Tumor Sequencing Is Useful to Refine the Analysis of Germline Variants in Unexplained High-Risk Breast Cancer Families - PubMed

Tumor Sequencing Is Useful to Refine the Analysis of Germline Variants in Unexplained High-Risk Breast Cancer Families - PubMed

Tumor Sequencing Is Useful to Refine the Analysis of Germline Variants in Unexplained High-Risk Breast Cancer Families

Cédric Van Marcke 1 2, Raphaël Helaers 2, Anne De Leener 3 4, Ahmad Merhi 5, Céline A Schoonjans 2, Jérôme Ambroise 6, Christine Galant 4 7, Paul Delrée 8, Françoise Rothé 9, Isabelle Bar 5, Elsa Khoury 10, Pascal Brouillard 2, Jean-Luc Canon 11, Peter Vuylsteke 12, Jean-Pascal Machiels 1, Martine Berlière 4, Nisha Limaye 10, Miikka Vikkula 2, François P Duhoux 13 14 15

Affiliations 

• PMID: 32295625
 
• PMCID: PMC7161277
 
• DOI: 10.1186/s13058-020-01273-y

Abstract

Background: Multigene panels are routinely used to assess for predisposing germline mutations in families at high breast cancer risk. The number of variants of unknown significance thereby identified increases with the number of sequenced genes. We aimed to determine whether tumor sequencing can help refine the analysis of germline variants based on second somatic genetic events in the same gene.

Methods: Whole-exome sequencing (WES) was performed on whole blood DNA from 70 unrelated breast cancer patients referred for genetic testing and without a BRCA1, BRCA2, TP53, or CHEK2 mutation. Rare variants were retained in a list of 735 genes. WES was performed on matched tumor DNA to identify somatic second hits (copy number alterations (CNAs) or mutations) in the same genes. Distinct methods (among which immunohistochemistry, mutational signatures, homologous recombination deficiency, and tumor mutation burden analyses) were used to further study the role of the variants in tumor development, as appropriate.

Results: Sixty-eight patients (97%) carried at least one germline variant (4.7 ± 2.0 variants per patient). Of the 329 variants, 55 (17%) presented a second hit in paired tumor tissue. Of these, 53 were CNAs, resulting in tumor enrichment (28 variants) or depletion (25 variants) of the germline variant. Eleven patients received variant disclosure, with clinical measures for five of them. Seven variants in breast cancer-predisposing genes were considered not implicated in oncogenesis. One patient presented significant tumor enrichment of a germline variant in the oncogene ERBB2, in vitro expression of which caused downstream signaling pathway activation.

Conclusion: Tumor sequencing is a powerful approach to refine variant interpretation in cancer-predisposing genes in high-risk breast cancer patients. In this series, the strategy provided clinically relevant information for 11 out of 70 patients (16%), adapted to the considered gene and the familial clinical phenotype.

Keywords: Breast cancer; Germline; Mutational signatures; Predisposition; Second hit; Variant of unknown significance.

Conflict of interest statement

The authors have declared no conflicts of interest related to this work.