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. 2022 Dec;33(12):1318-1327.
doi: 10.1016/j.annonc.2022.09.152. Epub 2022 Sep 17.

Analysis of rare disruptive germline mutations in 2135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes

C Loveday  1 , A Garrett  1 , P Law  1 , S Hanks  1 , E Poyastro-Pearson  1 , J W Adlard  2 , J Barwell  3 , J Berg  4 , A F Brady  5 , C Brewer  6 , C Chapman  7 , J Cook  8 , R Davidson  9 , A Donaldson  10 , F Douglas  11 , L Greenhalgh  12 , A Henderson  13 , L Izatt  14 , A Kumar  15 , F Lalloo  16 , Z Miedzybrodzka  17 , P J Morrison  18 , J Paterson  19 , M Porteous  20 , M T Rogers  21 , L Walker  22 ; Breast and Ovarian Cancer Susceptibility Collaboration; D Eccles  23 , D G Evans  16 , K Snape  24 , H Hanson  24 , R S Houlston  1 , C Turnbull  25
Collaborators, Affiliations
Free article

Analysis of rare disruptive germline mutations in 2135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes

C Loveday et al. Ann Oncol. 2022 Dec.
Free article

Abstract

Background: Breast cancer has a significant heritable basis, of which ∼60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility.

Patients and methods: We included 2135 invasive breast cancer cases recruited via the Breast and Ovarian Cancer Susceptibility study, a retrospective UK study of familial breast cancer.

Eligibility criteria: female, BRCA-negative, white European ethnicity, and one of: (i) breast cancer family history, (ii) bilateral disease, (iii) young age of onset (<30 years), and (iv) concomitant ovarian cancer. We undertook exome sequencing of cases and carried out gene-level burden testing of rare damaging variants against those from 51 377 ethnicity-matched population controls from gnomAD.

Results: 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2, and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk [odds ratio (OR) = 10.6] down to a population minor allele frequency of 4.6 × 10-5 (1 in 10 799, less than one-tenth that of BRCA1)and of PALB2-like risk (OR = 5.0) down to a population minor allele frequency of 2.8 × 10-4 (1 in 1779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (OR = 2-3) like CHEK2 and ATM.

Conclusions: This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.

Keywords: breast cancer; cancer susceptibility genes; genetic susceptibility; rare-variant burden testing; whole-exome sequencing.

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Conflict of interest statement

Disclosure The authors have declared no conflicts of interest.

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