Canonical and uncanonical pathogenic germline variants in colorectal cancer patients by next-generation sequencing in a European referral center

Abstract

Background: Despite increasing use of next-generation sequencing (NGS), data concerning the gain in germline pathogenic variants (PVs) remain scanty, especially with respect to uncanonical ones. We aimed to verify the impact of different cancer predisposition genes (CPGs) on colorectal cancer (CRC) in patients referred for genetic evaluation.

Materials and methods: We enrolled for NGS, by Illumina TruSight Cancer panel comprising 94 CPGs, 190 consecutive subjects referred for microsatellite instability (MSI) CRC, polyposis, and/or family history.

Results: Overall, 51 (26.8%) subjects carried 64 PVs; PVs coexisted in 4 (7.8%) carriers. PVs in mismatch repair (MMR) genes accounted for one-third of variant burden (31.3%). Four Lynch syndrome patients (20%) harbored additional PVs (HOXB13, CHEK2, BRCA1, NF1 plus BRIP1); such multiple PVs occurred only in subjects with PVs in mismatch syndrome genes (4/20 versus 0/31; P = 0.02). Five of 22 (22.7%) patients with MSI cancers but wild-type MMR genes harbored PVs in unconventional genes (FANCL, FANCA, ATM, PTCH1, BAP1). In 10/63 patients (15.9%) with microsatellite stable CRC, 6 had MUTYH PVs (2 being homozygous) and 4 exhibited uncanonical PVs (BRCA2, BRIP1, MC1R, ATM). In polyposis, we detected PVs in 13 (25.5%) cases: 5 (9.8%) in APC, 6 (11.8%) with biallelic PVs in MUTYH, and 2 (3.9%) in uncanonical genes (FANCM, XPC). In subjects tested for family history only, we detected two carriers (18.2%) with PVs (ATM, MUTYH).

Conclusion: Uncanonical variants may account for up to one-third of PVs, underlining the urgent need of consensus on clinical advice for incidental findings in cancer-predisposing genes not related to patient phenotype.

Keywords: DNA microsatellite instability; colorectal cancer; colorectal cancer genes; gene testing; inherited cancers.

Figure 1

Characteristics suggestive of inherited predisposition in 190 subjects undergoing NGS for CRC. CRC, colorectal cancer; EO, early onset; F, female; M, male; MMR, mismatch repair; MSI, microsatellite instability; NGS, next-generation sequencing.

Figure 2

Pathogenetic variants identified with reference to indication for genetic evaluation. CRC, colorectal cancer; LS, Lynch syndrome; MAP, MUTYH-associated polyposis; MS, microsatellite; MSI, microsatellite instability; MSS, microsatellite stability; PV, pathogenic variant. ^aBi, biallelic PV in MUTYH. ^bMono, mono-allelic PV in MUTYH.