Citations 1
Saturation genome editing-based functional evaluation and clinical classification of BRCA2 single nucleotide variants
Huang, Huaizhi , Abozaid, Mohamed , Rao, Tara, Tecleab, Yohannes A., Pesaran, Tina , Yadav, Siddhartha , Bandlamudi, Chaitanya , Chen, Wenan , Yadav, Siddhartha , Huang, Huaizhi , Couch, Fergus J. , Hu, Chunling , Na, Jie , Hart, Steven N. , Gnanaolivu, Rohan , Abozaid, Mohamed , Lyra, Paulo C. , Karam, Rachid , Domchek, Susan M. , Hoya, Miguel de la , Robson, Mark E. , Mehine, Miika , Mandelker, Diana L. , Monteiro, Álvaro N.A. , Boddicker, Nicholas , Richardson, Marcy E
No container title available | December 19, 2023 | Volume: No volume available | Issue: No issue available | Pages: No page available
Abstract Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to breast, ovarian, prostate and pancreatic cancer. However, variants of uncertain significance (VUS) (n>4000) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants. Here we report on comprehensive saturation genome editing-based functional characterization of 97% of all possible single nucleotide variants (SNVs) in the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants that is encoded by exons 15 to 26. The assay was based on deep sequence analysis of surviving endogenously targeted haploid cells. A total of 7013 SNVs were characterized as functionally abnormal (n=955), intermediate/uncertain, or functionally normal (n=5224) based on 95% agreement with ClinVar known pathogenic and benign standards. Results were validated relative to batches of nonsense and synonymous variants and variants evaluated using a homology directed repair (HDR) functional assay. Breast cancer case-control association studies showed that pooled SNVs encoding functionally abnormal missense variants were associated with increased risks of breast and ovarian cancer (odds ratio (OR) 3.89, 95%CI: 2.77-5.51). In addition, 86% of tumors associated with abnormal missense SNVs displayed loss of heterozygosity (LOH), whereas 26% of tumors with normal variants had LOH. The functional data were added to other sources of information in a ClinGen/ACMG/AMP-like model and 700 functionally abnormal SNVs, including 220 missense SNVs, were classified as pathogenic or likely pathogenic, while 4862 functionally normal SNVs, including 3084 missense SNVs, were classified as benign or likely benign. These classified variants can now be used for risk assessment and clinical care of variant carriers and the remaining functional scores can be used directly for clinical classification and interpretation of many additional variants.