Improved variant calling accuracy by merging replicates in whole-exome sequencing studies.
Improved variant calling accuracy by merging replicates in whole-exome sequencing studies.
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DOI：
10.1155/2014/319534
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发表时间：
2014
影响因子：
--
通讯作者：
Long J
中科院分区：
文献类型：
--
作者：
Zhang Y;Li B;Li C;Cai Q;Zheng W;Long J
在大规模的基于人群的全外显子组测序（WES）研究中，由于各种原因，有些样本偶尔会被测序两次或更多次。为了研究如何有效地利用这些重复的测序数据，我们对变异识别策略进行了全面评估。从大群体研究中选择92个样品进行两次WES。将这92个重复样品分成两组：H组由每个受试者的较高测序深度组成，L组由每个受试者的较低深度组成。将每个受试者的合并样本放入第三组M中。使用GATK多样本工具包，我们比较了三种策略之间的变异识别准确性。系统聚类分析表明，每个受试者的两个重复样本具有较高的同质性。基于杂合-纯合比（Hete/Homo）、转换-颠换比（Ti/Tv）和重叠率的比较分析与1000个基因组计划一致地表明，从M组检测到的SNPs的数据质量比从H和L组检测到的SNPs的数据质量更准确。这些结果表明，合并同质重复的外显子组而不是使用它们中的一个可以提高变体识别准确性。
In large scale population-based whole-exome sequencing (WES) studies, there are some samples occasionally sequenced two or more times due to a variety of reasons. To investigate how to efficiently utilize these duplicated sequencing data, we conducted comprehensive evaluation of variant calling strategies. 92 samples subjected to WES twice were selected from a large population study. These 92 duplicated samples were divided into two groups: group H consisting of the higher sequencing depth for each subject and group L consisting of the lower depth for each subject. The merged samples for each subject were put in a third group M. Using the GATK multisample toolkit, we compared variant calling accuracy among three strategies. Hierarchical clustering analysis indicated that the two replicates for each subject showed high homogeneity. The comparative analyses on the basis of heterozygous-homozygous ratio (Hete/Homo), transition-transversion ratio (Ti/Tv), and overlapping rate with the 1000 Genomes Project consistently showed that the data quality of the SNPs detected from the M group was more accurate than that of SNPs detected from the H and L groups. These results suggested that merging homogeneous duplicated exomes instead of using one of them could improve variant calling accuracy.
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来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
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DOI：
10.1126/science.1219240
发表时间：
2012-07-06
期刊：
Science (New York, N.Y.)
影响因子：
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作者：
Tennessen JA;Bigham AW;O'Connor TD;Fu W;Kenny EE;Gravel S;McGee S;Do R;Liu X;Jun G;Kang HM;Jordan D;Leal SM;Gabriel S;Rieder MJ;Abecasis G;Altshuler D;Nickerson DA;Boerwinkle E;Sunyaev S;Bustamante CD;Bamshad MJ;Akey JM;Broad GO;Seattle GO;NHLBI Exome Sequencing Project
通讯作者：
NHLBI Exome Sequencing Project
影响因子：
46.9
作者：
通讯作者：
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
12.3
作者：
Parla JS;Iossifov I;Grabill I;Spector MS;Kramer M;McCombie WR
通讯作者：
McCombie WR