algorithm BRCAPro1 and more recently BOADICEA2; however, the mutation detection rates for other indications for testing are not known. These include triple negative breast cancer <50 years, high grade, non-mucinous ovarian cancer <70 years, breast cancer diagnosed <35 years, and male breast cancer diagnosed at any age. Aim: A review of all breast cancer mutation detection testing performed by Austin Health Clinical Genetics between January 2009 and June 2015 was conducted to determine the clinical utility of current testing criteria. Results: In total, 667 individuals underwent testing of the BRCA1 and BRCA2 genes. Of these, 13.6% (n = 91) had a pathogenic mutation identified, 86.4% (n = 576) had an inconclusive result (variant of unknown significance or no mutation). Of all individuals tested, 27.6% (n = 184) did not meet any clinical criteria for testing. Of those with a known mutation, 33% (n = 30) had a BRCAPro score of <10%. Of those who met each clinical indication for testing, >10% had a pathogenic mutation identified. Among individuals who were offered testing on the basis of a clinical decision but did not meet any of the testing criteria, a mutation was detected in <10%. Conclusion: Testing for BRCA1 and BRCA2 mutations based on testing criteria is justified by >10% of individuals having a mutation in each of the categories. There appears little justification for testing outside the criteria.

ASGC Oral 12
YOUNG AUSTRALIAN WOMEN'S DECISION-MAKING ABOUT MANAGING BREAST AND OVARIAN CANCER RISK DUE TO A BRCA1/2 MUTATION

Laura Forrest ^1,2, Mary-Anne Young¹, Victoria Rasmussen¹, Gillian Mitchell^1,2

¹Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
² The University of Melbourne, VIC, Australia

Background: Young women aged 18–40 years with a BRCA1/2 mutation may experience their young adulthood, a formative developmental life stage, interwoven with an awareness of a significantly increased cancer risk. Psychosocial support needs may arise due to the tension between choosing which cancer risk management strategies to engage and when, and fundamental life events such as childbearing. This study explores how young Australian women with a BRCA1/2 mutation balance engagement with risk management strategies and young adulthood. Method: A grounded theory approach has been undertaken using qualitative, semi-structured interviews. The inclusion criteria included women who have a BRCA1/2 mutation, aged 18–40 years, who received their genetic test result more than 12 months prior. Data were analyzed iteratively and inductively to identify themes, ideas, concepts and categories. Results: Forty semi-structured interviews were conducted. Participants’ decision-making about how they managed their breast cancer risk was often informed by childbearing plans and/or the presence of children. Most participants chose annual breast screening after receiving their BRCA1/2 result but many were considering a bilateral prophylactic mastectomy (BPM) once they had completed childbearing. Nevertheless, attitudes towards, and perceptions of, BPM were variable. Participants who negatively perceived BPM described feeling a ‘physical revulsion’ to the removal of their breast tissue. However, participants were uniform in their acceptance of having a bilateral salpingo-oophorectomy once childbearing was complete. Discussion/Conclusion: These findings illustrate the psychosocial challenges young women with a BRCA1/2 mutation experience managing their cancer risk and balancing risk management strategies with childbearing.

Concurrent Session 6: Australasian Society for Inborn Errors of Metabolism

ASIEM Oral 7
PROPIONIC ACIDEMIA AFTER THE NEWBORN SCREENING

Eva Morava, Eric Debbold, Tamas Kozicz

Tulane University Medical School, Hayward Genetics Center, New Orleans, LA, USA

Propionic acidemia (PA) is a rare and severe inborn error of metabolism of branched chain amino acid degradation. Patient outcome in the past 20 years included early death in 25% of the patients, frequent growth-, developmental and speech delay. The long-term prognosis was complicated by the development of secondary mitochondrial dysfunction, myopathy and basal ganglia disease. The implementation of newborn screening has had a major impact in the occurrence of clinical symptoms and in the natural course of patients with PA. More and more children with PA are able to survive to adulthood. Still, most patients detected by newborn screening prior to the development of any metabolic disarrangement, and with the best possible treatment, seem to carry a risk for developing long term sequalae. We will evaluate the different metabolic factors playing a role in the development of features like cardiomyopathy, pancreatitis or muscle disease. We will discuss recent studies which suggest a novel approach for dietary treatment and new options in pharmacotherapy. The role of liver transplantation will be also discussed. We will also focus on the psychological outcome, behavioral anomalies and autism in propionic acidemia and make suggestions to optimize long term outcome.

ASIEM Oral 8
AN INFANT PRESENTING WITH LIFE-THREATENING ACUTE METABOLIC DECOMPENSATIONS WITH HYPOGLYCAEMIA, MARKED LACTIC ACIDOSIS AND HYPERAMMONAEMIA DUE TO TANGO2 DEFICIENCY

Jim McGill ^1,2,3, Anita Inwood¹, David Coman¹, Carolyn Bursle¹, Michelle Lipke¹, Karen Noy², Suzanne Chabowski², Christine Gurnsey², Avis McWhinney³, Tom Hurley⁴

¹Queensland Lifespan Metabolic Medicine Service, Lady Cilento Children's Hospital, Brisbane, QLD, Australia
² Division of Chemical Pathology, Pathology Queensland, Brisbane, QLD, Australia
³ Department of Clinical Chemistry, Mater Pathology, Brisbane, QLD, Australia
⁴ Department of Paediatrics, Nambour Hospital, Nambour, QLD, Australia

A female infant was the third child of non-consanguineous parents. She has had six acute metabolic decompensations requiring retrieval to the pediatric intensive care unit. Episodes are triggered by vomiting and start with hypoglycemia and then progress to severe acidosis (pH <7.0), lactic acidosis (up to16 mmol/L), hyperammonemia (up to 850umol/L) and coagulopathy with the first at 3.5 months of age. She required ventilatory support with recovery being dependent on re-establishing normal feeds. Her highest CK was 248 U/l. Urine organic acids showed marked ketoacidosis, dicarboxylic acids and lactate. In contrast, acylcarnitines showed a pattern suggestive of VLCAD deficiency. Transferrin isoforms were normal but she had a mildly elevated aglyco Apo C-III with normal mono- and disialo-Apo C-III. She has been treated with a low fat diet, medium chain triglycerides and overnight feeds. Several vomiting episodes have been aborted with ondansetron avoiding hypoglycemia. Her progress is better than her older twin siblings at the same age. These twins, a boy and a girl, presented with global developmental delay at 9 months, seizures, hypoglycemia with lactic acidosis and recurrent rhabdomyolysis with CK up to 97,500 U/l. Brain MRI in both showed generalized cerebral atrophy. The female twin developed hypertrophic cardiomyopathy. The twins died at 22 and 24 months of age. A mitochondrial disorder was suspected but whole exome sequencing showed homozygous mutations in the TANGO2 gene which is expressed in the Golgi and cytoplasm. Mutations are hypothesised to cause endoplasmic reticulum and Golgi disruption and stress.

ASIEM Oral 9
INBORN ERRORS OF THE VALINE PATHWAY

James Pitt

Victorian Clinical Genetics Services, Melbourne, VIC, Australia

Four enzymatic steps of the valine degradation pathway have an associated inborn error of metabolism: isobutyryl-CoA dehydrogenase (IBDH), short-chain enoyl-CoA hydratase (SCEH), 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) and methylmalonic semialdehyde dehydrogenase (MMSDHD). IBD is now generally considered to be a benign condition although it may be detected incidentally during newborn screening while MMSDHD is a very rare disorder that may be associated with microcephaly and developmental delay. IBDH and MMSDHD can be detected using conventional organic acid and acyl carnitine profiling methods. Following the recent discovery of SCEH, there has been considerable interest is this new disorder and HIBCH. Both disorders cause a variable, Leigh-like phenotype and have similar metabolic abnormalities which may be overlooked with conventional screening methods. Screening techniques have been developed for these two disorders that should stream-line their diagnosis in future. The metabolic profiles in HIBCH and SCEH, combined with their contrasting phenotypes compared to other valine pathway disorders, indicate that accumulating methacrylyl-CoA is a significant cause of pathology. Glutathione metabolism also appears to be involved with the detoxification of this reactive intermediate. These new metabolic findings also suggest potential treatments for HIBCH and SCEH.

ASIEM Oral 10
SLC39A8 DEFICIENCY: A CONGENITAL DISORDER OF GLYCOSYLATION WITH AN ASSOCIATED MITOCHONDRIAL DISORDER

Lisa Riley ¹, Mark Cowley², Vel Gayevskiy², Tony Roscioli², David Thorburn^3,4, Melanie Bahlo⁵, Shanti Balasubramaniam⁶, John Christodoulou^7,8

¹Genetic Metabolic Disorders Unit, The Children's Hospital at Westmead and Discipline of Paediatrics & Child Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
² Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
³ Murdoch Childrens Research Institute and Victorian Clinical Genetic Services, Royal Children's Hospital, Melbourne, VIC, Australia
⁴ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁵ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
⁶ Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
⁷ Genetic Metabolic Disorders Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead and Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
⁸ Neurodevelopmental Genomics Research Group, Murdoch Childrens Research Institute, Melbourne, VIC, Australia

Background: Mutations in SLC39A8 have recently been reported as the cause of a type II congenital disorder of glycosylation (CDG) in patients with intellectual disability and cerebellar atrophy. Here we report a novel SLC39A8 variant in two siblings with strong clinical, biochemical, radiological and enzymatic evidence of a mitochondrial disorder. Patients and Methods: Two sisters born to consanguineous Lebanese parents presented with profound developmental delay, dystonia, seizures and failure to thrive. Brain MRI of the proband revealed cerebral atrophy and bilateral basal ganglia hyperintensities. CSF lactate was elevated at 4.2 mmol/L. Complexes IV and II + III activity were low in liver, with elevated Complex I activity. Complex IV activity was borderline low in muscle and pyruvate dehydrogenase activity was reduced. Homozygosity mapping and whole genome sequencing (WGS) were performed to provide a genetic diagnosis, together with further biochemical tests. Results: WGS identified a novel homozygous c.338G>C (p.Cys113Ser) variant in SLC39A8, located in one of the eight regions identified by homozygosity mapping. In silico analyses predict the variant to be deleterious. SLC39A8 is absent from the MitoCarta2.0 database but encodes a manganese and zinc transporter which localises to both cell and mitochondrial membranes. Transferrin electrophoresis of patient serum revealed an isoform pattern consistent with a type II CDG defect. Blood and urine manganese levels were low. Conclusion: We report a novel SLC39A8 variant in siblings with profound developmental delay. In addition to symptoms previously reported in SLC39A8 deficiency, our patients had an apparently secondary mitochondrial disorder, expanding the clinical phenotype.

ASIEM Oral 11
A CASE REPORT OF IMPROVED NEUTROPHIL FUNCTION IN GLYCOGEN STORAGE DISEASE (GSD) 1B USING PROPHYLACTIC TRIMETHOPRIM/SULFAMETHOXAZOLE

Katherine Lewis ¹, Troy Dalkeith¹, Melanie Wong², Kaustuv Bhattacharya¹

¹Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Sydney, NSW, Australia
² Department of Allergy and Immunology, The Children's Hospital at Westmead, Sydney, NSW, Australia

Background: Neutropenia and impaired neutrophil function are well-known features of Glycogen Storage Disease (GSD) 1b, and are responsible for significant morbidity. Multiple mechanisms for impaired neutrophil function have been demonstrated regarding impaired motility and respiratory burst. Current standard treatment of neutropenia and related infections is with antimicrobial prophylaxis, most commonly trimethoprim/sulphamethoxazole when absolute neutrophil counts decline below 0.5, and increased neutrophil count with granulocyte colony-stimulating factor (G-CSF). There are, however, significant side effects with the use of G-CSF, including but not limited to worsening splenomegaly, hypersplenism, cutaneous vasculitis, and an increased risk of myelodysplasia and acute myelogenous leukemia. Trimethoprim/sulfamethoxazole has been shown to have demonstrated immunomodulatory effects in Wegener's granulomatosis and rheumatoid arthritis. As yet, there is no routine therapy direct at improving neutrophil function in GSDIb. Aim: To demonstrate the improvement in neutrophil respiratory burst and wound healing with prophylactic trimethoprim/sulphamethoxazole. Method: Prospective intervention with trimethoprim/sulfamethoxazole and immunological monitoring in a single patient with GSDIb. Results: Improvement in gastrostomy wound healing upon introduction of trimethoprim/sulfamethoxazole with concomitant increase of population of active neutrophil respiratory burst from 36% to 100%. After a dose increase 2 years later, proportion increased from 51% to 83% with concomitant gingival health improvement. Discussion/Conclusion: In this case study, trimethoprim/sulphamethoxazole was demonstrated to improve neutrophil function and clinical gum disease and wound healing despite declining absolute neutrophil counts. We postulate that the use of trimethoprim/sulphamethoxazole routinely in GSD1b may significantly reduce the morbidity associated with neutropenia in GSD1b patients and their subsequent reliance on G-CSF.

