Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues
Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues
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DOI：
10.1375/1832427054936673
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发表时间：
2005-08-01
影响因子：
0.9
通讯作者：
Martin, NG
中科院分区：
文献类型：
--
作者：
Montgomery, GW;Campbell, MJ;Martin, NG
高密度单核苷酸多态性（SNP）基因分型面板为基因组扫描提供了微卫星标记的替代方法。然而，基因型错误对检测连锁或关联的能力有重大影响，并且难以检测snp。我们使用Affymetrix GeneChip(R) SNP平台对来自一个单合子（MZ）和异合子（DZ）三胞胎混合家庭的样本进行了误差率估计，使用淋巴细胞、口腔DNA和使用多重位移扩增（MDA）技术的全基因组扩增样本。5个基因组样本58,960个snp的平均通达率为99.48%。MZ双胞胎的比较结果显示只有3个基因型不一致（一致性率为99.995%）。淋巴细胞和颊部DNA的平均一致性率为99.97%。孟德尔不一致性在46个snp中被发现，其中一个或多个家庭成员存在错误，发生率为0.022%。观察到的父母之间、父母与子女之间以及兄弟姐妹之间的基因型一致性率与先前报道的等位基因频率和Hardy-Weinberg平衡一致。使用MDA技术，两个样本的结果与基因组样本的结果具有同等的高准确性。而其余7个样本的SNP召唤率在72.5% ~ 99.5%之间，平均为86.11%。MDA反应后DNA样品的质量似乎是MDA样品SNP调用率的关键因素。我们的研究结果表明，Affymetrix基因芯片(R)在淋巴细胞和口腔DNA样本中具有高度精确和可重复性的基因分型。
High density single nucleotide polymorphism (SNP) genotyping panels provide an alternative to microsatellite markers for genome scans. However, genotype errors have a major impact on power to detect linkage or association and are difficult to detect for SNPs. We estimated error rates with the Affymetrix GeneChip(R) SNP platform in samples from a family with a mixed set of monozygotic (MZ) and dizygotic (DZ) triplets using lymphocyte, buccal DNA and samples from whole genome amplification using the multiple displacement amplification (MDA) technique. The average call rate from 58,960 SNPs for five genomic samples was 99.48%. Comparison of results for the MZ twins showed only three discordant genotypes (concordance rate 99.995%). The mean concordance rate for comparisons of samples from lymphocyte and buccal DNA was 99.97%. Mendelian inconsistencies were identified in 46 SNPs with errors in one or more family members, a rate of 0.022%. Observed genotype concordance rates between parents, between parents and children, and among siblings were consistent with previously reported allele frequencies and Hardy-Weinberg equilibrium. Using the MDA technique, results for two samples had equivalent high accuracy to results with genomic samples. However, the SNP call rate for the remaining seven samples varied from 72.5% to 99.5%, with an average of 86.11%. Quality of the DNA sample following the MDA reaction appears to be the critical factor in SNP call rate for MDA samples. Our results demonstrate highly accurate and reproducible genotyping for the Affymetrix GeneChip(R) Human Mapping Set in lymphocyte and buccal DNA samples.