PurposeTo evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors.MethodsBlood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio.ResultsMean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability. For the two vendors with mean depth of coverage >120 ×, analytic positive predictive values (aPPVs) exceeded 99.1% for single-nucleotide variants and homozygous indels, and sensitivities were 98.9-99.9%; however, heterozygous indels showed lower accuracy and sensitivity. Among the trios, FNRs in the offspring were 0.07-0.62% at well-covered variants concordantly called in both parents.ConclusionThe current standard of 120 × coverage for clinical WES may be insufficient for consistent breadth of coverage across the exome. Ordering clinicians and researchers would benefit from vendors' reports that estimate sensitivity and aPPV, including depth of coverage across the exome.Genetics in Medicine advance online publication, 12 April 2018; doi:10.1038/gim.2018.51.

中文翻译：

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在临床环境中测量全外显子组测序的覆盖率和准确性。

目的评估跨供应商的全外显子组测序 (WES) 的覆盖率和准确性。方法来自三个三重奏的血液样本在三个供应商处进行了 WES。三个 WES 服务的相对性能是根据覆盖的广度和深度来衡量的。使用每个三重奏中的分离模式估计假阴性率 (FNR)。结果三个供应商服务的所有基因的平均覆盖深度为 189.0、124.9 和 38.3。美国医学遗传学和基因组学学院 56 个基因中的 55 个，但 63 个药物基因中只有 56 个，在所有供应商的九个个体中至少有一个以 10 倍 100% 覆盖；然而，个体之间存在很大差异。对于平均覆盖深度 >120 × 的两家供应商，分析阳性预测值 (aPPV) 超过 99。单核苷酸变异和纯合插入缺失为 1%，灵敏度为 98.9-99.9%；然而，杂合插入缺失显示出较低的准确性和灵敏度。在三重奏中，后代的 FNR 在父母双方一致调用的覆盖良好的变体中为 0.07-0.62%。结论临床 WES 的当前 120 倍覆盖标准可能不足以实现整个外显子组的一致覆盖范围。订购临床医生和研究人员将从供应商的报告中​​受益，这些报告估计灵敏度和 aPPV，包括外显子组的覆盖深度。医学遗传学在线出版，2018 年 4 月 12 日；doi:10.1038/gim.2018.51。62% 的覆盖良好的变体在父母双方中一致调用。结论临床 WES 的当前 120 × 覆盖标准可能不足以实现整个外显子组的一致覆盖范围。订购临床医生和研究人员将从供应商的报告中​​受益，这些报告估计灵敏度和 aPPV，包括外显子组的覆盖深度。医学遗传学在线出版，2018 年 4 月 12 日；doi:10.1038/gim.2018.51。62% 的覆盖良好的变体在父母双方中一致调用。结论临床 WES 的当前 120 × 覆盖标准可能不足以实现整个外显子组的一致覆盖范围。订购临床医生和研究人员将从供应商的报告中​​受益，这些报告估计灵敏度和 aPPV，包括外显子组的覆盖深度。医学遗传学在线出版，2018 年 4 月 12 日；doi:10.1038/gim.2018.51。