Concurrent Session 7: Australasian Society of Diagnostic Genomics

ASDG Oral 7
A CROSS-CENTER APPROACH FOR CLINICAL EXOME VALIDATION

Sebastian Lunke ¹, Arthur Hsu¹, Clare Love¹, Kym Pham², Belinda Chong¹, Ksenia Nesic¹, Stefanie Eggers¹, Voula Dimitriadis², Leakhena Leas², Olga Kondrashova², Shannon Cowie¹, Sarah-Jane Pentaleo¹, Melissa Chow¹, Anna Ritchie¹, Desiree Du Sart¹, Damien Bruno¹, Paul Waring², Graham Taylor^1,2,3

¹Victorian Clinical Genetics Services (VCGS), Melbourne, VIC, Australia
² University of Melbourne, Melbourne, VIC, Australia
³ Guy's and St Thomas' Hospitals NHS Trust, London, UK

Background: As massively parallel sequencing continues to become more and more established in diagnostic laboratories around the country, many labs are beginning to shift from targeted sequencing panels to whole exome sequencing. However, despite various guidelines being available on the implementation of the technology, there are neither established standards for validating the performance of the technology nor a framework for analysis and interpretation of the ensuing variant data. Here we present our approach for the validation and implementation of clinical exome sequencing; a collaborative study between the Victorian Clinical Genetics Services and the Centre for Translational Pathology at the University of Melbourne. Methods: A total of over one hundred Illumina Nextera whole exome data sets were generated across the two sites on three different instruments (NextSeq500, HiSeq2500 and HiSeq4000) using both Corriell gold standards and previously analyzed clinical samples. The data was extensively analyzed to establish analytical parameters of the assay. The performance characteristics of our in-house, ACMG-based variant curation scheme were established by having multiple curators at both sites independently interpret variants identified in the relevant target regions of all 116 clinical samples. Results and Conclusions: Using this approach to clinical exome validation we were able to establish the performance of our clinical exome assay in extensive detail, achieving >99% analytical sensitivity, specificity and reproducibility. At the same time, the implemented variant curation scheme allowed us to achieve >95% reproducibility of variant interpretation within and between the two sites.

ASDG Oral 8
EVALUATION OF AN ALTERNATIVE TESTING ALGORITHM INVOLVING CHROMOSOME MICROARRAY AND FISH IGH ANALYSIS IN MULTIPLE MYELOMA

Dale Wright ¹, Artur Darmanian¹, Dorothy Hung¹

¹The Children's Hospital at Westmead, Sydney, NSW, Australia

Background: Multiple myeloma occurs in ~10% of adult hematological malignancies. A range of prognostic chromosome abnormalities can be found, which can include whole chromosome gains only, IGH rearrangements, chromosome 1q gain, loss of TP53, and other complex abnormalities. Our standard testing algorithm included karyotyping with FISH analysis of CD138+ plasma cells for t(11;14), loss of chromosome 13q and TP53. Karyotype abnormalities were limited (~25%) due poor plasma cell proliferation compared to FISH abnormality rates (~60%). Improved diagnostic yields (~90%) have been reported using FISH; however, extensive and labour intensive analysis of multiple probe panels is required. Aim: Evaluate an alternative testing algorithm involving microarray and FISH for IGH rearrangements for multiple myeloma. Method: A prospective cross-sectional myeloma cohort was investigated by karyotype using 24-hr synchronized and 72-hr unsynchronized cultures, FISH analysis for IGH rearrangements and chromosome microarray. The CD138+ EasySep kit (STEMCELL Technologies) was used to enrich plasma cells. Chromosome microarray was performed using the ISCA design (Agilent Technologies) but analyzed at low (1.0Mb) mean resolution. Unless of known prognostic relevance, copy number abnormalities <5Mb were not reported. Results: Altogether, 62 patients had karyotype, FISH and chromosome microarray analysis performed. The abnormality rate for karyotyping was 15/62 (24%), compared to 24/62 (39%) for FISH and 53/62 (86%) for microarray. Combined FISH and microarray abnormality rate was 56/62 (90%). Conclusion: Compared to our standard testing algorithm, increased chromosome abnormalities were found in90% of myeloma patients using IGH FISH supplemented by microarray. We no longer perform karyotyping for multiple myeloma patients.

ASDG Oral 9
EXPLORING THE USE OF WHOLE GENOME SEQUENCING AS A DIAGNOSTIC APPROACH FOR MITOCHONDRIAL DISEASES

Kishore Raj Kumar ^1,2, Ryan Davis¹, Christina Liang¹, Kate Ahmad¹, Jin-Sung Park¹, Andre Minoche², Clare Puttick², Velimir Gayevskiy², John Christodoulou³, Marcel Dinger², Tony Roscioli², Mark Cowley², Carolyn Sue¹

¹Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and The University of Sydney, Sydney, NSW, Australia
² Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
³ Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia

Aim: Mitochondrial diseases are common inherited metabolic disorders with complex and heterogeneous clinical manifestations. Mitochondrial disease can be caused by mutations in both the nuclear or mitochondrial genome. Diagnosis can be challenging, time consuming and expensive and frequently involves invasive tests such as a muscle biopsy. Whole genome sequencing (WGS) promises to be a highly effective diagnostic tool in mitochondrial disease due to its ability to simultaneously sequence both the nuclear and mitochondrial genome. Methods: Over 250 patients with mitochondrial disease were recruited through the Neurogenetics Department at the Royal North Shore Hospital. We included both genetically diagnosed cases (positive controls) and undiagnosed cases. WGS was performed on a Hi Seq X Ten, with small variants identified using the GATK HaplotypeCaller, copy number variants using CNVnator, and structural variants using LUMPY. Using Seave, an in-house variant filtration platform, variants were filtered against the MITOMAP and Mitocarta2.0 databases, prevalence in healthy populations, functional impact, and the likely mode of inheritance. Results: WGS provided very high coverage across the mitochondrial genome allowing for detection of mitochondrial point mutations and small deletions. Furthermore, we were able to estimate heteroplasmy and detect very low levels of heteroplasmic variants. Nuclear mutations were also identified, including new genetic diagnoses for several cases after the identification of mutations in the MFN2, OPA1, POLG, and SPG7 genes. Conclusion: WGS allows for accurate detection of variants in both the nuclear and mitochondrial genomes. This single, streamlined test promises to transform the diagnosis of mitochondrial diseases.

ASDG Oral 10
COST-EFFECTIVENESS OF SINGLETON WHOLE EXOME SEQUENCING COMPARED WITH STANDARD DIAGNOSTIC CARE

Zornitza Stark ¹, Deborah Schofield^1,2,3, Khurshid Alam^1,4, William Wilson^5,6, Nessie Mupfeki^1,5, Ivan Macciocca^1,5, Susan M White^1,5, Clara Gaff^4,5

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
³ Graven Institute of Medical Research, Sydney, NSW, Australia
⁴ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁵ Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
⁶ CSIRO, Melbourne, VIC, Australia

Translation of genomic sequencing technologies from research to appropriately funded clinical practice requires evidence for cost effectiveness and optimal timing of testing. We report the results of a prospective clinical study that addressed this gap by evaluating the cost effectiveness of singleton whole exome sequencing in 40 infants with suspected monogenic disorders who underwent standard diagnostic investigations in parallel. The mean duration of the diagnostic trajectory was 13 months. A molecular diagnosis was achieved in seven infants (18%) through standard diagnostic care, with a cost per successful diagnosis of AU$27,050 (95% CI: 15,366 to 68,530). By contrast, a molecular diagnosis was achieved in 25 infants (63%) using singleton WES, with a cost per diagnosis of AU$5,047. Integrating singleton WES after exhaustive standard investigation results in an incremental cost per additional diagnosis of AU$8,112 (95% CI: 5,851 to 11,967), whereas integrating WES as a first-line test results in an incremental cost per additional diagnosis of AU$2,182 (95%CI: -5,855 to 130). When used as a first-tier test in infants with suspected monogenic disorders, singleton WES not only outperforms standard diagnostic care in terms of diagnostic utility, but is also most cost-effective.

ASDG Oral 11
WHOLE GENOME SEQUENCING AS A MOLECULAR DIAGNOSTIC METHOD FOR AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE — OVERCOMING THE CHALLENGES OF PSEUDOGENE HOMOLOGY AND HIGH GC CONTENT

Amali Mallawaarachchi ¹, Yvonne Hort¹, Mark Cowley^1,2, Mark McCabe^1,2, Andre Minoche¹, Marcel Dinger^1,2, John Shine¹, Timothy Furlong^1,3

¹Garvan Institute of Medical Research, Sydney, NSW, Australia
² St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
³ Department of Renal Medicine, St Vincent's Hospital, Sydney, NSW, Australia

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic kidney disorder, with a prevalence of 1 in 500. ADPKD is caused by mutations in PKD1 or PKD2. Molecular diagnosis is challenging due to six pseudogenes that share 95–97% homology to PKD1 and several regions of high GC-content. Hypothesis: That WGS, given its avoidance of capture and amplification bias, uniform coverage and longer read-lengths, would be better able to uniquely sequence these difficult genomic areas. Method: DNA-libraries were made for a cohort of 29 unrelated-patients with an ADPKD phenotype. 150bp paired-end sequencing was performed using an Illumina HiSeq X sequencer. A second pilot cohort of 4 patients underwent WGS after PCR-free library-preparation. In-house bioinformatics-pipeline aligned unique reads to the reference genome. Analysis of SNPs and CNVs was targeted to PKD1 and PKD2. Long-range PCR amplification and Sanger Sequencing or MLPA was performed to confirm all disease-causing variants. Segregation analysis was performed in 34 additional patients. Results: Molecular diagnosis was made in 29/33 (88%) patients. Interrogation of mapping quality demonstrated unique alignment of reads over pseudogene-homologous regions. In the standard library-preparation cohort, coverage over 4/61 exons was relatively reduced and correlated with GC-content >80%. In the PCR-free cohort, coverage was uniform across all exons. Two multi-exon deletions were also identified. All disease-causing variants were identified via Sanger sequencing or MLPA without false- positives. Conclusion: We demonstrate that WGS can be utilised in ADPKD. The method can overcome pseudogene homology and areas of high GC-content, which has implications for other disease groups.

ASDG Oral 12
THALASSAEMIC SYNDROME RESULTING FROM CO-INHERITANCE OF HAEMOGLOBIN ALPHA (HBA) GENE MULTIPLICATIONS WITH PATHOGENIC HAEMOGLOBIN BETA (HBB) GENE VARIANTS

Catherine Nicholls ¹, Aygul Simsek¹, Keryn Simons¹, Lucas Dejong¹, Mike Attwell¹, Lisa Worgan³, Kate Wraight³, Heather Tapp², Manika Pal², Christopher Barnett⁴, Eleanor Ludington⁴, Hamish S. Scott¹

¹SA Pathology, Adelaide, SA, Australia
² Haematology/Oncology Department, Women's and Children's Hospital, Adelaide, SA, Australia
³ Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia,
⁴ Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, SA, Australia

We report two cases of novel HBA (hemoglobin alpha) gene multiplication co-inherited with a pathogenic HBB (hemoglobin beta) variant. Most clinically significant thalassemic syndromes arise from globin chain imbalance in either the HBA or HBB genes. The two cases presented are remarkable as the risk of a thalassemic syndrome derives from co-inheritance of variants from both the HBA loci and HBB gene. Common HBA1/2 gene deletions were detected using gap PCR. Sequence analysis of the HBA1/2 and HBB genes was performed using Sanger Sequencing with exon dosage detected by MLPA. Case 1: A male (dob 12/07/2006) with transfusion dependent beta thalassemia. Family study detected heterozygosity for HBB:c.93-21G>A in the proband and his father. No other abnormality was detected in his parents HBA1/2 or HBB genes. Alpha globin MLPA and microarray in the proband, however, detected an apparent de novo multiplication of his HBA1/2 genes, resulting in 8 rather than the normal 4 copies of his HBA genes. Case 2: A family of four presenting in the first trimester of the mother's third pregnancy. The mother was heterozygous for HBB:315+1G>A and the father for an alpha globin 3.7kB deletion (-a/). HBA MLPA detected seven HBA genes in the father (i.e., -a/aaaaaa and not a-/aa), eight in one child (aa/aaaaaa) and three in the other (-a/aa). These two cases highlight the necessity of considering HBA1/2 multiplications as the underlying cause of chain imbalance and pathology in suspected cases of beta thalassemia where only one pathogenic variant is detected in the HBB gene.

