Despite clear technical superiority of genome sequencing (GS) over other diagnostic methods such as exome sequencing (ES), few studies are available regarding the advantages of its clinical application. We analyzed 1007 consecutive index cases for whom GS was performed in a diagnostic setting over a 2-year period. We reported pathogenic and likely pathogenic (P/LP) variants that explain the patients’ phenotype in 212 of the 1007 cases (21.1%). In 245 additional cases (24.3%), a variant of unknown significance (VUS) related to the phenotype was reported. We especially investigated patients which had had ES with no genetic diagnosis (n = 358). For this group, GS diagnostic yield was 14.5% (52 patients with P/LP out of 358). GS should be especially indicated for ES-negative cases since up to 29.6% of them could benefit from GS testing (14.5% with P/LP, n = 52 and 15.1% with VUS, n = 54). Genetic diagnoses in most of the ES-negative/GS-positive cases were determined by technical superiority of GS, i.e., access to noncoding regions and more uniform coverage. Importantly, we reported 79 noncoding variants, of which, 41 variants were classified as P/LP. Interpretation of noncoding variants remains challenging, and in many cases, complementary methods based on direct enzyme assessment, biomarker testing and RNA analysis are needed for variant classification and diagnosis. We present the largest cohort of patients with GS performed in a clinical setting to date. The results of this study should direct the decision for GS as standard second-line, or even first-line stand-alone test.

尽管基因组测序 (GS) 与外显子组测序 (ES) 等其他诊断方法相比具有明显的技术优势，但关于其临床应用优势的研究很少。我们分析了 2 年期间在诊断环境中进行 GS 的 1007 个连续指标病例。我们报告了致病性和可能致病性 (P/LP) 变异，这些变异可以解释 1007 例病例中的 212 例 (21.1%) 患者的表型。在另外 245 个病例 (24.3%) 中，报告了与表型相关的意义不明的变异 (VUS)。我们特别调查了没有基因诊断的 ES 患者（n = 358）。对于该组，GS 诊断率为 14.5%（358 名患者中有 52 名患有 P/LP）。GS 应特别适用于 ES 阴性病例，因为其中高达 29.6% 的患者可以从 GS 检测中受益（P/LP 为 14.5%，n  = 52，VUS 为 15.1%，n = 54）。大多数 ES 阴性/GS 阳性病例的遗传诊断取决于 GS 的技术优势，即可访问非编码区域和更均匀的覆盖范围。重要的是，我们报告了 79 个非编码变体，其中 41 个变体被归类为 P/LP。非编码变异的解释仍然具有挑战性，在许多情况下，变异分类和诊断需要基于直接酶评估、生物标志物测试和 RNA 分析的补充方法。我们展示了迄今为止在临床环境中进行的最大的 GS 患者队列。这项研究的结果应该指导 GS 作为标准二线甚至一线独立测试的决定。