Detecting genotyping errors at Schistosoma japonicum microsatellites with pedigree information

Gao, Y.-M., Lu, D.-B., Ding, H. and Lamberton, P. H.L. (2015) Detecting genotyping errors at Schistosoma japonicum microsatellites with pedigree information. Parasites and Vectors, 8(1), 452. (doi: 10.1186/s13071-015-1074-0) (PMID:26350750) (PMCID:PMC4563838)

Abstract

Background: Schistosomiasis japonica remains a major public health problem in China. Integrating molecular analyses, such as population genetic analyses, of the parasite into the on-going surveillance programs is helpful in exploring the factors causing the persistence and/or spread of Schistosoma japonicum. However, genotyping errors can seriously affect the results of such studies, unless accounted for in the analyses. Methods: We assessed the genotyping errors (missing alleles or false alleles) of seven S. japonicum microsatellites, using a pedigree data approach for schistosome miracidia, which were stored on Whatman FTA cards. Results: Among 107 schistosome miracidia successfully genotyped, resulting in a total of 715 loci calls, a total of 31 genotyping errors were observed with 25.2 % of the miracidia having at least one error. The error rate per locus differed among loci, which ranged from 0 to 9.8 %, with the mean error rate 4.3 % over loci. With the parentage analysis software Cervus, the assignment power with these seven markers was estimated to be 89.5 % for one parent and 99.9 % for a parent pair. One locus was inferred to have a high number of null alleles and a second with a high mistyping rate. Conclusion: To the authors’ knowledge, this is the first time that S. japonicum pedigrees have been used in an assessment of genotyping errors of microsatellite markers. The observed locus-specific error rate will benefit downstream epidemiological or ecological analyses of S. japonicum with the markers.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Lamberton, Professor Poppy
• Authors: Gao, Y.-M., Lu, D.-B., Ding, H., and Lamberton, P. H.L.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Parasites and Vectors
• Publisher: BioMed Central
• ISSN: 1756-3305
• ISSN (Online): 1756-3305
• Published Online: 08 September 2015
• Copyright Holders: Copyright © 2015 Gao et al.
• First Published: First published in Parasites and Vectors 8(1):452
• Publisher Policy: Reproduced under a Creative Commons License