Concurrent Session 8: Australasian Association of Clinical Geneticists

AACG Oral 7
DE NOVO AND INHERITED MUTATIONS IN THE X-LINKED GENE CLCN4 ARE ASSOCIATED WITH SYNDROMIC INTELLECTUAL DISABILITY AND BEHAVIOUR AND SEIZURE DISORDERS IN MALES AND FEMALES

Elizabeth Palmer ¹, Stefanie Weinert³, Till Stuhlmann³, Eric Haan⁴, Hilde Van Esch⁵, Maureen Holvoet⁵, Jacqueline Boyle¹, Melanie Leffler¹, Martine Raynaud⁶, Claude Moraine⁶, Hans van Bokhoven⁷, Tjitske Kleefstra⁷, Kimia Kahrizi⁸, Hossein Najmabadi⁸, Hans-Hilger Ropers⁹, Mauricio R. Delgado¹⁰, Deepa Sirisi¹⁰, Sailaja Golla¹⁰, Annemarie Sommer¹¹, Marguerite P. Pietryga¹¹, Wendy K Chung¹², Julia Wynn¹², Luis Rohena¹³, Erika Bernardo¹³, Damara Hamlin¹³, Brian M. Faux¹³, Dorothy K. Grange¹⁴, Linda Manwaring¹⁴, John Tolmie¹⁵, Sbelagh Joss¹⁵, DDD study¹⁶, Floor A.M. Duijkers¹⁷, Jan M. Cobben¹⁷, Jessica M. Goehringer¹⁸, Thomas D. Challman¹⁸, Friederike Hennig¹⁹, Ute Fischer¹⁹, Astrid Grimme¹⁹, Vanessa Suckow¹⁹, Luciana Musante¹⁹, Jillian Nicholl²⁰, Marie Shaw²¹, Suhrid P. Lodh², Zhiyv Niu²², Jill A. Rosenfeld²², Pawel Stankiewicz²², Thomas J. Jentsch³, Jozef Gecz²¹, Michael Field¹, Vera M. Kalscheuer⁹

¹Genetics of Learning Disability Service, Waratah, Newcastle, NSW, Australia
² University of New South Wales, Sydney, NSW, Australia
³ Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
⁴ School of Medicine, The University of Adelaide, Adelaide, SA, Australia
⁵ Center for Human Genetics, University Hospitals, Leuven, Belgium
⁶ Inserm U930 ‘Imaging and Brain’, France
⁷ Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
⁸ Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
⁹ Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
¹⁰ University of Texas Southwestern Medical Center, Dallas, TX, USA
¹¹ Nationwide Children's Hospital, Columbus, OH, USA
¹² Columbia University, New York, NY, USA
¹³ Department of Pediatrics, San Antonio Military Medical Center, Fort Sam, Houston, TX, USA
¹⁴ Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO, USA
¹⁵ West of Scotland Clinical Genetics Service, Southern General Hospital, Glasgow, UK
¹⁶ Wellcome Trust Sanger Institute, Hinxton, UK
¹⁷ Department of Pediatrics, AMC University Hospital Amsterdam, Amsterdam, the Netherlands
¹⁸ Autism & Developmental Medicine Institute, Geisinger Health System Lewisburg, PA, USA
¹⁹ Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Germany
²⁰ SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
²¹ Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
²² Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA

Variants in CLCN4, which encodes the chloride/hydrogen ion exchanger CIC-4 prominently expressed in brain, were recently described to cause X-linked intellectual disability and epilepsy. We present detailed phenotypic information on 52 individuals from 16 families with CLCN4 related disorder: 5 affected females and 2 affected males with a de novo variant in CLCN4 (6 individuals previously unreported) and 27 affected males, 3 affected females and 15 asymptomatic female carriers from nine families with inherited CLCN4 variants (four families previously unreported). Intellectual disability ranged from borderline to profound. Behavioral and psychiatric disorders were common in both child- and adulthood, and included autistic features, mood disorders, obsessive compulsive behaviors and hetero and autoagression. Epilepsy was common, with severity ranging from epileptic encephalopathy to well-controlled seizures. Several affected individuals showed white matter changes on cerebral neuroimaging and progressive neurological symptoms, including movement disorders and spasticity. Heterozygous females can be as severely affected as males. The variability of symptoms in females is not correlated with the X-inactivation pattern studied in their blood. The mutation spectrum includes frameshift, missense and splice site variants and one single-exon deletion. All missense variants were predicted to affect CLCN4’s function based on in silico tools and either segregated with the phenotype in the family or were de novo. Pathogenicity of all previously unreported missense variants was further supported by electrophysiological studies in Xenopus levis oocytes. We compare CLCN4-related disorder to conditions related to dysfunction of other members of the CLC family.

AACG Oral 8
IDENTIFICATION OF A NOVEL AUTOSOMAL DOMINANT SLOWLY PROGRESSIVE LATE ONSET ATAXIA CO-SEGREGATING WITH A CHROMOSOME 14 DELETION/DUPLICATION

Melanie Bahlo², Rick Tankard², Mac Gardner³, Elsdon Storey⁴, Trent Burgess⁵, Amber Boys⁵, Michael Fahey⁴, Greta Gillies¹, Stephen Robertson⁶, Martin Delatycki ¹, Paul Lockhart¹

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Walter and Eliza Hall Institute, Melbourne, VIC, Australia
³ Genetic Health Service NZ
⁴ Monash University, Melbourne, VIC, Australia
⁵ Victorian Clinical Genetics Service, Melbourne, VIC, Australia
⁶ Otago University, Dunedin, New Zealand

Background: Autosomal dominant spinocerebellar ataxias are a group of disorders that present with largely adult onset ataxia with variable speed of progression, and variable associated neurological symptoms. At least 42 types with an associated chromosomal locus have been described and in a number of these, the underlying genetic basis has been identified. Methods: We have identified a family with at least 22 individuals affected by a relatively pure cerebellar ataxia. Onset of ataxia is generally beyond 40 years and does not limit lifespan. The disease is very slowly progressive with individuals often ambulant many years after symptom onset. MRI of brain revealed atrophy of the superior and dorsal cerebellar vermis and mild atrophy of the cerebellar hemispheres. The brain stem was normal. Results: Eight individuals with ataxia from the family, separated by a total of 20 meioses, have been shown to have a novel deletion/duplication of 14q32.13 using chromosomal microarray. The deletion and duplication each include four OMIM genes. None of the eight genes are known disease genes and none are obvious candidates for the phenotype. Linkage mapping within a branch of the family shows that the del/dup co- segregates with the phenotype. Discussion: It is most likely that one of the deleted genes is responsible for the phenotype in this family. RNA-seq and assessment of the eight genes in WES/WGS data from individuals with unsolved ataxia are underway. Microarray can occasionally identify the cause of ataxia and should be included in the work up of individuals with this presentation.

AACG Oral 9
CLINICAL AND MOLECULAR CHARACTERIZATION OF FRONTONASAL DYSPLASIA

Patrick Yap ¹, Stefanie Eggers^3,4, Naomi Baker^3,4, David Amor^1,3,4, George McGillivray^1,3, Kate Pope³, Martin Delatycki^1,3,4, Matthew Hunter^5,6, Alicia Oshlack³, Peter Farlie^3,4, Tiong Yang Tan^1,3,4

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Genetic Health Service New Zealand, Auckland, New Zealand
³ Murdoch Childrens Research Institute, Melbourne, VIC, Australia
⁴ Dept of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁵ Austin Health Clinical Genetics Services, Melbourne, VIC, Australia
⁶ Dept of Paediatrics, Monash University, Melbourne, VIC, Australia

Objectives: (1) To clinically characterise a cohort of patients with FND to identify phenotypic subgroups. (2) To use microarray, a custom targeted craniofacial panel and whole exome sequencing to identify the molecular spectrum of mutations in known genes and novel FND genes. Methods: We used the databases of the Victorian Clinical Genetics Services and Royal Children's Hospital Craniofacial Clinic to identify potential participants with FND. We also recruited patients prospectively from outpatient clinics, inpatient referrals and international collaborators. We used a standardized assessment and 3-dimensional photography for clinical phenotyping. We undertook microarrays and a custom SureSelect NGS panel to screen for variants in known FND genes. Exome sequencing was used to identify novel genes in mutation-negative patients. Results: Our cohort of 17 probands comprises Craniofrontonasal dysplasia (6), FND (7) and Oculoauricolofrontonasal syndrome (3), as well as a 3-generational family with a novel Xq13.1 duplication involving the EFNB1 gene. We also characterized three provisionally unique FND phenotypes. We identified one novel mutation in EFNB1, and functional studies are underway to determine the clinical significance of the variant identified by exome sequencing. Conclusions: Our findings confirm that FND is a clinically and genetically heterogeneous group that requires detailed phenotyping in order to establish the causative molecular lesion.

AACG Oral 10
THE GENETIC CAUSES OF AICARDI SYNDROME: X MAY NOT MARK THE SPOT

Thuong Ha ¹, Rosie Burgess², Morgan Newman³, Melody Li⁴, Alison Gardner⁵, Duyen Pham⁵, Raman Kumar⁵, Christopher Reid^4,6, Steven Petrou⁴, Nicholas Smith^5,7, Sam Berkovic^2,8, Clare van Eyk⁹, Michael Lardelli³, Ingrid Scheffer⁶, Jozef Gecz^1,5, Mark Corbett⁵

¹School of Biological Sciences, University Of Adelaide, Adelaide, SA, Australia
² Epilepsy Research Centre, University of Melbourne, Melbourne, VIC, Australia
³ Alzheimer's Disease Genetics Laboratory, University of Adelaide, Adelaide, SA, Australia
⁴ Florey Department of Neuroscience and Mental Health, Melbourne, VIC, Australia
⁵ School of Medicine, University of Adelaide, Adelaide, SA, Australia
⁶ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁷ Department of Neurology, Women's and Children's Hospital, Adelaide, SA, Australia
⁸ Department of Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
⁹ Australian Collaborative Cerebral Palsy Research Group, University of Adelaide, Adelaide, SA, Australia

Aicardi syndrome (OMIM 304050; AIC) is a rare, almost female exclusive, severe neurodevelopmental disorder defined by chorioretinal lacunae, infantile spasms and a characteristic malformation of cortical development that includes agenesis of the corpus callosum. AIC is traditionally thought to be an X-linked male lethal disorder however, despite numerous investigations the causes of AIC remain largely enigmatic. This study aim to identify the genetic causes underlying AIC. We performed whole exome sequencing (WES) on eight parent-proband trios and four additional individuals diagnosed with AIC. We enriched for likely causative variants based on: predicted pathogenicity, amino acid conservation, variant allele frequency and clinical significance. In four different individuals we identified de novo variants in the ANKRD32, HCN1, SZT2 and WNT8B genes respectively. We showed, using in vitro assays that the HCN1 variant left-shifted the voltage-dependence of activation resulting in a loss of function, while the WNT8B variant had a dominant negative effect on WNT signaling; the functions of SZT2 and ANKRD32 are as yet unknown. We used morpholino knockdowns of all the genes we implicated in AIC and a recently published AIC gene (TEAD1) in zebrafish. We identified a unifying morphant phenotype of AIC-like eye and brain defects among 2/3 genes tested so far. Our study demonstrates that AIC is genetically heterogeneous and, importantly, we challenge the dogma that AIC is X-linked. We show that the WNT signalling pathway, which is already well known for its roles in eye and brain development, is a contributor to the molecular pathogenesis of AIC.

AACG Oral 11
CHILDREN DIAGNOSED WITH TUBEROUS SCLEROSIS ANTENATALLY/ BEFORE SEIZURES — ARE THEY A LESS SEVERE GROUP OF PATIENTS?

Clara Chung ¹, John Lawson^1,4, Vanessa Sarkozy^1,4, Sean Kennedy^1,4, Kate Riney², Orli Wargon¹, Stephen Cooper¹, Antonia Shand³, David Mowat^1,4

¹Sydney Children's Hospital, Sydney, NSW, Australia
² Lady Cilento Children's Hospital, Brisbane, QLD, Australia
³The Royal Hospital for Women, Sydney, NSW, Australia
⁴School of Women's and Children's Health, The University of New South Wales, Sydney, NSW, Australia

Background: Tuberous sclerosis complex (TSC) is an autosomal dominant condition caused by mutations in the TSC1 or TSC2 gene with a birth incidence of 1 in 6,000. TSC is associated with variable neurodevelopmental outcomes, seizures and benign tumours in various organs. In most cases, the diagnosis is made after seizures have occurred. Approximately 17% are diagnosed antenatally. Neurodevelopment outcome is linked to seizure severity. Trials aimed at improving outcome with early use of vigabatrin and mTOR inhibitors are underway. Early diagnosis of TSC, preferably prior to seizure onset, will be needed to maximize benefit. Aim/Methods: Retrospective medical records review of all TSC patients born between 2001 and 2015 who were seen in the TSC clinic at Sydney Children's Hospital. We compared those diagnosed pre- and post- seizure to determine if a pre-seizure TSC diagnosis results in better long-term neurodevelopmental outcome. Results: 74 patients were ascertained: 34 diagnosed pre-seizure (21 antenatally), 40 diagnosed post-seizure. (1) Of those diagnosed pre-seizure, 77% presented with cardiac rhabdomyoma(s). (2) 72% of the pre-seizure cohort developed clinical seizures — 53% by 12 months of age, compared with 87% of the post-seizure cohort. (3) 47% of the pre-seizure patients had developmental disability (DD) compared with 68% of the post- seizure patients (p = .027). Conclusion: (1) Pre-seizure TSC cases have a milder clinical course with less severe DD and fewer seizures. (2) Fetuses/children with cardiac rhabdomyomas ought to be assessed for possible diagnosis of TSC. 3. Pre-seizure TSC infants need active management to identify onset of seizures and provide early treatment.

