Identification of Mendelian inconsistencies between SNP and pedigree information of sibs.
Identification of Mendelian inconsistencies between SNP and pedigree information of sibs.
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DOI：
10.1186/1297-9686-43-34
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发表时间：
2011-10-11
期刊：
影响因子：
--
通讯作者：
Bastiaansen JW
中科院分区：
文献类型：
--
作者：
Calus MP;Mulder HA;Bastiaansen JW
利用SNP基因型进行基因组选择已成为育种中的普遍做法。需要编辑和检查基因型数据质量的工具。检查孟德尔的不一致性使得有可能识别出系谱信息和基因型信息不一致的动物。存在检测孟德尔不一致性的简单测试，其计算亲本和后代之间相反的纯合标记（例如SNP）基因型的数量（PAR-OFF）。在这里，我们开发了两个测试，以确定孟德尔兄弟姐妹之间的不一致。第一个测试计数在同胞对之间具有相反纯合基因型的SNP（SIBs）。第二个测试比较了系谱和基于SNP的关系（SIBREL）。所有测试都基于不一致的父母和后代或兄弟姐妹的数量减少而迭代地移除动物。PAR-OFF检验，然后是SIB检验，应用于包含2，078头基因分型奶牛和211头基因分型公畜的数据集。计算所有三个测试的测试统计量分布的理论预期，并与经验得出的值进行比较。在对编辑的数据进行检验后计算I型和II型错误率，而孟德尔不一致性则是通过对不同比例动物的基因型数据进行系谱置换而引入的。两种SIB测试都通过目视检查成对谱系和基于SNP的关系的散点图来鉴定谱系和基因组关系可被认为不一致的动物对。通过PAR-OFF试验移除235只动物后，SIBREL（SIBREL）识别出另外18（22）只不一致的动物。通过两种方法鉴定了17只动物。两种方法的错误删除动物（I型错误）数量同样低，而SIBREL的错误非删除动物（II型错误）数量明显高于SIBREL。测试，以消除兄弟姐妹之间的孟德尔不一致之前，应测试亲子不一致。这种亲子检验不仅要考虑基于系谱数据的亲子对，还要考虑基于SNP信息的亲子对。这两个SIB测试可以识别孟德尔不一致的同胞对。基于I型和II型错误率，计算同胞之间的相对纯合子（SIBREL）似乎比比较基因组和系谱关系（SIBREL）更精确，以检测同胞之间的孟德尔不一致。
Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement. Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals. Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals. Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT. Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.
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影响因子：
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作者：
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