Detecting genotyping errors at Schistosoma japonicum microsatellites with pedigree information.
Detecting genotyping errors at Schistosoma japonicum microsatellites with pedigree information.
复制标题
利用谱系信息检测日本血吸虫微卫星的基因分型错误。
DOI：
10.1186/s13071-015-1074-0
复制
发表时间：
2015-09-08
影响因子：
3.2
通讯作者：
Lamberton PH
中科院分区：
文献类型：
--
作者：
Gao YM;Lu DB;Ding H;Lamberton PH
日本血吸虫病仍然是中国的一个重大公共卫生问题。将寄生虫的分子分析（例如群体遗传分析）纳入正在进行的监测计划有助于探索导致日本血吸虫持续存在和/或传播的因素。然而，除非在分析中加以考虑，否则基因分型错误可能会严重影响此类研究的结果。我们使用血吸虫毛蚴谱系数据方法评估了 7 个日本血吸虫微卫星的基因分型错误（缺失等位基因或假等位基因），这些数据存储在 Whatman FTA 卡上。在成功进行基因分型的 107 个血吸虫毛蚴中，共有 715 个位点识别，总共观察到 31 个基因分型错误，其中 25.2% 的毛蚴至少有一个错误。每个位点的错误率因位点而异，范围为 0 至 9.8%，各个位点的平均错误率为 4.3%。使用亲子关系分析软件 Cervus，这七个标记的分配能力估计对于一个亲本为 89.5%，对于一对亲本为 99.9%。推断一个基因座具有大量无效等位基因，而第二个基因座则具有较高的错误打字率。据作者所知，这是首次使用日本血吸虫谱系来评估微卫星标记的基因分型错误。观察到的位点特异性错误率将有利于使用标记对日本血吸虫进行下游流行病学或生态学分析。本文的在线版本 (doi:10.1186/s13071-015-1074-0) 包含补充材料，可供授权用户使用。
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. 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. 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. 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. The online version of this article (doi:10.1186/s13071-015-1074-0) contains supplementary material, which is available to authorized users.