AACG Oral 12
ANTENATAL DIAGNOSIS OF MARKED HYDROCEPHALUS (CCDC88C-RELATED) CAN HAVE A SURPRISINGLY GOOD OUTCOME

Mathew Wallis ¹, Allessandra Baumer², Erica Jacobson³, Wiam Smaili⁵, David Mowat⁴, Anita Rauch²

¹Department of Clinical Genetics, Austin Health, Melbourne, VIC, Australia
² Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
³ Department of Neurosurgery, Sydney Children's Hospital, Sydney, NSW, Australia
⁴ Department of Medical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia,
⁵ Department of Genetic Medicine, National Institute of Hygiene, Rabat, Morocco

Background: Non-syndromic congenital hydrocephalus is etiologically diverse. A genetic cause is often suspected but cannot always be confirmed. The most common genetic cause is the L1CAM-related X-linked hydrocephalus and that explains only 5–10% of all male cases. This underlines a current limitation in our understanding of the genetic burden of non-syndromic congenital hydrocephalus, especially for those cases with likely autosomal recessive inheritance. The prognosis for most cases of severe congenital hydrocephalus is poor, with a majority of surviving infants displaying significant intellectual impairment despite surgical intervention. It is for this reason that couples with a prenatal diagnosis are given the option, and may opt, for termination of the pregnancy. Aim and Method: We aim to review the neurodevelopmental outcomes of patients with CCDC88C-related autosomal recessive hydrocephalus by analyzing all previously reported cases and presenting two new families. Results: Individuals who did not require multiple surgical revisions and had a more distal truncating mutation of the CCDC88C gene had normal neurodevelopment in most cases. Conclusion: These reported cases suggest that children with CCDC88C-related autosomal recessive hydrocephalus can have a normal neurodevelopmental outlook despite severe hydrocephalus on antenatal and neonatal imaging studies. The likelihood of a normal outcome may be mutation-specific and/or relate to the presence of additional surgical complications. We recommend including CCDC88C analysis in cases of severe non-syndromic congenital hydrocephalus with possible recessive inheritance, especially when aqueduct stenosis with or without a medial diverticulum are seen.

Concurrent Session 9 — Submitted Orals

Oral 1
THE EVOLVING ROLE OF GENOMIC DYSMORPHOLOGY

Susan Marie White ¹, Zornitza Stark¹, Maie Walsh¹, Patrick Yap¹, David Amor^1,2, Alison Yeung¹, George McGillivray¹, Ravi Savarirayan^1,2, Clara Gaff^3,4, Ivan Macciocca^1,3, A/Tiong Yang Tan^1,2

¹Victorian Clinical Genetics Service, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
³ Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
⁴ Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia

Next-generation sequencing is changing the practice of dysmorphology. In the Melbourne Genomics Health Alliance, we undertook a prospective study of singleton whole exome sequencing (WES) in parallel with standard care in 145 syndromic children. Results on 80 infants are complete, with a molecular diagnosis by WES reached in 47 (59%), compared with 14% by standard care. One third of diagnoses resulted in a change to the child's medical care. This presentation will reflect upon the many ways that the WES project has changed our dysmorphology practice. 80% of diagnoses were in genes suspected clinically, emphasizing the importance of accurate phenotyping. We were also reminded of its limits: 20% of our diagnoses were in genes thought clinically unlikely or not suspected at all. Clinical geneticists worked closely with laboratory scientists to facilitate phenotype-driven selection of variants for curation and accurate interpretation of the clinical validity of genomic data. This improved the genomic literacy within our clinical team. Dysmorphology meetings broadened scope to include discussion of patient suitability for exome testing and generation of patient-specific gene lists. We introduced multidisciplinary meetings with clinical and molecular genetics, bio-informatics and researchers to reach consensus on variant pathogenicity. We started a genomics clinic to integrate WES into clinical care and employed a genomics genetic counselor who coordinated workflow processes, laboratory liaison and case management. In addition to the benefits of improved diagnosis rates and patient outcomes, integrating genomics into our practice is revolutionizing the way we work.

Oral 2
A CLINICALLY DRIVEN VARIANT PRIORIZATION SCHEME OUTPERFORMS IN SILICO APPROACHES FOR THE DIAGNOSTIC ANALYSIS OF WES DATA

Zornitza Stark ¹, Tiong Yang Tan^1,2, Natalie Thorne^1,2,3, Alicia Oshlack^1,2, Simon Sadedin¹, Melbourne Genomics Health Alliance³, Susan M White^1,2, Paul A James⁴

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² University of Melbourne, Melbourne, VIC, Australia
³ Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
⁴ Royal Melbourne Hospital, Melbourne, VIC, Australia

Background: Rapid identification of clinically significant variants is key to the successful application of next generation sequencing technologies in clinical practice. Methods: The Melbourne Genomics Health Alliance (MGHA) variant prioritization scheme employs a gene prioritization index (GPI) based on clinician-generated a priori gene lists, and a variant prioritization index (VPI) based on rarity, conservation and protein effect. We used data from 46 diagnosed patients to test the scheme's ability to rank disease-causing variants highly. The phenotypic and WES data from the same patients was used to evaluate the performance of other gene and variant prioritization tools such as Exomiser, CADD and Condel scores, PhenoTips and Phenomizer. Results: The average rank of disease-causing variants using the MGHA prioritization scheme was 2.48, with 51 of 58 variants (87.9%) ranked within the top 5 variants in the patient datasets. Exomiser, CADD and Condel did not score or rank some disease-causing variants at all. For the variants that were ranked, the average rank of the disease-causing variant provided by Exomiser was 15.6, CADD was 12.7 and Condel was 13.1. Exomiser outperformed CADD and Condel in placing more disease-causing variants within the top 5 (53% vs. 36% and 33% respectively). Clinicians included 40 of the 48 WES diagnoses in their a priori list of differential diagnoses (83%). The lists generated by PhenoTips and Phenomizer contained 14 (29%) and 18 (37.5%) of these diagnoses respectively. Conclusions: These results highlight the benefits of structured phenotyping and clinically-driven variant prioritization in increasing the efficiency of WES data analysis.

Oral 3
EXOME SEQUENCING HAS HIGHER DIAGNOSTIC YIELD COMPARED TO DISEASE-SPECIFIC PANELS IN 145 CHILDREN SUSPECTED OF HAVING MONOGENIC DISORDERS

Oliver Dillon ¹, Zornitza Stark^2,3, Belinda Chong², Dean Phelan^2,3, Miss Gemma R Brett^2,3, Miss Emma Creed³, Maie Walsh^2,3, Lilian Downie^2,3, David J Amor^1,2,3, Ravi Savarirayan^1,2,3, George McGillivray^2,3, Alison Yeung^2,3, Heidi Peters^3,4, Susan Robertson⁴, Aaron J Robinson⁴, Ivan Macciocca^2,3, Natalie Thorne⁵, Clara Gaff^3,5, Susan M White^1,2,3, Tiong Yang Tan^1,2,3

¹University Of Melbourne Department of Paediatrics, Melbourne, VIC, Australia
² Victorian Clinical Genetics Service, Melbourne, VIC, Australia
³ Murdoch Children's Research Institute, Melbourne, VIC, Australia
⁴ The Royal Children's Hospital, Melbourne, VIC, Australia
⁵ Walter and Eliza Hall Institute, Melbourne, VIC, Australia

Background: With the falling cost of exome sequencing, its worth in clinical diagnostics is increasingly evident. In patients for whom exome sequencing is considered, the alternative testing option is a commercial gene panel. Objective: We sought to compare the diagnostic yield of exome sequencing against hypothetical disease-specific gene panels in 145 prospectively recruited children suspected of having a monogenic disorder. Methods: We undertook exome sequencing with targeted phenotype-driven analysis in all children. At recruitment, each child's primary clinician was required to report the alternative testing options being considered in each case, if an exome were not available. In those diagnosed by exome sequencing, we analyzed the alternative test options to determine if the causative gene would have been identified. For each panel, we selected three commercial providers for analysis. We also evaluated the costs of alternative testing options compared to exome sequencing. Results: Clinicians proposing children for exome sequencing included pediatric neurologists, metabolic physicians, and clinical geneticists. The majority of children had dysmorphic features with congenital anomalies, or a neurometabolic disorder. Specific disease subgroups included skeletal dysplasias, eye, gastrointestinal or dermatological disorders. Overwhelmingly, exome sequencing was superior to gene panels in identifying the causative mutation. This was particularly evident in children with less specific phenotypes or dual diagnoses. Conclusions: We found that exome sequencing has higher diagnostic yield and is a more cost-effective strategy compared to a gene panel. Our data also provide insights into which children are most likely to benefit from exome sequencing over a gene panel.

Oral 4
THE GENOMIC AUTOPSY: USING WHOLE GENOME SEQUENCING TO SOLVE COMPLEX FETAL AND NEONATAL PRESENTATIONS

Christopher Barnett ¹, Alicia Byrne^2,3, Lynette Moore⁴, Jill Lipsett⁴, Nicholas Manton⁴, Yee Khong⁴, Sui Yu², Marcel Dinger⁵, Babic Milena^2,3, Peter Brautigan^2,3, Quentin Schwartz³, P Thomas⁶, Christopher Hahn^2,3, F Feng^6,7, Andreas Schreiber^6,7, Karin Kassahn^2,3, Hamish Scott^2,3,6,7

¹Women's And Children's Hospital/SA Pathology, Adelaide, SA, Australia
²Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
³ Centre for Cancer Biology, An alliance between SA Pathology & University of South Australia, Adelaide, SA, Australia
⁴ Department of Anatomical Pathology, SA Pathology at the Women's and Children's Hospital, Adelaide, SA, Australia
⁵ Kinghorn Centre for Clinical Genomics, the Garvan Institute, Sydney, NSW, Australia
⁶ School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
⁷ ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia

Background: Congenital abnormalities are the most frequent reason for mid-term stillbirth and termination of pregnancy. Unexplained late fetal deaths in utero, or in the newborn period, affect ~4/1000 births. Formal post-mortem examination is performed in these settings in South Australia in ~60% of cases (200/year), but despite this no definitive cause of the congenital abnormalities or death is found in 25–50% of cases. Aim: To use whole genome sequencing (WGS) to identify genetic causes of fetal and newborn abnormalities that result in termination of pregnancy, death due to congenital abnormalities, death in utero or death in the newborn period, in view to providing families with answers regarding cause and recurrence risk. Methods: WGS will be performed on 40 samples per year for 3 years, using the IlluminaHiSeq X Ten System. High priority cases are fetuses with congenital abnormalities with consanguineous parents (proband sample only); fetuses with multiple malformations; and unexplained fetal/newborn death (trio samples). Tertiary bioinformatics and primary functional assays will be used to confirm causality of variants. Results: This project is in its first year. Pilot data will be presented from the first WGS's performed, with specific focus on our discovery of a new autosomal recessive polycystic kidney disease gene, leading to a successful reproductive outcome for a family.

Discussion: Genomic autopsy using WGS offers enormous potential as an adjunct to traditional autopsy in providing accurate genetic counseling for families who have experienced pregnancy loss, death in utero, termination of pregnancy or death in the newborn period.

