Analysis workflow to assess de novo genetic variants from human whole-exome sequencing.
Analysis workflow to assess de novo genetic variants from human whole-exome sequencing.
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DOI：
10.1016/j.xpro.2021.100383
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发表时间：
2021-03-19
期刊：
影响因子：
--
通讯作者：
Jin SC
中科院分区：
文献类型：
--
作者：
Diab NS;King S;Dong W;Allington G;Sheth A;Peters ST;Kahle KT;Jin SC
在这里，我们提出了一种分析从先证者-父母三人组的全外显子组测序(WES)中获得的从头遗传变异的方案。我们提供了使用现有管道调用从头突变(DNM)的逐步说明，并确定观察到的此类突变的数量是否相对于预期数量有所丰富。该方案可以扩展到任何基于人类疾病TRIO的队列。队列大小是发现高置信度致病DNMS的限制性决定因素。有关本议定书的使用和执行的完整细节，请参阅。我们展示了从整个外显子组测序数据中调用从头突变的能力。该协议被应用于由先证者和父母双方组成的队列中的WE。我们演示了如何使用去核糖核酸进行富集化分析。基于三个组的队列的大小是该协议准确性的限制因素。这里，我们提出了一个分析从先证者和父母三个组的全外显子组测序(WES)中获得的从头基因变异的协议。我们提供了使用现有管道调用从头突变(DNM)的逐步说明，并确定观察到的此类突变的数量是否相对于预期数量有所丰富。该方案可以扩展到任何基于人类疾病TRIO的队列。队列大小是发现高置信度致病DNMS的限制性决定因素。
Here, we present a protocol to analyze de novo genetic variants derived from the whole-exome sequencing (WES) of proband-parent trios. We provide stepwise instructions for using existing pipelines to call de novo mutations (DNMs) and determine whether the observed number of such mutations is enriched relative to the expected number. This protocol may be extended to any human disease trio-based cohort. Cohort size is a limiting determinant to the discovery of high-confidence pathogenic DNMs. For complete details on the use and execution of this protocol, please refer to. We demonstrate the ability to call de novo mutations from whole-exome sequencing data This protocol is applied to WES from cohorts composed of proband and both parents We demonstrate how to perform enrichment analysis using denovolyzR The size of the trio-based cohort is a limiting determinant of this protocol’s accuracy Here, we present a protocol to analyze de novo genetic variants derived from the whole-exome sequencing (WES) of proband-parent trios. We provide stepwise instructions for using existing pipelines to call de novo mutations (DNMs) and determine whether the observed number of such mutations is enriched relative to the expected number. This protocol may be extended to any human disease trio-based cohort. Cohort size is a limiting determinant to the discovery of high-confidence pathogenic DNMs.
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影响因子：
30.8
作者：
Kircher, Martin;Witten, Daniela M.;Jain, Preti;O'Roak, Brian J.;Cooper, Gregory M.;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
30.8
作者：
Jin SC;Homsy J;Zaidi S;Lu Q;Morton S;DePalma SR;Zeng X;Qi H;Chang W;Sierant MC;Hung WC;Haider S;Zhang J;Knight J;Bjornson RD;Castaldi C;Tikhonoa IR;Bilguvar K;Mane SM;Sanders SJ;Mital S;Russell MW;Gaynor JW;Deanfield J;Giardini A;Porter GA Jr;Srivastava D;Lo CW;Shen Y;Watkins WS;Yandell M;Yost HJ;Tristani-Firouzi M;Newburger JW;Roberts AE;Kim R;Zhao H;Kaltman JR;Goldmuntz E;Chung WK;Seidman JG;Gelb BD;Seidman CE;Lifton RP;Brueckner M
通讯作者：
Brueckner M
影响因子：
5.8
作者：
Wei, Qiang;Zhan, Xiaowei;Li, Bingshan
通讯作者：
Li, Bingshan
影响因子：
64.8
作者：
1000 Genomes Project Consortium;Auton A;Brooks LD;Durbin RM;Garrison EP;Kang HM;Korbel JO;Marchini JL;McCarthy S;McVean GA;Abecasis GR
通讯作者：
Abecasis GR
影响因子：
7
作者：
McKenna, Aaron;Hanna, Matthew;DePristo, Mark A.
通讯作者：
DePristo, Mark A.