HBOC multi-gene panel testing: comparison of two sequencing centers

Abstract

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.

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

“…CHEK2 (2.5% of the patients), ATM (0.8%), and TP53 (0.8%) were the most frequently mutated genes in breast cancer, whereas ovarian cancer patients carried mutations in BRIP1 (1.7%) and MSH6 (1.3%) [34]. Similar results were obtained by other centres [39,61] including Invitae [41], where 1062 subjects tested with a 29-gene-panel because of HBOC confirmed ATM , PALB2 , CHEK2 and some MMR genes as the most frequently mutated genes, plus MUTYH [42] with a possible recessive behaviour. Also, when a higher number of genes was screened, mutations were detected in the same set of genes.…”

“…Complete concordance with the reference methods was also demonstrated using a 29-gene-panel on 1062 subjects, in which over 750 variants were identified, including technically challenging classes of sequence and copy number alterations [42]. The reproducibility between two separate German centres that used different gene-panels and library preparation methods was tested on 12 specimens with over 99.5% concordance (one non-pathogenic variant was called in discordance between the centres and it turned out that this specific alteration mapped in a region without sufficient coverage) [39]. …”

The transfer of multigene panel testing for hereditary breast and ovarian cancer to healthcare: What are the implications for the management of patients and families?

“…The frequency of BRCA1/2, PALB2, ATM and CHEK2 mutations were comparable to those in published series with the same inclusion criteria. Table 3A and 3B summarizes the primary aim of these studies, the inclusion criteria, the list of genes included in the selected panels and the results of ten published studies that included more than 500 patients who had undergone diagnostic multigene panel testing for HBOC [18-20, 22-23, 25, 27-28, 30-31]. One study was excluded from this review despite the high number of patients, because the authors chose to study only 36 known pathogenic mutations in the selected HBOC genes [14].…”

The transfer of multigene panel testing for hereditary breast and ovarian cancer to healthcare: What are the implications for the management of patients and families?

“…In the last 2 years, the literature assessing the contribution of multigene panel testing in cohorts of patients with HBOC has grown. The results have been consistent even though the inclusion criteria sometimes differ [17][18][19][20][21][22][23][24][25][26][27][28][29][30]. The next challenge is to determine the consequences of these results on clinical management [NCCN clinical practice Guidelines-see URL].…”