Oral 5
COST-EFFECTIVENESS OF THE DIAGNOSTIC WHOLE EXOME SEQUENCING APPROACH IN EPILEPTIC ENCEPHALOPATHY

Rani Sachdev^1,2, Elizabeth E. Palmer^2,3, Deborah Schofield^5,6, Rupendra Shrestha⁵, Tejaswi Kandula^1,2, Rebecca Macintosh¹, Hugo Sampiao^1,2, Ian Andrews^1,2, John Lawson^1,2, Alexandra Johnson^1,2, Michael Cardamone^1,2, Michelle Farrar^1,2, William Lo⁴, George Elakis⁴, Ying Zhu^3,4, Michael Buckley⁴, Marcel Dinger⁶, Mark Cowley⁶, Edwin P Kirk^1,2,4, Tony Roscioli^1,6, Ann Bye^1,2

¹Sydney Children's Hospital, Sydney, NSW, Australia
² Department of Women and Children's Health, Randwick Campus, University of New South Wales, Sydney, NSW, Australia
³ Genetics of Learning Disability Service, Waratah, Newcastle, NSW, Australia
⁴ SEALS Pathology, Sydney, NSW, Australia
⁵ Charles Perkins Centre University of Sydney, Sydney, NSW, Australia
⁶ The Kinghorn Centre for Clinical Genomics, Garvan Institute, Sydney, NSW, Australia

Diagnostic whole exome sequencing (ES) is rapidly becoming integrated in clinical practice. Comparison of the ES approach to the previous ‘traditional’ testing approach has been repeatedly postulated to be cost-effective, mainly due to improved diagnostic yield and the potential to avoid an invasive and expensive ‘diagnostic odyssey’. However, there is a paucity of health costing data to support this assertion. We present a comprehensive health-costings comparison for a well phenotyped cohort of 32 patients with epileptic encephalopathy (EE), using a counterfactual model, of a ‘trio ES’ model and ‘traditional’ diagnostic approach. EEs are severe epilepsies impacting cognition in which rapid establishment of etiology is important; however, traditional diagnostic approaches are invasive and expensive because of genetic heterogeneity and limited genotype-phenotype correlation. The cohort comprises EE patients seen at the Sydney Children's Hospital, born between 2000 and 2014, who remained undiagnosed after ‘first-tier’ testing. We determined the diagnostic yields (2/32;6.2% for the ‘traditional’ arm compared to 18/32;56.2% for the ‘trio ES’ arm), the comparative costs per patient ($11,937 ‘traditional arm’; $9,550 ‘trio ES’ arm) and per diagnosis ($190,999 per diagnosis ‘traditional’ arm and $16,978 ‘trio ES’ arm). We also present an analysis of projected diagnostic yields and costs for a variety of commercial trio exomes and EE panels. This study uniquely compares the diagnostic yield and cost of an ES and traditional approach for EE, and has important health policy implications for the diagnosis of Mendelian conditions in the next generation sequencing age.

Oral 6
USING MASSIVELY PARALLEL SEQUENCING TO DETERMINE THE GENETIC BASIS OF LEIGH SYNDROME, THE MOST COMMON PAEDIATRIC MITOCHONDRIAL DISORDER

Nicole J. Lake ^1,2, Alison G. Compton^1,2, Sarah E. Calvo^3,4,5, Vamsi K. Mootha^3,4,5, David R. Thorburn^1,2,6

¹Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
³ Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
⁴ Department of Systems Biology, Harvard Medical School, Boston, MA, USA
⁵ Broad Institute of Harvard and MIT, Cambridge, MA, USA
⁶ Victorian Clinical Genetic Services, Royal Children's Hospital, Melbourne, VIC, Australia

Aim: To identify the maximum diagnostic yield of massively parallel sequencing (MPS) in patients with Leigh syndrome (LS), the most common pediatric mitochondrial disease. Background: LS is a neurodegenerative disorder caused by mutations in >75 genes, encoded by both mitochondrial (mt) and nuclear DNA, with maternal, autosomal recessive or X-linked inheritance. This study focused on a published cohort of 67 patients with LS or Leigh-like disease. Methods: DNA from all 33 patients lacking a genetic diagnosis underwent whole exome sequencing supplemented with mtDNA baits, followed by targeted analysis of ~2200 genes (known and candidate mitochondrial disease genes, and differential diagnosis genes). Variants were identified using GATK Best Practices. Functional effects of rare variants were determined in silico, and through analyzing RNA and protein extracted from patient tissue and cells. Results: Pathogenic variants in 11 genes were identified in 16 of 33 patients, including multiple novel mutations. Careful analysis of MPS data, supplemented with identification of copy number variants using ExomeDepth, enabled genetic diagnosis where routine filtering yielded no candidates. We have now established the genetic basis in 75% of the total cohort (67 patients), including 34 of 35 LS patients and 16 of 32 Leigh-like patients. Possible genetic diagnoses, including in differential diagnosis genes, are under evaluation in 10 patients. Conclusions: Our results show that MPS can potentially identify the genetic basis in nearly 100% of patients with tightly defined LS, despite marked genetic and clinical heterogeneity. They also emphasize utility of a broader gene list, particularly in atypical patients.

Concurrent Session 10 — Submitted Orals

Oral 7
MAINSTREAMING GENOMICS — A THEORY-INFORMED SYSTEMATIC REVIEW OF CLINICIANS’ GENETIC TESTING PRACTICES

Jean Paul ¹, Hanna Leslie², Alison Trainer^3,4,5, Clara Gaff^1,5,6

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Paediatric & Reproductive Unit, SA Clinical Genetics Service, Adelaide, SA, Australia
³ Familial Cancer Centre, The Royal Melbourne Hospital, Melbourne, VIC, Australia
⁴ Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
⁵ The University of Melbourne, 6Melbourne Genomics Health Alliance, Melbourne, VIC, Australia

Background: Advances in genomic tests have increased technical efficiency and sensitivity of variant detection. Incorporating new tests into existing practice involves a change in clinical practice and a significant lag has previously existed between development of a genetic test and its adoption into mainstream healthcare. Lessons from monogenetic testing may help us anticipate clinicians’ needs and concerns towards offering more comprehensive genomic tests, facilitating the effective introduction of such tests into mainstream healthcare. Aim: To identify factors affecting appropriate use of genetic tests by non-genetic-trained clinicians through a systematic review grounded in behaviour change theory. Methods: Studies which investigated non-genetic-trained clinicians’ experience with offering genetic tests were identified from five electronic databases. These were critically appraised and using content analysis, were mapped to the Theoretical Domains Framework (TDF). Results: Twenty-five studies met inclusion criteria. The majority were conducted in the United States, used quantitative design, and investigated cancer genetic testing. Many had low response rates, and survey design lacked a theoretical basis. TDF factors identified which may impact upon clinicians’ decisions to offer genetic tests included: knowledge, genetic test factors (uncertainty, incidental results), patient factors, organizational factors, professional factors, and ethical, legal, social and systemic factors. Conclusions: Using the TDF, we have produced a comprehensive overview of factors influencing clinicians’ testing decisions, identifying areas for possible change to support mainstreaming genomic testing. Our findings demonstrate that more than education is required to incorporate new tests into clinical practice, and further theory-based research is needed to inform the successful introduction of genomic testing.

Oral 8
‘WHAT DOES THIS RESULT MEAN FOR ME?’ EXPERIENCE WITH CHANGING INTERPRETATION OF COPY NUMBER VARIANTS ON THE X CHROMOSOME 2008–2015 AND CHALLENGES IN GENETIC COUNSELING

Melanie Leffler ¹, Elizabeth Emma Palmer^1,2, Louise Christie¹, Jackie Boyle¹, Carolyn Rogers¹, Rosie Fell¹, Tracy Dudding-Byth^1,3, Nicole Bain⁴, Greg Peters^5,6, Artur Darmanian⁵, Trent Burgess^7,8, Amber Boys⁷, Jozef Gecz^8,9, Michael Field^1,3, Anna Hackett^1,3

¹The Genetics of Learning Disability (GOLD) Service, Waratah, Newcastle, NSW, Australia
² University of New South Wales, Sydney, NSW, Australia
³ Grow Up Well Priority Research Centre, University of Newcastle, Newcastle, Australia,
⁴ Pathology North — Hunter, Newcastle, NSW, Australia
⁵ Children's Hospital at Westmead, Sydney, NSW, Australia
⁶ University of Sydney, Sydney, NSW, Australia
⁷ VCGS Pathology, Melbourne, VIC, Australia
⁸ University of Melbourne Department of Paediatrics, Royal Children's Hospital, Melbourne, VIC, Australia
⁹ School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
¹⁰ Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia

Chromosomal microarray (CMA) is considered a standard ‘first-line’ investigation for the cause of intellectual disability (ID) and autism spectrum disorder (ASD), and is increasingly requested for a diverse range of indications including in the prenatal setting. The detection of variants of uncertain clinical significance (VOUS), especially on the X chromosome, results in a substantial clinical dilemma. Clinicians are often uncertain how to best counsel the individual or family, or further investigate the significance of findings. The Genetics of Learning Disability (GOLD) Service is a unique clinical genetics service that has seen over 600 families with all forms of familial ID. Our referral criteria include individuals with VOUS/potentially pathogenic CNV on the X chromosome. Our service benefits from the ability to perform detailed segregation analysis and collaborative links with diagnostic and research genetics laboratories. We present a retrospective case series of 40 families seen through our service since 2007 who had a CNV identified on the X chromosome. 75% (n = 30) of the initial laboratory reports classified the CNV as VOUS, with 25% (n = 10) classifying the CNV as pathogenic. After further investigation, and reclassification of 28 results, we currently regard 45% (n=18) as pathogenic/likely pathogenic, 47% (n = 19) as benign/likely benign, and only 8% (n = 3) as VOUS. We report the clinical and molecular strategies that have been most helpful in assessing variant pathogenicity and highlight particular challenges in genetic counseling regarding complex and uncertain genetic results, using a recent prenatal case as an example of how families utilize revised reporting of CMA.

Oral 9
GENETIC COUNSELING CHALLENGES WITH REPRODUCTIVE GENETIC CARRIER SCREENING FOR CYSTIC FIBROSIS, FRAGILE X SYNDROME AND SPINAL MUSCULAR ATROPHY: EXPERIENCE WITH 10,000 PATIENTS

Alison Archibald ^1,2,3, Katrina Scarff¹, Melanie Smith¹, Justine Elliott¹, Clare Hunt¹, Zoe McDonald¹, Caitlin Barns-Jenkins¹, Chelsea Holt¹, Karina Sandoval¹, Vanessa Siva Kumar¹, Lisa Ward¹, Shannon Cowie¹, Trent Burgess^1,2, David Amor^1,2,3,4, Eppie Yiu^2,3,4, John Massie^2,3,4, Desiree Du Sart^1,2, Damien Bruno^1,2

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Murdoch Childrens Research Institute, Melbourne, VIC, Australia
³ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
⁴ Royal Children's Hospital, Melbourne, VIC, Australia

For the past 3 years Victorian Clinical Genetics Services (VCGS) has been offering the Reproductive Genetic Carrier Screen (RGCS) for: cystic fibrosis (CF), fragile X syndrome (FXS) and spinal muscular atrophy (SMA). This novel screen is offered due to high carrier frequencies, the significant impact on affected individuals and their families, accurate tests and research indicating support for screening. RGCS is offered in general practice, obstetrics, fertility and genetics settings in pre-pregnancy and/or early pregnancy. Carriers are offered genetic counseling and partner testing with prenatal testing available to pregnant couples at increased risk for any of the conditions. Appointments with physicians specializing in the condition are also offered. Screening of 10,000 people has revealed 516 carriers of one or more conditions (5.2%; 1 in 19): 293 CF (56%), 28 FXS (5%), 204 SMA (39%), including 9 carriers of 2 conditions. At least 86% of partners of CF and SMA carriers were tested. Thirty-seven couples were at increased risk of having a child with one of these conditions (11 CF, 25 FXS and 1 SMA) and 25 were pregnant. Of these, 22 opted for prenatal diagnosis (6 affected: 3 CF, 2 FXS, 1 SMA). Increased risk couples utilized prenatal diagnosis and/or PGD for subsequent pregnancies. Genetic counseling challenges will be discussed including: cascade testing, managing ‘low’ FXS permutation results (<60 CGG repeats), and the clinical utility of SMN2 testing in prenatal diagnosis for SMA carrier couples. Successful carrier screening for these conditions requires the availability of appropriate genetic counseling support.

