背景：检测导致异常剪接的致病性内含子变异在常规基因检测中仍然是一个挑战。我们描述了种系全外显子组测序（WES）分析，并将其应用于家族性卵巢癌（OC）病例的计算机预测工具，这些病例被报道为致病性BRCA1和BRCA2变异的临床阴性。方法：分析了27例家族性OC患者的WES数据，这些患者报告临床上对致病性BRCA1和BRCA2变体呈阴性，并分析了53例散发性早发性OC患者的BRCA1或BRCA2的致病性变体。对来自致病性BRCA1或BRCA2变体携带者的WES数据进行了10个其他OC易感基因中的致病性变体分析。对来自变异携带者的肿瘤DNA进行杂合性缺失分析。结果：BRCA1c.5407-25T>一个内含子变体，在两个受影响的姐妹和一个零星的OC病例中发现，预测会产生影响BRCA1转录的新剪接。来自BRCA1c.5407-25T>A携带者的WES数据显示在其他OC易感基因中没有致病性变异的证据。对来自变体载体的肿瘤DNA进行测序显示野生型等位基因完全丧失。结论：研究结果支持BRCA1c.5407-25T>A作为可能的致病变异，并强调了研究内含子序列作为OC家族的因果变异的重要性，其中BRCA1的参与是高度提示的。
Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.
