Schroeder Christopher, Faust Ulrike, Sturm Marc, Hackmann Karl, Grundmann Kathrin, Harmuth Florian, Bosse Kristin, Kehrer Martin, Benkert Tanja, Klink Barbara, Mackenroth Luisa, Betcheva-Krajcir Elitza, Wimberger Pauline, Kast Karin, Heilig Mechthilde, Nguyen Huu Phuc, Riess Olaf, Schröck Evelin, Bauer Peter, Rump Andreas
Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
Breast Cancer Res Treat. 2015 Jul;152(1):129-136. doi: 10.1007/s10549-015-3429-9. Epub 2015 May 29.
Multi-gene panels are used to identify genetic causes of hereditary breast and ovarian cancer (HBOC) in large patient cohorts. This study compares the diagnostic workflow in two centers and gives valuable insights into different next-generation sequencing (NGS) strategies. Moreover, we present data from 620 patients sequenced at both centers. Both sequencing centers are part of the German consortium for hereditary breast and ovarian cancer (GC-HBOC). All 620 patients included in this study were selected following standard BRCA1/2 testing guidelines. A set of 10 sequenced genes was analyzed per patient. Twelve samples were exchanged and sequenced at both centers. NGS results were highly concordant in 12 exchanged samples (205/206 variants = 99.51 %). One non-pathogenic variant was missed at center B due to a sequencing gap (no technical coverage). The custom enrichment at center B was optimized during this study; for example, the average number of missing bases was reduced by a factor of four (vers. 1: 1939.41, vers. 4: 506.01 bp). There were no sequencing gaps at center A, but four CCDS exons were not included in the enrichment. Pathogenic mutations were found in 12.10 % (75/620) of all patients: 4.84 % (30/620) in BRCA1, 4.35 % in BRCA2 (27/620), 0.97 % in CHEK2 (6/620), 0.65 % in ATM (4/620), 0.48 % in CDH1 (3/620), 0.32 % in PALB2 (2/620), 0.32 % in NBN (2/620), and 0.16 % in TP53 (1/620). NGS diagnostics for HBOC-related genes is robust, cost effective, and the method of choice for genetic testing in large cohorts. Adding 8 genes to standard BRCA1- and BRCA2-testing increased the mutation detection rate by one-third.
多基因检测板用于在大量患者队列中识别遗传性乳腺癌和卵巢癌（HBOC）的遗传病因。本研究比较了两个中心的诊断流程，并对不同的下一代测序（NGS）策略提供了有价值的见解。此外，我们展示了在两个中心进行测序的620名患者的数据。两个测序中心都是德国遗传性乳腺癌和卵巢癌联盟（GC-HBOC）的一部分。本研究纳入的所有620名患者均按照标准的BRCA1/2检测指南进行选择。每位患者分析一组10个测序基因。12个样本在两个中心进行交换测序。在12个交换样本中，NGS结果高度一致（205/206个变异=99.51%）。由于测序缺口（无技术覆盖），中心B遗漏了一个非致病性变异。在本研究期间，中心B的定制富集得到了优化；例如，缺失碱基的平均数量减少了四倍（版本1：1939.41，版本4：506.01 bp）。中心A没有测序缺口，但有四个CCDS外显子未包含在富集范围内。在所有患者中，12.10%（75/620）发现了致病突变：BRCA1中为4.84%（30/620），BRCA2中为4.35%（27/620），CHEK2中为0.97%（6/620），ATM中为0.65%（4/620），CDH1中为0.48%（3/620），PALB2中为0.32%（2/620），NBN中为0.32%（2/620），TP53中为0.16%（1/620）。HBOC相关基因的NGS诊断可靠、具有成本效益，是大型队列基因检测的首选方法。在标准的BRCA1和BRCA2检测中增加8个基因，使突变检测率提高了三分之一。