Oral 10
IMPACT OF A POSITIVE HYPERTROPHIC CARDIOMYOPATHY GENE RESULT IN ASYMPTOMATIC FAMILY MEMBERS

Catherine Spinks ¹, Carissa Bonner², Christopher Semsarian^1,3,4, Alexandra Barratt², Kirsten McCaffery², Jodie Ingles^1,3,4

¹Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, NSW, Australia
² School of Public Health, The University of Sydney, Sydney, NSW, Australia
³ Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
⁴ Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia

Aim: When a genetic diagnosis is made in a hypertrophic cardiomyopathy (HCM) proband, first-degree relatives are offered cascade genetic testing in addition to clinical screening. Adult family members with no clinical evidence of HCM who receive a positive genetic test result are considered ‘at-risk’, but no therapies are initiated in the absence of a phenotype. This study explored the experience of genetic testing for this new group of ‘genotype positive, phenotype negative’ (G+P-) patients. Method: Nineteen G+P- patients were recruited from a specialist genetic heart disease clinic. Semi-structured interviews were conducted face to face or by phone, and transcribed audio-recordings were coded using Framework Analysis. Results: Participants reported the main benefit of genetic testing was for the next generation, and worried more about children than themselves. Genetic test results were viewed as beneficial yet had multiple subtle but potentially important impacts on participants’ lives, including: avoiding strenuous exercise, monitoring their heart rate, and increased awareness of heart symptoms. Advice from medical professionals was often contradictory, leading to uncertainty about risk and management. Implications for insurance and family planning related to whether participants self-identified as having a current medical condition/disease. Conclusion: While genetic testing has clear potential to benefit relatives who receive a negative result, the meaning of a positive result in the absence of clinical signs or prevention strategies is unclear, and can lead to misconceptions about disease status and management. Better understanding of the patient experience is needed to inform pre-test counseling and post-result clinical management of families.

Oral 11
GENOMES AND PREGNANCY, THE GAP STUDY: PROVIDING CHOICE OF FETAL GENOMIC RESULTS TO WOMEN HAVING PRENATAL DIAGNOSIS

Jane Halliday ^1,2, Taryn Charles¹, Joanne Kennedy¹, Sharon Lewis^1,2, Cecile Muller^1,3, Susan Fawcett⁴, Sian Smith⁵, Della Forster^6,7, Susan Walker⁸, Bettina Meiser⁵, David Amor^2,4, Howard Slater⁴, Fiona Norris⁴

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
³ School of Psychology, University of Surrey, Guildford, UK,
⁴ Victorian Clinical Genetics Services, Melbourne, VIC, Australia
⁵ Psychosocial Research, University of New South Wales, Sydney, NSW, Australia
⁶ Judith Lumley Centre, La Trobe University, Melbourne, VIC, Australia
⁷ Maternity Services, Royal Women's Hospital, Melbourne, VIC, Australia
⁸ Perinatal Medicine, Mercy Hospital for Women, Melbourne, VIC, Australia

Background: Use of chromosome microarrays for prenatal diagnosis can detect copy number variants of unknown or uncertain significance (VOUS). The Genomics and Pregnancy study (GaP) aims to find out if parents want information on VOUS in pregnancy. Methods: Women having prenatal diagnosis were recruited, but not when there was report of fetal abnormality on ultrasound. Participants were given a study-specific decision aid and asked to choose between receiving targeted (pathogenic only) or extended (plus VOUS) fetal genomic information. Two surveys were completed, one before the procedure assessing decisional conflict, state/trait anxiety, intolerance of uncertainty and health literacy. Another survey, sent approximately ten days after receiving the result, assessed decisional regret, satisfaction with decision and state anxiety. Results: Of 111 participants, 40.5% chose targeted and 59.5% chose extended analysis. Choice was not associated with maternal age, parity, religion, ethnicity, education, and financial situation; however those trying to conceive for ≥12 months and using fertility treatments were significantly more likely to choose extended (78% and 92% respectively). Women choosing extended had significantly higher trait anxiety (mean score of 39.5 (SD 9.3)), compared to women who chose targeted (mean score 36.2 [SD 6.8]), p < .05. Conclusion: While current practice typically involves extended analysis, GaP demonstrates this does not reflect the true preference of those having prenatal diagnostic testing when there are normal ultrasound findings. Provision of choice in pregnancy about reporting of genomic results is ideal; if laboratories are prepared to offer such choice, decision-support methods before collection of genetic material could be adopted to facilitate this.

Oral 12
GENETIC RISK FACTORS FOR VULVAR CANCER IN YOUNG INDIGENOUS WOMEN IN ARNHEM LAND

Rebekah McWhirter ^1,2, Jo Dickinson¹, Debbie Taylor-Thomson², James Marthick¹, Alice Rumbold³, John Condon²

¹Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
² Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
³ Obstetrics and Gynaecology, University of Adelaide, Adelaide, SA, Australia

Background: Vulvar cancer is usually rare, and occurs most often in postmenopausal women. Among young (<50 years) Indigenous women living in remote Aboriginal communities in Arnhem Land; however, the incidence of this malignancy is more than 70 times the national Australian rate for the same age group. Previously, we found that neither excess human papillomavirus (HPV) incidence nor a particularly virulent strain of HPV could explain the very high incidence of vulvar cancer in this population. Reports from the Gynaecology Outreach Service that cases appeared to cluster in family groups suggested a genetic susceptibility, either to the effects of HPV or another cause of vulvar cancer. Methods: To investigate the role of genetic risk factors, 30 cases and 61 controls, matched on age and community of residence, were recruited to the study. DNA was extracted from saliva samples, and genotyped to provide information on approximately 2.5 million variants. These data were analyzed using both genome- wide association and identity-by-descent techniques. Results: We found clear evidence for the involvement of a genetic risk factor predisposing this population to vulvar cancer, and identified three genomic regions of interest. Discussion: Bioinformatic analysis prioritised biologically plausible candidate genes within these regions. Sequencing and functional studies to further elucidate the role of genetic variants in the etiology of vulvar cancer are currently underway. This is the first genetic study of this population, and these findings continue to inform health care delivery in Arnhem Land, especially vaccination policy and screening strategies.

Australasian Association of Clinical Geneticists SIG Meeting

KBG SYNDROME: AN AUSTRALIAN EXPERIENCE

Natalia Murray ¹, Miss Bronwyn Burgess¹, Julie McGaughran², Sulekha Rajagopalan³, Alison Colley³, Himanshu Goel ¹

¹Hunter Genetics Unit, Waratah, Newcastle, NSW, Australia
² Genetic Health Qld, Brisbane, QLD, Australia
³ Liverpool Clinical Genetics, Liverpool, Sydney, NSW, Australia

A syndrome of intellectual disability, macrodontia of the upper central incisors and distinct craniofacial dysmorphisms was first described in 1975 by Hermann et al. and KBG syndrome was coined based on the initials of the affected families’ surnames. In 2011, Sirmaci et al through whole exome sequencing identified heterozygous mutations in the ANKRD11 gene in affected individuals. Since then, around 60 cases have been described in the literature with the expansion of the clinical phenotype. The role of mutations in affecting degradation of the mutant protein with a possible dominant negative mechanism has been delineated (Walz et al., 2015). Here we present an Australian cohort of 9 KBG affected individuals, all with pathogenic mutations in the ANKRD11 gene on chromosome 16 confirmed on DNA sequencing. Data was collected from participating geneticists across Australia. The clinical phenotype was defined according to a proforma based on the diagnostic features described by Skjei et al. DNA sequencing was performed using individual HGSA accredited laboratories. Mutations were analyzed according to effect on protein based on USCS genome browser and pathogenicity was determined based on ACMG guidelines. Several novel heterozygous variants have been described and the genotype-phenotype correlations have been explored. These cases highlight the need for thorough examination and investigation of the dental and skeletal systems in the approach to syndromic intellectual disability. KBG remains an under-diagnosed entity in the Australian population and exhibits intra- and interfamilial variability. The description of further cases of KBG syndrome is needed to further delineate this condition.

MUTATIONS IN CDC45, ENCODING AN ESSENTIAL COMPONENT OF THE PRE-INITIATION COMPLEX, CAUSE MEIER-GORLIN SYNDROME AND CRANIOSYNOSTOSIS

Louise Bicknell ¹, Aimee Fenwick², Maciej Kliszczak², Fay Cooper³, Jennie Murray³, Luis Sanchez-Pulido³, Stephen Twigg², Anne Goriely², Simon McGowan², Kerry Miller², Indira Taylor², Clare Logan³, Sevcan Bozdogan⁴, Sumita Danda⁵, Joanne Dixon⁶, Solaf Elsayed⁷, Ezzat Elsobky⁷, Alice Gardham⁸, Mariette Hoffer⁹, Marije Koopmans⁹, Donna McDonald-McGinn¹⁰, Gijs Santen⁹, Ravi Savarirayan¹¹, Deepthi de Silva¹², Steven Wall¹³, Louise Wilson⁸, Olivier Vanakker¹⁴, Ozge Ozalp Yuregir¹⁵, Elaine Zackai¹⁰, Chris Ponting³, Andrew Jackson³, Andrew Wilkie^2,13, Wojciech Niedzwiedz²

¹University Of Otago, Dunedin, New Zealand
² MRC Weatherall Institute of Molecular Medicine, Oxford, UK
³ MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
⁴ Mersin University, Mersin, Turkey
⁵ Christian Medical College and Hospital, Vellore, India
⁶ Genetic Health Service NZ-South Island Hub, Christchurch, New Zealand
⁷ Ain Shams University, Cairo, Egypt
⁸ Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
⁹ Leiden University Medical Center, Leiden, The Netherlands
¹⁰ The Children's Hospital of Philadelphia, Philadelphia, PA, USA
¹¹ Murdoch Children's Research Institute, Melbourne, VIC, Australia
¹² University of Kelaniya, Ragama, Sri Lanka
¹³ Oxford University Hospitals NHS Foundation Trust, Oxford, UK
¹⁴ Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
¹⁵ Adana Numune Training and Research Hospital, Adana, Turkey

DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier- Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1 or CDC6) as well as de novo activating mutations in the licencing inhibitor, GMNN, cause MGS. We have identified mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required respectively for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, hence is functionally distinct from previously identified MGS genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in patient cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS, and connect the core ce nome replication with growth, chondrogenesis and cranial suture homeostasis.

Australasian Society of Diagnostic Genomics SIG Meeting

INCIDENCE OF GONADAL MOSAICISM IDENTIFIED BY MICROARRAY TESTING OF PARENTS AND CHILDREN

Matthew Regan, Matthew Hunter

Monash Health, Melbourne, VIC, Australia

The current dogma in gonadal mosaicism is to counsel for a less than 1% recurrence risk. It is known that highly penetrant autosomal dominant conditions may be masked in phenotypically unaffected parents by somatic mosaicism. Recent literature shows that somatic mosaicism in an unaffected parent maybe higher than previously reported. If so, the risk of recurrence (RR) may be significantly underestimated and parents falsely reassured. The aim of our study was to assess parental mosaicism to generate our own gonadal mosaicism risk and replicate recent published results. We performed a retrospective study in all patients referred to the Clinical Genetics service at a metropolitan hospital over a 1-year period to quantify incidence parental somatic mosaicism. The main inclusion criteria was a prenatal micro array via CVS or amniocentesis, and a micro array test on at least one of the parents if positive or two parents if negative. The micro array report itself was used to classify a parent as mosaic for a specific change, identified as non-mosaic in the foetus. We report out findings in 1,109 individuals referred in 2015, of whom 265 were referred for prenatal assessment. As per previously reported data, we expected a 4% RR versus the previously quoted less than 1% RR.

ARRAY CGH IN PRENATAL DIAGNOSIS: A REVIEW OF VARIATIONS OF UNKNOWN SIGNIFICANCE REPORTING, TIME TO LOOK FOR AN ALTERNATIVE APPROACH?

Abhijit Kulkarni ¹, Matthew Hunter², Paul Sheckleton³, Fabricio Costa⁴, Nikki Gelfand², Melody Menezes⁴

¹Monash Pathology, Monash Medical Centre, Melbourne, VIC, Australia
² Monash Genetics, Monash Health, Melbourne, VIC, Australia
³ Fetal Diagnostic Unit, Monash Health, Melbourne, VIC, Australia
⁴ Monash Ultrasound for Women, Melbourne, VIC, Australia

In Australia, Array CGH has replaced conventional cytogenetic analysis as the first line of investigation in prenatal diagnosis. One drawback is the detection of VoUS (Variations of Unknown Significance). There are now well established international guidelines for test indications, result interpretation and report writing for prenatal chromosomal analysis by Array CGH. Many laboratories take an approach to process all the prenatal samples by both FISH and Array CGH. We present data from the cytogenetics department at Monash Health, where array CGH was introduced in 2013 with a similar policy. There was a total of 850 prenatal specimens tested to date and 100 reports (11.7%) with VoUS issued, with parental studies completed in the majority of them. We review the indications and fetal outcome for these cases. The internationally recommended approach of restricting array CGH testing to selected high risk cases with abnormal ultrasound scan and/or nuchal translucency of more than 3.5 mm will be discussed. A new processing workflow for prenatal chromosome testing will be proposed. Interpretation criteria's for neurosusceptibilty loci in prenatal samples will be reviewed. The existing data will be compared with the proposed workflow. The clinical and economic impact of the proposed approach with special emphasis in a public hospital setup will be summarized.

