Setting a diagnostic benchmark for tumor BRCA testing: detection of BRCA1 and BRCA2 large genomic rearrangements in FFPE tissue – A pilot study

Nadejda Valtcheva,Bich Doan Nguyen-Sträuli,Ulrich Wagner,Sandra N Freiberger,Zsuzsanna Varga,Christian Britschgi,Konstantin J Dedes,Markus P Rechsteiner

doi:10.1016/j.yexmp.2021.104705

Nadejda Valtcheva, Bich Doan Nguyen-Sträuli + Show 6 more

Open Access

https://doi.org/10.1016/j.yexmp.2021.104705

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Abstract

PARP inhibitors are used for treatment of tumors lacking function of the double-strand DNA break repair proteins BRCA1 or BRCA2 and are already approved for several cancer types. Thus, it is clinically crucial to determine germline as well as somatic BRCA1/2 mutations in those patients. The amplicon-based Oncomine BRCA1 and BRCA2 Assay is a test routinely used in diagnostics with FFPE specimens. The assay is validated for the detection of mutations, however, data on its performance in detecting large genomic rearrangements in FFPE tissue, is scarce.We cross-validated Oncomine BRCA1 and BRCA2 Assay in blood samples and/or FFPE tissue with multiplex ligation-dependent probe amplification (MLPA) for exon deletions and with OncoScan and an in-house hybridization-based target capture assay (MelArray) with a customized pipeline for the detection of loss of heterozygosity (LOH) and heterozygous versus complete gene loss.The Oncomine BRCA1 and BRCA2 Assay could detect both exon deletion and mono- and bi-allelic losses of the BRCA1/2 genes.We show that the therapeutically relevant large genomic rearrangements are reliably detected with the amplicon-based Oncomine BRCA1 and BRCA2 Assay in FFPE tumor tissue. Based on our data, we suggest tumor BRCA testing as standard diagnostic prescreening prior to germline BRCA testing.

Highlights

With the growing understanding of the molecular characteristics of cancer, novel treatment options targeting tumor vulnerabilities have emerged (Mateo et al, 2019)
We show that the therapeutically relevant large genomic rearrangements are reliably detected with the amplicon-based Oncomine BRCA1 and BRCA2 Assay in FFPE tumor tissue
Performance of the Oncomine BRCA1 and BRCA2 Assay for exon deletions First, we tested the performance of the Oncomine BRCA1 and BRCA2 assay in detecting exon deletions and duplications by sequencing three patients with known germline exon deletions

Summary

Introduction

With the growing understanding of the molecular characteristics of cancer, novel treatment options targeting tumor vulnerabilities have emerged (Mateo et al, 2019). In order to detect both somatic and Journal Pre-proof germline BRCA variants and capture all patients who may benefit from PARPi treatment, a rapid, affordable and reliable BRCA1/2 mutational test including detection of large genomic rearrangements, which can be applied in formalin-fixed paraffin-embedded (FFPE) tumor tissue is needed. Single nucleotide variants (SNV) and small insertions and deletions (indels), ranging from one nucleotide to small nucleotide stretches, are reliably detected with a comparable performance by both amplicon-based and hybridization-capture based assays Another class of alterations referred to as large genomic rearrangements (LGR) (Judkins et al, 2012), are challenging for testing in FFPE tissue and for amplicon-based NGS assays.

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