title: 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.
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany. christopher.schroeder@med.uni-tuebingen.de.
authors.forename: Christopher
authors.initials: C
authors.lastname: Schroeder
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Faust
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Sturm
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Karl
authors.initials: K
authors.lastname: Hackmann
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Grundmann
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Harmuth
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Kristin
authors.initials: K
authors.lastname: Bosse
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kehrer
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Tanja
authors.initials: T
authors.lastname: Benkert
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Klink
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Luisa
authors.initials: L
authors.lastname: Mackenroth
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Elitza
authors.initials: E
authors.lastname: Betcheva-Krajcir
authors.affiliation: Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Pauline
authors.initials: P
authors.lastname: Wimberger
authors.affiliation: Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Karin
authors.initials: K
authors.lastname: Kast
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Mechthilde
authors.initials: M
authors.lastname: Heilig
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Huu Phuc
authors.initials: HP
authors.lastname: Nguyen
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Olaf
authors.initials: O
authors.lastname: Riess
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Evelin
authors.initials: E
authors.lastname: Schröck
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Bauer
authors.affiliation: Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Rump
mesh_terms: D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000592:standards; D004252:DNA Mutational Analysis / Q000592:standards / Q000639:trends; D005260:Female; D005820:Genetic Testing / Q000379:methods* / Q000592:standards*; D023281:Genomics / Q000379:methods / Q000592:standards; D061325:Hereditary Breast and Ovarian Cancer Syndrome / Q000175:diagnosis* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D015203:Reproducibility of Results