UTILITY OF SNP MICROARRAY FOR ELUCIDATING CAUSATIVE RECESSIVE GENES AND FOR CREATING PATIENT SPECIFIC CANDIDATE GENE LISTS FOR WHOLE EXOME SEQUENCING

Amber Boys ¹, Zornitza Stark¹, Natasha Brown², Martin Delatycki^2,4, Richard Leventer^3,4, Jeremy Freeman³, Ralph Oertel¹, Mrs Paula Lall¹, Lorna Williams¹, Fiona Norris¹, Howard Slater¹

¹Victorian Clinical Genetics Services, Melbourne, VIC, Australia
² Department of Clinical Genetics, Austin Health, Melbourne, VIC, Australia
³ Royal Children's Hospital, Melbourne, VIC, Australia
⁴ Murdoch Childrens Research Institute, Melbourne, VIC, Australia

The introduction of chromosome microarray (CMA) into diagnostic genetic testing instigated a new era of genetic interpretation, in particular for disorders caused by copy number variants with incomplete penetrance and variable expressivity. Through the use of SNP-based CMA, long continuous stretches of homozygosity (LCSH) have provided an additional clinical resource for identifying genes associated with recessive disorders. LCSH are detected in individuals with consanguineous parents as expected, but also in individuals from apparently outbred populations. In our cohort of 60,000 individuals, approximately 10% have at least 1 LCSH greater than 5 megabases in length. We will showcase, using a range of clinical examples, how the medical scientist can work with the clinical geneticist/ medical specialist to successfully identify the pathogenic mutation in an affected individual or multiple family members. The approach taken can vary depending on the number of affected and unaffected family members, the size of the proposed candidate gene list, and the genomic percentage of the LCSH. If a strong candidate gene has been identified with this approach, as in the majority of the examples presented here, single gene sequencing can confirm causative homozygous mutations. If a single strong candidate gene does not emerge, then review of the LCSH gene content can be invaluable in generating candidate gene lists to direct the analysis of whole exome and whole genome data, either in the clinical setting or as part of gene discovery projects.

APPLICATION OF NGS FOR THE INVESTIGATION OF ABNORMALITIES OF THE Y CHROMOSOME

Nicole Martin, Peter Field, Melinda Richter

Virtus Diagnostics, Brisbane, QLD, Australia

There are a number of genes involved in infertility; we have developed a custom designed, targeted panel with amplicons for coding regions covering genes for the investigation of both males and females. The gene covered on the Y chromosome include SRY, ZFY, amelogenin Y, USP9Y, EIF1AY, BPY2 and DAZ. The Y chromosome is unique in that it does not have a homologue for complete pairing and recombination at meiosis. It shows size variability due to differing amounts of heterochromatin in the q arm. It also contains regions of palindromes and inversions that are capable of recombining, resulting in duplications and deletions. Deletions in the AZF region of Yq are associated with absent or reduced sperm production. Best practice guidelines to date (2013) only recommend looking at micro satellite markers for deletions in this region. Three of our patients who have been shown to be deleted for AZF a,b and c by microsatellite markers, have been shown not to be deleted for any of the relevant genes in these regions by NGS and are also FISH positive for probes for the three regions. One case of a 46,XY female has been shown not to have any base pair alterations in SRY suggesting her androgen insensitivity is not related to SRY. One case of a cytogenetic 46,XX male was initially detected by NGS as he had only SRY and amelogenin X present. Subsequent cytogenetic studies determined a 46,XX karyotype and FISH showed SRY translocated to Xp.

IDENTIFYING NOVEL GENETIC CAUSES OF 46,XY DISORDERS OF SEX DEVELOPMENT USING TARGETED SEQUENCING TECHNOLOGIES

Katie Ayers ^1,2, Jocelyn Van Den Bergen¹, Gorjana Robevska¹, Stefanie Eggers¹, Thomas Ohnesorg¹, Andrew Sinclair^1,2

¹Murdoch Childrens Research Institute, Melbourne, VIC, Australia
² Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia

Background: Disorders of sex development (DSDs) are congenital conditions in which development of chromosomal, gonadal, or anatomical sex is atypical. DSDs include a wide range of anomolies and together account for 7.5% of all birth defects. Indeed, 1 in 4,500 babies worldwide is born with significant ambiguous genitalia. Currently only 30% of all DSDs are diagnosed at the genetic level. In particular 46,XY DSDs (including patients with gonadal dysgenesis or under-virilisation) have a poorly defined etiology, perhaps due to gaps in the understanding of the molecular pathways required for testis development. Methods: To address these gaps we have recruited a cohort of around 420 46,XY DSD patients, including patients with gonadal dysgenesis, androgen insensitivity and hypospadias. We are screening these patients for novel mutations in genes using a variety of methods including a targeted massively parallel sequencing panel of around 1,000 known or candidate DSD genes, whole exome sequencing and a targeted DSD CGH array. Results: We have thus far analyzed 270 46,XY patients. A likely pathogenic variant in a diagnostic DSD gene has been found in 45% of these patients illustrating the diagnostic power of our screening methods. These include novel mutations in rare DSD genes such as GATA4 and FOG2. In addition, we have identified several candidate DSD genes, including a negative regulator of the WNT signaling pathway and androgen receptor interacting proteins. Functional testing is underway and we will present the mounting evidence that these genes play a role in the development of testis and in DSD.

NEXT GENERATION SEQUENCING IN PATIENTS WITH OVERGROWTH

Benjamin Kamien

The University of Newcastle, Newcastle, NSW, Australia

Background: Overgrowth is a sign in clinical genetics practice used to help diagnose a group of heterogenous conditions where excessive growth, developmental delay, dysmorphic features, and increased risk of neoplasia are prominent. In this study, overgrowth was defined as requiring at least two of three parameters (height, weight, head circumference) significantly greater than the 97th centile. Aims and hypotheses: It was hypothesized that due to genetic heterogeneity and subtle phenotypic distinctions, overgrowth syndromes are difficult to clinically diagnose and that a next generation sequencing (NGS) gene panel may improve rates of diagnosis. Another aim was to allow for phenotypic expansion of some of the overgrowth syndromes. Methods: An audit of all patients seen over a 5-year period at Hunter Genetics occurred to determine current diagnostic rates. 24 undiagnosed patients identified by the audit were then retrospectively recruited and an additional 14 patients were prospectively recruited. A NGS panel examining 30 genes was applied to the cohort. Results: The audit identified that 21/61 overgrowth patients had a secure clinical or molecular diagnosis and that most of these diagnoses were chromosomal deletions or duplications detected by array CGH while few syndromic diagnoses were made. The NGS panel found 5 variants of uncertain significance including a family with a SETD2 variant and a family with both a PTEN and PTCH1 variant. These findings expand the phenotypic possibilities of mutations in these genes. Conclusion: Our findings show that overgrowth is a non-specific clinical sign where achieving a molecular diagnosis is challenging.

GENOTYPER: AN ALIGNMENT FREE APPROACH FOR THE IDENTIFICATION OF VARIANTS IN RAW MASSIVELY PARALLEL SEQUENCING DATA

Sebastian Lunke ¹, Clare Love¹, Graham Taylor^1,2,3, Damien Bruno¹, Arthur Hsu^1,2

¹Victorian Clinical Genetics Services (VCGS), Melbourne, VIC, Australia
²University of Melbourne, Melbourne, VIC, Australia
³Guy's and St Thomas’ Hospitals NHS Trust, London, UK

Variant calling in massively parallel sequencing (MPS) data is virtually always preceded by multiple bioinformatic processing steps, including the alignment of millions of sequencing reads to a reference genome. Due to the vast amount of data generated and the complexity of the task, by necessity the utilized alignment algorithms have to trade off the accuracy of read placement against the speed of the analysis. While most of the currently available tools are doing an excellent job, even very low error rates can result in false positive variant calls (alignment artefacts), which are not actually present in the raw data. We have developed and tested a tool (Genotyper) that is able to quickly and reliably scan sequencing raw (FASTQ) data for previously known variants. While Genotyper is not able to identify novel variants in the data, it is designed to take results generated by a conventional variant calling pipeline and confirm their presence in the raw data, thereby increasing the specificity of variant calling through alignment artefact identification. At the same time, it can be used for fast identity checking of MPS data against known patient SNPs before running expensive analyses. Perhaps most interestingly, our tool can be used to quickly screen every MPS dataset for known pathogenic variants (e.g., ClinVar, HGMD) and thereby not only increase the specificity, but also the speed and sensitivity of pathogenic variant identification.

IMPLEMENTATION OF A 174-GENE CAPTURE PANEL FOR GENETIC DIAGNOSIS OF CARDIAC DISORDERS

Michael Fietz, Jamie-Lee Ricciardi, Fathimath Faiz, Edward Edkins, Karen Carpenter

Pathwest Laboratory Medicine WA, Perth, WA, Australia

Background: The Department of Diagnostic Genomics at PathWest provides molecular diagnostic services for a range of genetic disorders. Since 2012, the Department has begun the introduction of Massively Parallel Sequencing (MPS) technologies to improve the efficacy and efficiency of these services. In June 2015 we commenced the use of a specialist gene panel for the analysis of a broad range of cardiac disorders. Aim: To examine the efficacy of MPS analysis for the genetic diagnosis of cardiac disorders. Methods: Patient samples were examined using the 174-gene Illumina TruSight Cardio Sequencing Kit, which utilises capture probes for isolation of target sequences. Libraries were sequenced on an Illumina MiSeq Desktop Sequencer with alignment and variant calling performed using BWA-MEM and GATK, respectively. Variant analysis was performed with Cartagenia Bench Lab NGS and Alamut Visual. Results: The Cardio Sequencing Kit yields at least 20-fold coverage for greater than 99% of target sequences, with a mean coverage across all currently tested samples of 400-fold. Validation with known control samples demonstrated efficacy in detection of single nucleotide variants and indels of up to 36bp in length. Complete analysis of 150 diagnostic patient samples has detected a clinically significant variant in 23% of cases, with 30% of structural disorders yielding a clinically significant variant. Conclusion: The use of a specialist gene panel for cardiac disorders has enabled the efficient analysis of a large range of relevant genes and proved highly effective in the detection of significant genetic variants.

TRIAGING COMPLEX CASES FOR GENETIC TESTING IN SOUTH AUSTRALIA: A MULTIDISCIPLINARY TEAM APPROACH

Peter Kaub, Karin Kassahn, Janice Fletcher

SA Pathology, Adelaide, SA, Australia

New genetic testing platforms offer much promise, but remain a limited resource in diagnostic settings. To maximize clinical utility, our diagnostic service has implemented a structured triage process. Tests are determined to be either ‘standard testing’ or ‘case requiring review’ (complex or panel precedent cases). The review process uses a multidisciplinary team (MDT) forum, with structured case presentations and decision criteria to assist determination of the most appropriate testing. The review process includes consideration of management implications, evidence supporting genetic testing indication and utility, test availability, service capacity and in-house expertise, as well as expected turnaround time. A recommendation for each case is formed after open and robust discussion between the MDT meeting members (primary clinicians, pathologists, medical scientists and bioinformaticians). In 18 months, next-generation sequencing has replaced classical genetic testing as the platform of choice for more than 800 standard tests (especially for large genes). In addition, the consensus-based, open discussion MDT platform has reviewed 80 complex clinical cases over this period. The majority of complex cases have been pediatric patients, with the greatest number referred from clinical geneticists, however immunologists, neurologists, cardiologists, metabolic, renal and general physicians have also been represented. a summary of the MDT system, with range of outcomes, phenotypes and results encountered will be presented. This approach reflects a paradigm shift in clinical review meetings, where embedding medical scientists with pathologists and primary physicians in an active clinical conversation maximises the utility of diagnostic services and assists best clinical outcome for patients.

A CUSTOM GENE PANEL FOR INTERROGATING PEDIATRIC OVERGROWTH DISORDERS AND TUMOUR PREDISPOSITION

Elizabeth Algar¹, Priscillia Siswara¹, Nadine Taubenheim ¹, Hamilton Fraval²

¹Monash Health, Melbourne, VIC, Australia
² Integrated Sciences, Melbourne, VIC, Australia

The Genetics and Molecular Pathology laboratory at Monash Health is the predominant Australian testing laboratory for pediatric overgrowth disorders associated with increased cancer risk in childhood, including Beckwith Wiedemann syndrome (BWS) and hemihypertrophy (HH). Cascade testing typically involves SNP microarray, methylation analysis of imprinting centres on 11p15.5 and CDKN1C (P57) mutation screening.

