PMS2 c.2117del (p.Lys706Serfs*19) is the Most Frequent Cancer-Associated Founder Pathogenic Variant in the French-Canadian Population of Quebec, Canada

Abstract

We identified a PMS2 variant (NM_000535.7:c.2117del, p.Lys706Serfs*19) in 22 French-Canadian (FC) families from Quebec with Lynch syndrome (LS; n = 21) or constitutional mismatch repair deficiency (CMMRD; n = 1). We aimed to (a) confirm its founder origin, (b) assess its allele frequency in the FC population, and (c) determine its contribution to the risk of developing various cancers in this population. We identified a haplotype common to all c.2117del alleles spanning 666 kb to 1.37 Mb, confirming the founder nature of the variant. In affected cases, the variant was found in 0 out of 821 breast cancer cases, 8 out of 693 (1.15%) endometrial cancer (EC) cases, and 1 out of 191 (0.52%) colorectal cancer (CRC) cases. In unaffected persons, the variant was identified in 22/6347 newborns (0.35%) and in 21/18129 FC CARTaGENE cohort participants (0.12%). Within this cohort, an excess of CRC (odds ratio: 10.7; 95% CI: 1.42-80.1; p value = 0.022), but not EC, was seen among heterozygotes for the PMS2 founder variant. Analysis of the variant in 24 subregions of Quebec showed over-representation in 5 of them. Here, we report the most frequent genetic cause of mismatch repair deficiency syndromes identified thus far in the FC population of Quebec.

Keywords: French‐Canadian variant; ancestral recombination graph; colorectal cancer; endometrial cancer; imputation.

FIGURE 1

Carrier frequency estimation using ISGen. Heatmap showing the carrier frequency in 24 historic regions of Quebec. Scale is given in number of carriers per 1000 individuals. Five regions display a higher frequency than the rest of Quebec: Saguenay, Côte de Beaupré, Charlevoix, Beauce, and Côte‐du‐Sud.