Department of Haematology-Oncology, National University Cancer Institute, Singapore (NCIS), Singapore.
ACT Genomics Co., Ltd.
Gynecol Oncol. 2019 Nov;155(2):275-279. doi: 10.1016/j.ygyno.2019.08.027. Epub 2019 Aug 31.
Clinical genetic testing to diagnose germline mutations often requires blood sample or saliva smear from a cancer-affected individual. This rules out testing in families when cancer-affected individuals are deceased. We explored the use of a next-generation sequencing (NGS) platform to diagnose germline pathogenic mutations from tumors.
Archival tumors (ovarian = 26, breast = 25, others = 9) were retrieved from 60 cancer patients who have undergone multi-gene panel blood testing. Genomic DNA was extracted and sequenced for BRCA1/2 using a NGS platform. 41/60 specimens were sequenced for 5 other genes (APC, ATM, PALB2, PTEN, TP53). Tumor testing and results interpretation were performed blinded to the blood test result.
All 38 patients with no BRCA1/2 mutations on blood testing were correctly tested negative on tumor. Tumor testing correctly diagnosed BRCA1/2 pathogenic mutations in 15/22 (68%) patients while in 7/22 (32%) patients, the mutation was either detected but incorrectly classified as VUS (n = 3) or not detected at all (n = 4). Overall concordance rate for tumor and blood testing for BRCA1/2 mutations was 88%, with 0% false positive and 32% false negative rate for pathogenic mutations. Tumor testing correctly diagnosed 1/2 pathogenic germline ATM mutation, 1/1 pathogenic germline PALB2 mutation and 2/2 pathogenic germline TP53 mutations. False positive germline mutations were diagnosed in 4 genes at a rate of 2.4%-10.3% (APC = 2.4%, PALB2 = 2.4%, PTEN = 4.9%, TP53 = 10.3%).
Tumor testing for BRCA1/2 germline mutations using an NGS platform is fairly reliable with no false positive findings, and correctly diagnosed more than two-thirds of pathogenic germline BRCA1/2 mutations. However, it is not reliable to diagnose pathogenic germline mutations in genes frequently mutated in sporadic cancers, such as PTEN and TP53.
临床基因检测诊断种系突变通常需要癌症患者的血液样本或唾液涂片。这排除了癌症患者去世的家庭进行检测的可能性。我们探索了使用下一代测序（NGS）平台从肿瘤中诊断种系致病性突变。
从接受多基因panel 血液检测的 60 名癌症患者中获取存档肿瘤（卵巢=26，乳腺=25，其他=9）。提取基因组 DNA 并使用 NGS 平台对 BRCA1/2 进行测序。41/60 个标本对 5 个其他基因（APC、ATM、PALB2、PTEN、TP53）进行测序。肿瘤检测和结果解释是在不了解血液检测结果的情况下进行的。
所有在血液检测中无 BRCA1/2 突变的 38 名患者在肿瘤检测中均正确地检测为阴性。肿瘤检测正确诊断出 22 名患者中的 15 名（68%）BRCA1/2 致病性突变，而在 7 名（32%）患者中，突变要么被检测到但错误地归类为 VUS（n=3），要么根本未被检测到（n=4）。BRCA1/2 突变的肿瘤和血液检测的总一致性率为 88%，致病性突变的假阳性率为 0%，假阴性率为 32%。肿瘤检测正确诊断出 1 种致病性种系 ATM 突变、1 种致病性种系 PALB2 突变和 2 种致病性种系 TP53 突变。在 4 个基因中诊断出假阳性种系突变，发生率为 2.4%-10.3%（APC=2.4%，PALB2=2.4%，PTEN=4.9%，TP53=10.3%）。
使用 NGS 平台对 BRCA1/2 种系突变进行肿瘤检测的可靠性较高，没有假阳性发现，正确诊断了超过三分之二的致病性种系 BRCA1/2 突变。然而，在经常发生散发性癌症突变的基因（如 PTEN 和 TP53）中诊断致病性种系突变并不可靠。
