Abstract

A majority of BRCA1/2 (BRCA) pathogenic variants (PVs) are single nucleotide substitutions or small insertions/deletions. Copy number variations (CNVs), also known as large genomic rearrangements (LGRs), have been identified in BRCA genes. LGRs detection is a mandatory analysis in hereditary breast and ovarian cancer families, if no predisposing PVs are found by sequencing. Next generation sequencing (NGS) may be used to detect structural variation, since quantitative analysis of sequencing reads, when coupled with appropriate bioinformatics tools, is capable of estimating and predicting germline LGRs (gLGRs). However, applying this approach to tumor tissue is challenging, and the pipelines for determination of CNV are yet to be optimized. The aim of this study was to validate the Next Generation Tumor Sequencing (NGTS) technology to detect various gLGRs of BRCA1 locus in surgical tumor tissue samples. In this study, seven different BRCA1 gLGRs, previously found in high-grade serous ovarian cancers (HGSOC) patients, were detected in tumor samples collected from the patients at a time of HGSOC surgery. This study demonstrated that NGS can accurately detect BRCA1 gLGRs in primary tumors, suggesting that gLGR evaluation in BRCA1 locus should be performed in cases when the screening for BRCA alterations starts from tumor instead of blood. NGS sequencing of tumor samples may become the preferred method to detect both somatic and germline gLGRs in BRCA-encoding loci.

中文翻译：

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通过下一代肿瘤测序检测BRCA1的大种系重排

摘要

大多数BRCA1 / 2（BRCA）致病性变异体（PVs）是单核苷酸取代或小的插入/缺失。在BRCA中已经确定了拷贝数变异（CNV），也称为大型基因组重排（LGR）基因。如果未通过测序发现易感性PV，则LGR检测是遗传性乳腺癌和卵巢癌家族的一项强制性分析。下一代测序（NGS）可用于检测结构变异，因为与适当的生物信息学工具结合使用时，测序读数的定量分析能够估计和预测种系LGR（gLGR）。然而，将这种方法应用于肿瘤组织是具有挑战性的，并且用于确定CNV的管道尚待优化。这项研究的目的是验证下一代肿瘤测序（NGTS）技术，以检测外科肿瘤组织样本中BRCA1基因座的各种gLGR 。在这项研究中，七个不同的BRCA1gLGRs以前在高级别浆液性卵巢癌（HGSOC）患者中发现，在HGSOC手术时从患者收集的肿瘤样本中被检测到。这项研究表明NGS可以准确检测原发性肿瘤中的BRCA1 gLGR，这表明如果从肿瘤而非血液开始筛查BRCA改变，则应该在BRCA1基因座中进行gLGR评价。肿瘤样品的NGS测序可能成为检测BRCA编码基因座中体细胞和种系gLGRs的首选方法。