Sensitivity of BRCA1/2 testing in high-risk breast/ovarian/male breast cancer families: little contribution of comprehensive RNA/NGS panel testing.
The sensitivity of testing BRCA1 and BRCA2 remains unresolved as the frequency of deep intronic splicing variants has not been defined in high-risk familial breast/ovarian cancer families. This variant category is reported at significant frequency in other tumour predisposition genes, including NF1 and MSH2. We carried out comprehensive whole gene RNA analysis on 45 high-risk breast/ovary and male breast cancer families with no identified pathogenic variant on exonic sequencing and copy number analysis of BRCA1/2. In addition, we undertook variant screening of a 10-gene high/moderate risk breast/ovarian cancer panel by next-generation sequencing. DNA testing identified the causative variant in 50/56 (89%) breast/ovarian/male breast cancer families with Manchester scores of ≥50 with two variants being confirmed to affect splicing on RNA analysis. RNA sequencing of BRCA1/BRCA2 on 45 individuals from high-risk families identified no deep intronic variants and did not suggest loss of RNA expression as a cause of lost sensitivity. Panel testing in 42 samples identified a known RAD51D variant, a high-risk ATM variant in another breast ovary family and a truncating CHEK2 mutation. Current exonic sequencing and copy number analysis variant detection methods of BRCA1/2 have high sensitivity in high-risk breast/ovarian cancer families. Sequence analysis of RNA does not identify any variants undetected by current analysis of BRCA1/2. However, RNA analysis clarified the pathogenicity of variants of unknown significance detected by current methods. The low diagnostic uplift achieved through sequence analysis of the other known breast/ovarian cancer susceptibility genes indicates that further high-risk genes remain to be identified.
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.
Helen
H
Byers
West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
Yvonne
Y
Wallis
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.|Radboud University Nijmegen Medical Centre, Radboud University Nijmegen, Nijmegen, The Netherlands.
Elke M
EM
van Veen
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.
Fiona
F
Lalloo
West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
Kim
K
Reay
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.
Philip
P
Smith
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.
Andrew J
AJ
Wallace
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.
Naomi
N
Bowers
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.|Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
William G
WG
Newman
Genomic Medicine, Institute of Human Development, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, University of Manchester, Manchester, UK.|Genesis Breast Cancer Prevention Centre, University Hospital of South Manchester NHS Trust, Manchester, UK.|Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
D Gareth
DG
Evans
D000328:Adult; D000368:Aged; D064007:Ataxia Telangiectasia Mutated Proteins / Q000235:genetics; D019313:BRCA1 Protein / Q000235:genetics*; D024682:BRCA2 Protein / Q000235:genetics*; D018567:Breast Neoplasms, Male / Q000175:diagnosis / Q000235:genetics*; D064447:Checkpoint Kinase 2 / Q000235:genetics; D005260:Female; D005820:Genetic Testing / Q000592:standards*; D006801:Humans; D007438:Introns; D008297:Male; D008875:Middle Aged; D010051:Ovarian Neoplasms / Q000175:diagnosis / Q000235:genetics*; D010375:Pedigree; D012326:RNA Splicing; D051135:Rad51 Recombinase / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000592:standards*
D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D024682:BRCA2 Protein; C551750:BRCA2 protein, human; D064447:Checkpoint Kinase 2; C576324:ATM protein, human; D064007:Ataxia Telangiectasia Mutated Proteins; C578634:CHEK2 protein, human; C495153:RAD51 protein, human; D051135:Rad51 Recombinase