Rare point mutations in NSD1, NLRP2, DNMT1 and ZFP57 have been described in BWS and like disorders as well as deletions and insertions within the 11p15.5 imprinting centres IC1 (H19/IGF2) and IC2 (KCNQ1OT1/CDKN1C). Tumor risk is increased in most genetic and epigenetic subtypes of BWS and HH however degree of risk and tumor type varies between groups. Parents of affected children are often understandably anxious to know the recurrence risk for these conditions and as the number of childhood cancer survivors increases, the possibility for transmission of a causative mutation is becoming an increasingly important issue. To improve our capacity to detect predisposing mutations in BWS, HH and in the pediatric tumors that have been described in these conditions, we have designed a gene panel comprising 37 genes as well as intergenic regions spanning imprinting centres on 11p15.5 and 11p13. We have used the Haloplex target enrichment system with sequences run on an Illumina MiSeq. We have performed pilot testing to show that the panel has clinical utility and demonstrates excellent sequence coverage of the 11p imprinting centres. Analysis of results to date has revealed novel mutations including OCT-4 binding site disruption in IC1 and subregions of homozygosity.

A NEW APPROACH TO MEASURING BONE MARROW TRANSPLANT CHIMERISM BASED ON UBIQUITOUS, HIGHLY HETEROZYGOUS COPY NUMBER VARIATION AND DIGITAL DROPLET PCR

Howard Slater ¹, John B. Whitlam¹, Ling Ling¹, Michael Swain², Vida Petrovic¹, Jackie Challis¹, Ian Brooks¹, Sara Cronin¹, Tom Harrington¹, Damien Bruno¹, Rachel Conyers²

¹Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
² Children's Cancer Centre, Royal Children's Hospital, Melbourne, VIC, Australia

Background: Chimerism analysis is used for assessment of engraftment, minimal residual disease and relapse in allogenic bone marrow transplantation (BMT). Serial analysis is also used to guide treatment intensity so as to maximize graft-versus-tumour effect and minimize graft rejection, opportunistic infection and graft-versus-host disease risk. Aim: To develop a panel of DNA copy number deletion (CND) markers for monitoring any allogeneic bone marrow transplant, especially those with multiple or close relative donors and a highly sensitive and robust chimerism assay to potentiate early detection of relapse and minimal residual disease. Methods: The key advantage of the CND approach is the use of homozygous copy number deletions in either the donor or recipient to provide a ‘zero background’ for the assay and digital droplet PCR for absolute quantification. Unlike all other polymorphic markers in use (SNPs, indels, STRs), CNDs are monoallelic, a feature that provides significant improvements in quantification. Results: Validation studies indicate ready availability of multiple CND markers (at least 3 informative markers in 99% of typical unrelated donor-recipient transplants) and assay sensitivity down to 0.01% chimerism with good inter- and intra-assay reproducibility and concordance with SNP and FISH methods of chimerism analysis. Discussion: The assay is now in clinical use for routine transplants including measuring chimerism in genetically complex, multiple-relative donor transplants and on flow-sorted leukocyte subpopulations. The simplicity of this approach, combined with the advantages of ddPCR technology, recommend it as an improved approach to monitoring of allogeneic BMT chimerism.

LIMITATIONS OF PYROSEQUENCING FOR DETECTION OF SOMATIC MUTATIONS IN A CLINICAL SETTING

Helen Scales, Wendy Lewis, Susan Dooley, Rodney Scott

Molecular Medicine, Pathology North Hunter, New Lambton Heights, NSW, Australia

Background: In December 2015, our laboratory implemented the use of CE-IVD marked Therascreen Kits for testing KRAS, BRAF and EGFR gene mutations in FFPE tissue. The PyroMark analysis software was implemented to assist with processing data; however, there have been three KRAS cases where it has either called the mutation incorrectly, or not at all. These cases were repeated using the PyroMark platform, and results confirmed by Sanger Sequencing. Aim: To investigate somatic mutations called incorrectly by the PyroMark analysis software. Method: DNA was extracted using the QiaSymphony tissue protocol, and amplified and sequenced using the Therascreen PyroMark kits as per the prescribed method. All samples were re extracted and repeated using the method above, and by Sanger sequencing on the ABI 3730 analyzer. Case 3, a particularly rare mutation, was repeated by both methods on normal tissue to exclude the possibility of a germline mutation. Results: Cases 1 and 2; software called as c.35G>T, found to be c.37G>T. Case 3: software failed to analyze, found to be c.36_38dup. Normal tissue was wildtype. Conclusion/Discussion: This highlights the importance of manually checking the program against the histogram when analyzing pyrosequencing. When relying on a software program that calls only common mutations, there is a chance that rarer mutations may be missed or called incorrectly. Rarer mutations at a lower level are difficult to confirm using other methodology, that is, Sanger sequencing has a sensitivity of ~20%, Pyrosequencing ~5-10%.

FAMILIAL LEUKAEMIA, THE NEXT GENERATION — REDEFINING FAMILIAL HEMATOLOGICAL RISK THROUGH THE AUSTRALIAN FAMILIAL HEMATOLOGICAL CANCER STUDY

Hamish Scott ¹, Anna Brown¹, Devendra Hiwase², Andreas Schreiber¹, Jinghua Feng¹, Milena Babic¹, Nicola Poplawski², Graeme Suthers², Miriam Fine², Lesley Rawlings², Richard D'Andrea¹, Christopher Hahn¹

¹Centre for Cancer Biology, an alliance between SA Pathology and The University of South Australia Adelaide, SA, Australia
² SA Pathology, Adelaide, SA, Australia

The Australian Familial Haematological Cancer Study (AFHCS) was founded in 2004 when only one familial hematological malignancy (FHM) gene was known, RUNX1 causing thrombocytopenia and predominantly an MDS/AML HM phenotype. Today, there are at least 12 known FHM genes. We have a still growing collection of over 80 families as well as access to large numbers of sporadic hematological malignancies (HM). Many of these families have now been solved through our identification of mutations in genes such as GATA2 and PAX5 and the characterisation of novel RUNX1, CEBPA and DDX41 families. Interestingly, phenotypic heterogeneity is now evident across families with the same gene mutated, presumably due to differential alteration of function caused by different mutations in the same gene. One example of this is our recent identification of a family with a lymphoma phenotype segregating with a novel mutation in DDX41 (p. R164W), where most other DDX41 families identified to-date have predominantly MDS/AML. Accumulating evidence also suggests that in addition to characterised mutations segregating in FHM, there are further genetic modifiers at play. First, the observation of anticipation in many families may suggest the introduction of additional pathogenic variants thus accounting for the decreasing age of diagnosis in subsequent generations. Second, phenotypic diversity and incomplete penetrance of phenotypes within and across families with identical mutations in the same FHM gene are readily observable. He presentation will provide an overview and an update of our work showing germline genetic variants contributing not only to FHM but also sporadic HMs.

TRANSLATING RESEARCH IN TO THE PEDIATRIC ONCOLOGY CLINIC: A PERSONALISED MEDICINE TRIAL TO ASSESS THE FEASIBILITY AND CLINICAL VALUE OF A DIAGNOSTIC PLATFORM FOR IDENTIFYING NOVEL TARGETED THERAPEUTIC AGENTS FOR HIGH RISK PEDIATRIC AND AYA CANCER PATIENTS USING A MULTIDISCIPLINARY INTEGRATIVE APPROACH

Vanessa Tyrrell ¹, Loretta Lau^1,2, Michelle Haber¹, Glenn Marshall^1,2, Carol Wadham¹, Emily Mould¹, Amit Kumar^1,3, Angela Xie¹, Richard Lock¹, Karen Mac Kenzie¹, Paul Ekert^1,4, Andrew Fellowes³, David Ziegler^1,2, Toby Trahair^1,2

¹Children's Cancer Institute, Sydney, NSW, Australia
² Sydney Children's Hospital, Sydney, NSW, Australia
³ Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
⁴ Murdoch Children's Research Institute, Melbourne, VIC, Australia

~1000 children in Australia are diagnosed with cancer each year, among the highest incidence Internationally (Baade et al., 2010British Journal of Cancer, 102 ¹, and cancer remains the leading cause of death by disease in children. Most cancer chemotherapeutics used to treat childhood cancers have non-specific cytotoxicity to both normal and cancer cells, resulting in significant health care costs (20-25% of the work in children's hospitals in Australia). 30% of survivors will suffer one or more serious life-altering health conditions as a result of the toxicity of current treatments (http://curesearch.org/Childhood-Cancer-Statistics). A personalised medicine trial is being undertaken to assess the feasibility of a diagnostic platform for the identification of novel therapeutic agents for high-risk pediatric malignancies with expected overall survival ≤30%.

Patients’ tumour and germline samples are being collected at diagnosis and/or relapse and analyzed using: (1) Genetic analysis (targeted molecular profiling [DNA, RNA], WGS, RNASeq); (2) In vitro high throughput drug sensitivity screening; (3) In vivo drug response testing using patient-derived xenograft models. Since the launch of the feasibility study, 24 children have been enrolled, and where sufficient and appropriate tissue samples have been available, methods described above have been performed, and results combined and correlated with clinical data. The proportion of patients where results inform an alteration of treatment leading to improved clinical outcome will be assessed. This study may provide the evidence that personalised cancer therapy has the potential to improve outcome and reduce treatment-related toxicities, and hence reduce the burden to the health care system.

Australasian Society of Genetic Counsellors SIG Meeting

PRENATAL GENOMIC SEQUENCING: HOW MUCH INFORMATION IS TOO MUCH?

Allison Werner-Lin

School of Social Policy and Practice, University of Pennsylvania, Philadelphia, PA, USA

The American College of Obstetrics and Gynecology considers prenatal chromosomal microarray analysis (CMA) an appropriate first-tier test following detection of an ultrasound anomaly. The increased diagnostic yield of CMA is, however, accompanied by the possibility of finding copy number variants (CNVs) of uncertain clinical significance, incomplete penetrance, or variable expressivity, with phenotypes ranging from apparently normal to severely affected. Carrying a pregnancy to term without understanding or knowledge of the full implications of an uncertain CNV may come at great emotional and financial cost to the parent and to the child. Little is known about the experiences of parenting an infant following such findings. Our team conducted semi-structured telephone interviews with 23 mothers of 6–12 month old infants diagnosed prenatally with a potentially pathogenic CNV to elicit perspectives on the child's health and development, support needs, and intent to share their child's results with others. Most mothers reported that their infants were developing typically (n = 24, 73%). Yet, the majority of mothers expressed ongoing concern about their child's development, leading a few to seek out early intervention or ongoing assessments by pediatricians. Approaches to parenting were stratified across three levels of intensity, ranging from perseverant vigil to unworried. All interviewees shared the result with the either the child's pediatrician, their relatives, and/or with friends. The few who did not cited fear of stigma, lack of understandings, an inability to explain the CNV, or presumptions that the child was not affected. Belief that a child is perpetually at risk may incite fear that cannot be completely assuaged due to the limits of our understanding of CNVs of unknown significance. And without any symptoms other than a positive test result, families remain in a state of prolonged uncertainty, physicians lack the diagnostic schema that permits clear conceptualization and action, and children may be perceived as vulnerable in ways that are unfounded. The potential for over-medicalization of the child's development heightens the risk of parental, and potentially of the physician's, perception that the child is vulnerable, and may come to shape the child's social experiences or identity.

GENOMICS: NEW WAYS OF THINKING FOR NEW TECHNOLOGIES

Paul James

Genetic Medicine, Royal Melbourne Hospital; Familial Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia

In recent years clinical genetics has witnessed major technological changes involving a massive expansion in genetic sequencing capacity. As a result, the focus of researchers and clinicians has very quickly moved from single genes to whole genomes, and a ‘new’ clinical speciality of genomics has come into being. We are only now beginning to consider how the genomic information generated by these new technologies differs from more conventional genetic data and how this will impact on the practice of clinical genetics and genetic counseling. In this talk I will be considering these changes from the point of view the fundamental tool kit needed for clinical genomics, as well as reflecting more broadly on implications for the foundations of the way we practice.

IMPACT OF GENOMIC TECHNOLOGIES ON THE ROLE OF THE GENETIC COUNSELOR

Clara Gaff

The University of Melbourne and Melbourne Genomics Health Alliance, Melbourne, VIC, Australia

Although not yet available as a funded test, genomic sequencing is increasingly available to patients in Australasia. Some patients participate in gene discovery research, while others receive testing as part of programs identifying and addressing the barriers to the use of genomics in clinical practice. International experience has shown a direct impact of genomics on the profession of genetic counselors. In the United States, the introduction of genomics has led both to expanded roles and a shortage of genetic counselors. In the United Kingdom, profound changes to the genetic counseling training and registration process have been driven by the anticipated impact of genomics on their national health system. Locally, genetic counselors are playing key roles in the transition of genomic technologies from research to practice. As well as providing clinical genetic counseling, genetic counselors are trialing new roles, conducting research, educating other professionals and contributing to policy. Genetic counselors are therefore well placed to shape the way in which genomics is incorporated into the role of the genetic counselor. These themes will be explored as I consider the current impact and future role of genetic counselors in the era of genomic medicine.