Classification of Missense Variants in XRCC2 by Functional Analysis: Implications for Breast Cancer Association Studies.

Abstract

XRCC2 belongs to the family of RAD51 paralogs, which are involved in homologous recombination repair (HRR) of DNA double-strand breaks. Variants in XRCC2 have recently been suggested to increase the risk for breast cancer. However, this finding could not be confirmed in a second study. Both case-control studies lacked power due to the rarity of deleterious XRCC2 mutations, and therefore rare missense variants predicted to be damaging by in silico analysis had been included in the analyses. But is incorporating purely in silico predictions for variant pathogenicity advised when conducting association studies? In this issue, Hilbers et al. (Hum Mutat 37:914–925, 2016) examined 23 previously reported XRCC2 missense variants with four different in silico prediction algorithms, including AlignGVGD, SIFT, PolyPhen2, and CADD, to estimate whether the variants were likely to be pathogenic. The functional effects of the XRCC2 missense variants were subsequently examined by testing their ability to complement the DNA repair phenotype of XRCC2-deficient cells, as well as measuring the efficiency of the variants to perform HRR in hamster and human cells. The experiments revealed that the in silico predictions correlated poorly with the observed functional effects. When the novel functional data were included in case-control studies, there no longer was an association with breast cancer. The authors conclude that if XRCC2 variants predispose to breast cancer, the associated variants are likely to be restricted to protein-truncating mutations as well as few missense variants. Next-generation sequencing is expected to increase the number of rare variants identified in novel cancer-predisposing genes, which poses challenges to risk estimation through patient cohorts and cosegregation analysis. The study by Hilbers et al. highlights the importance of functional analysis of variants of unknown clinical significance and demonstrates the pitfalls in establishing an association between rare missense variants and disease risk.