Exome sequencing explained: a practical guide to its clinical application
Exome sequencing explained: a practical guide to its clinical application
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DOI：
10.1093/bfgp/elv054
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发表时间：
2016-09-01
影响因子：
4
通讯作者：
Ennis, Sarah
中科院分区：
文献类型：
--
作者：
Seaby, Eleanor G.;Pengelly, Reuben J.;Ennis, Sarah
下一代测序将医疗保健带入了革命性的基因组学时代。其中一种技术，全外显子组测序，靶向基因组的蛋白质编码区，已被证明成功地确定了以前未知病因的疾病的新的因果突变。随着最近研究中罕见疾病的成功诊断率接近25%，其临床实用性越来越受欢迎。然而，全外显子组测序数据的解释需要基因组信息学和临床医学方面的专业知识，以确保将结果准确和安全地报告给床边。这受到了大量测序数据的挑战，每个测序个体包含约25000个变异。因此，需要计算策略和挑剔的过滤框架来从常见多态性的海洋中提取候选变体。一旦确定了优先级，就需要在生物学水平上进行深入细致的审查，并需要与临床表型一起进行明智的评估。在最后一步，所有证据都与致病性指南一起整理和记录，以产生返回临床的外显子组报告。这篇综述为临床医生和基因组信息学家提供了全外显子组测序临床应用的实用指南。我们解决测序捕获和方法，在测序分析的不同阶段的质量控制参数，并提出了一个外显子组数据过滤策略，包括初级过滤（用于去除可能的良性变异）和二级过滤剩余的候选人的优先级。
Next-generation sequencing has catapulted healthcare into a revolutionary genomics era. One such technology, whole-exome sequencing, which targets the protein-coding regions of the genome, has proven success in identifying new causal mutations for diseases of previously unknown etiology. With a successful diagnostic rate approaching 25% for rare disease in recent studies, its clinical utility is becoming increasingly popular. However, the interpretation of whole-exome sequencing data requires expertise in genomic informatics and clinical medicine to ensure the accurate and safe reporting of findings back to the bedside. This is challenged by vast amounts of sequencing data harbouring approximately 25 000 variants per sequenced individual. Computational strategies and fastidious filtering frameworks are thus required to extricate candidate variants in a sea of common polymorphisms. Once prioritized, identified variants require intensive scrutiny at a biological level, and require judicious assessment alongside the clinical phenotype. In the final step, all evidence is collated and documented alongside pathogenicity guidelines to produce an exome report that returns to the clinic. This review provides a practical guide for clinicians and genomic informaticians on the clinical application of whole-exome sequencing. We address sequencing capture and methodology, quality control parameters at different stages of sequencing analysis and propose an exome data filtering strategy that includes primary filtering (for the removal of probable benign variants) and secondary filtering for the prioritization of remaining candidates.