Value of the loss of heterozygosity to BRCA1 variant classification

Elizabeth Santana Dos Santos,Sarah Beck,Étienne Rouleau ,Giovana Tardin Torrezan ,Melissa C Southey ,Keltouma Driouch,Françoise Révillion ,Ambre Petitalot,Carole Brewer,Dominique Stoppa‐Lyonnet ,Alison Callaway,Athalie Melville,Anne Vincent‐Salomon ,Michael T Parsons,Philippe Lafitte,Raphaël Leman ,Didier Meseure,Adrien Briaux,Ivan Bièche ,Amanda B Spurdle,Heather Thorne,Sandrine M Caputo,Dirce Maria Carraro ,Maria Aparecida Azevedo Koike Folgueira ,Lucy Side,Null Author_Id

doi:10.1038/s41523-021-00361-2

Abstract

At least 10% of the BRCA1/2 tests identify variants of uncertain significance (VUS) while the distinction between pathogenic variants (PV) and benign variants (BV) remains particularly challenging. As a typical tumor suppressor gene, the inactivation of the second wild-type (WT) BRCA1 allele is expected to trigger cancer initiation. Loss of heterozygosity (LOH) of the WT allele is the most frequent mechanism for the BRCA1 biallelic inactivation. To evaluate if LOH can be an effective predictor of BRCA1 variant pathogenicity, we carried out LOH analysis on DNA extracted from 90 breast and seven ovary tumors diagnosed in 27 benign and 55 pathogenic variant carriers. Further analyses were conducted in tumors with PVs yet without loss of the WT allele: BRCA1 promoter hypermethylation, next-generation sequencing (NGS) of BRCA1/2, and BRCAness score. Ninety-seven tumor samples were analyzed from 26 different BRCA1 variants. A relatively stable pattern of LOH (65.4%) of WT allele for PV tumors was observed, while the allelic balance (63%) or loss of variant allele (15%) was generally seen for carriers of BV. LOH data is a useful complementary argument for BRCA1 variant classification.

Highlights

Monoallelic germline BRCA1/2 pathogenic variants (PV) substantially increase the risk of developing breast (BC) and/or ovarian cancer (OC), but at least 10% of BRCA1/2 tests result in a variant of unclassified/uncertain/unknown significance (VUS)[1]
We evaluated 97 tumor samples (90 breast and seven ovarian) from carriers of 26 distinct BRCA1 germline variants using a pipeline to identify genomic markers of BRCA1 locus-specific Loss of heterozygosity (LOH) and other possible mechanisms of gene inactivation
The loss of the remaining WT allele is the last event before entering germline BRCA1-related tumorigenesis

Summary

Introduction

Monoallelic germline BRCA1/2 pathogenic variants (PV) substantially increase the risk of developing breast (BC) and/or ovarian cancer (OC), but at least 10% of BRCA1/2 tests result in a variant of unclassified/uncertain/unknown significance (VUS)[1]. The distinction between germline pathogenic and benign nature of a missense variant remains problematic, while the classification of a rare germline missense variant remains challenging[2]. In addition to genetic counseling implications, BRCA1/2 variant classification has an important impact on therapeutic decisions as well as predicting the benefit from PARPi3,4 and DNA-damaging agents[5]. Recent data suggest that in addition to the germline PV, locus-specific LOH may be necessary to predict sensitivity to DNA-damaging agents for better outcomes[6,7,8]. The estimations of the second event have been biased, as most of the LOH reported have copyneutral allelic imbalance[12]

Methods

Results

Conclusion