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Microsatellite analysis of pooled Schistosoma mansoni DNA: an approach for studies of parasite populations

Published online by Cambridge University Press:  28 October 2005

L. K. SILVA ,
S. LIU  and
R. E. BLANTON
L. K. SILVA
Affiliation:
Center for Global Health and Diseases, 2103 Cornell Road, Case University, Cleveland, OH 44106-7286, USA Centro Universitário da Bahia (FIB), R. Xingu, 179, STIEP, Salvador, BA 41770-130, Brazil União Metropolitana de Educação e Cultura (UNIME), Av. Luís Tarquínio Pontes, 600, Centro, Lauro de Freitas, BA 42700-000, Brazil
S. LIU
Affiliation:
Center for Global Health and Diseases, 2103 Cornell Road, Case University, Cleveland, OH 44106-7286, USA
R. E. BLANTON
Affiliation:
Center for Global Health and Diseases, 2103 Cornell Road, Case University, Cleveland, OH 44106-7286, USA
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Abstract

Human parasites are often distributed in metapopulations, which makes random sampling for genetic epidemiology difficult. The typical approach to sampling Schistosoma mansoni involves laboratory passage to obtain individual worms with small sample size and selection bias as a consequence. By contrast, the naturally pooled samples from egg output in stool or urine directly represent the genetic composition of current populations. To test whether pooled samples could be used to estimate population allele frequencies, DNA from individual cloned parasites was pooled and amplified by PCR for 7 microsatellites. By polyacrylamide gel analysis, the relative band intensities of the products from the major alleles in the pooled samples differed by 0–6% from the summed intensities of the individual clones (mean=2·1%±2·1% S.D.). The number of PCR cycles (25–40) did not influence the accuracy of the estimate. Varying the frequency of 1 allele in pooled samples from 32 to 69% likewise did not affect accuracy. Allele frequency estimates from aggregate samples such as eggs will be a better foundation for studies of parasite population dynamics as well as the basis for large-scale association studies of host and parasite characteristics.

Keywords

allele frequencyPCRpooled samplesgeneticsmetapopulation
Type
Research Article
Information
Parasitology , Volume 132 , Issue 3 , March 2006 , pp. 331 - 338
Copyright
© 2005 Cambridge University Press

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References

REFERENCES

Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. ( 1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.CrossRefGoogle Scholar
Bush, A. O., Lafferty, K. D., Lotz, J. M. and Shostak, A. W. ( 1997). Parasitology meets ecology on its own terms: Margolis et al. revisited. The Journal of Parasitology 83, 575–583.CrossRefGoogle Scholar
Christensen, K. ( 2003). Genetic calculation applets 3/31/01. [Online.]
Collins, H. E., Li, H., Inda, S. E., Anderson, J., Laiho, K., Tuomilehto, J. and Seldin, M. F. ( 2000). A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Human Genetics 106, 218–226.CrossRefGoogle Scholar
Daniels, J., Holmans, P., Williams, N., Turic, D., McGuffin, P., Plomin, R. and Owen, M. J. ( 1998). A simple method for analyzing microsatellite allele image patterns generated from DNA pools and its application to allelic association studies. American Journal of Human Genetics 62, 1189–1197.CrossRefGoogle Scholar
Hoogendoorn, B., Owen, M. J., Oefner, P. J., Williams, N., Austin, J. and O'Donovan, M. C. ( 1999). Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography. Human Genetics 104, 89–93.CrossRefGoogle Scholar
Hughes, C. R. and Queller, D. C. ( 1993). Detection of highly polymorphic microsatellite loci in a species with little allozyme polymorphism. Molecular Ecology 2, 131–137.CrossRefGoogle Scholar
Jarne, P. and Theron, A. ( 2001). Genetic structure in natural populations of flukes and snails: a practical approach and review. Parasitology 123, S27–S40.CrossRefGoogle Scholar
Le Hellard, S., Ballereau, S. J., Visscher, P. M., Torrance, H. S., Pinson, J., Morris, S. W., Thomson, M. L., Semple, C. A., Muir, W. J., Blackwood, D. H., Porteous, D. J. and Evans, K. L. ( 2002). SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Research 30, e74.CrossRefGoogle Scholar
Pritchard, J. K., Stephens, M. and Donnelly, P. ( 2000). Inference of population structure using multilocus genotype data. Genetics 155, 945–959.Google Scholar
Sambrook, J. and Russell, D. W. ( 2001). Molecular Cloning: A Laboratory Manual, 3rd Edn. Cold Spring Harbor Press, New York.
Schneider, S., Roessli, D. and Excoffier, L. ( 2000). ARLEQUIN: a software for population genetics data analysis. University of Geneva 2.000. [Online.]
Sham, P., Bader, J. S., Craig, I., O'Donovan, M. and Owen, M. ( 2002). DNA pooling: a tool for large-scale association studies. Nature Reviews Genetics 3, 862–871.CrossRefGoogle Scholar
Shaw, S. H., Carrasquillo, M. M., Kashuk, C., Puffenberger, E. G. and Chakravarti, A. ( 1998). Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Research 8, 111–123.CrossRefGoogle Scholar
Smit, A. F. ( 2003). RepeatMasker open-3.0. [Online.]
Utter, F. and Ryman, N. ( 1993). Genetic markers and mixed stock fisheries. Fisheries 18, 11–21.2.0.CO;2>CrossRefGoogle Scholar
Wang, J. ( 2001). A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research 78, 243–257.CrossRefGoogle Scholar