Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes-猫眼课题宝

DOI：

发表时间：

2016

期刊：

Vaccine

影响因子：

5.5

通讯作者：

中科院分区：

医学3区

文献类型：

作者：

Sarah B. H. Ng;Emily H. Turner;P. Robertson;Steven Flygare;A. Bigham;Choli Lee;T. Shaffer;Michelle Wong

全基因组关联研究表明，常见的遗传变异只解释了一小部分常见疾病的遗传风险，这就提出了一个问题，即罕见变异是否占了无法解释的遗传性的很大一部分？虽然DNA测序的成本已经大幅下降，但要想在大规模人群中常规地在全基因组范围内识别罕见的和新的变异，它们还远远不够。因此，我们寻求开发第二代方法，对所有蛋白质编码区域（“外显子组”）进行靶向测序，以降低成本，同时丰富高渗透变异的发现。在这里，我们报告了12人的外显子组的靶向捕获和大规模平行测序。其中包括代表三个种群的8个HapMap个体，以及4个没有血缘关系的个体，他们患有一种罕见的显性遗传性疾病——弗里曼-谢尔登综合征（FSS）。我们在超过300兆碱基（Mb）的编码序列中展示了对罕见和常见变异的敏感和特异性识别。使用FSS作为概念验证，我们表明单基因疾病的候选基因可以通过对少数不相关的受影响个体的外显子组测序来鉴定。通过更大的样本量和通过预测功能影响对非同义变异的适当加权，该策略可以扩展到具有更复杂遗传学的疾病。蛋白质编码区占人类基因组的约1%，约30 Mb，分布在约18万个外显子中。用户可以查看、打印、复制和下载这些文档中的文本和数据挖掘内容，用于学术研究，并始终遵守完整的使用条件：http://www.nature.com/authors/editorial_policies/license.html#terms对材料的通信和请求应发送给J.S. （shendure@u.washington.edu）或S.B.N. （sarahng@u.washington.edu）。本项目由S.B.N.、e.h.t.、a.b.、e.e.e.、m.b.、d.a.n.和J.S.构思和策划实验。实验由S.B.N.、e.h.t.、c.l.和M.W.完成。算法开发和数据分析由S.B.N.、p.d.r.、s.d.f.、a.w.b.、t.s.、m.b.、d.a.n.和J.S.完成。手稿由S.B.N.和J.S.撰写。作者声明竞争的经济利益：详细信息随论文的完整HTML版本在www.nature.com/nature。补充信息链接到该论文的在线版本www.nature.com/nature。HHS公共访问作者手稿自然。作者的手稿;可在PMC 2010年3月23日。最终定稿：Nature. 2009年9月10日；461(7261): 272 - 276。doi: 10.1038 / nature08250。一个作家的手稿

Genome-wide association studies suggest that common genetic variants explain only a small fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability1,2. While DNA sequencing costs have fallen dramatically3, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions (`exomes'), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of twelve humans. These include eight HapMap individuals representing three populations4, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS)5. We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases (Mb) of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of nonsynonymous variants by predicted functional impact. Protein coding regions constitute ~1% of the human genome or ~30 Mb, split across ~180,000 exons. A brute-force approach to exome sequencing with conventional Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms Correspondence and requests for material should be addressed to J.S. (shendure@u.washington.edu) or S.B.N. (sarahng@u.washington.edu).. Author Contributions The project was conceived and experiments planned by S.B.N., E.H.T., A.B., E.E.E., M.B., D.A.N., and J.S. Experiments were performed by S.B.N., E.H.T., C.L., and M.W. Algorithm development and data analysis were performed by S.B.N., P.D.R., S.D.F., A.W.B., T.S., M.B., D.A.N., and J.S. The manuscript was written by S.B.N. and J.S. Author Information Reprints and permissions information is available at www.nature.com/reprints. The authors declare competing financial interests: details accompany the full HTML version of the paper at www.nature.com/nature. Supplementary Information is linked to the online version of the paper at www.nature.com/nature. HHS Public Access Author manuscript Nature. Author manuscript; available in PMC 2010 March 23. Published in final edited form as: Nature. 2009 September 10; 461(7261): 272–276. doi:10.1038/nature08250. A uhor M anscript

Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes

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