Whole-exome sequencing identifies new pathogenic germline variants in patients with colorectal polyposis

Abstract

Background: Adenomatous polyposis confers an increased risk of developing colorectal cancer. APC and MUTYH are the major genes investigated in patients suspected of having polyposis. In addition to APC and MUTYH genes, other genes, such as POLE, POLD1, NTHL1, MBD4, MSH3 and MLH3, have recently been associated with polyposis phenotypes, conferring heterogeneity in terms of the clinical, etiological and heritable aspects of patients with polyposis.

Aim: To investigate the underlying variant landscape in patients with suspected polyposis who lack variants in the APC and MUTYH genes using whole-exome sequencing.

Methods: Twenty-seven participants were included in the study and subjected to germline whole-exome sequencing. In addition, their clinical-pathological, personal, and family history data were collected.

Results: The mean age at diagnosis was 51 years, and most participants had attenuated forms of polyposis (88.9%), with 63.0% diagnosed with a primary tumor, mostly colorectal cancer (76.5%). Among the variants identified, 17 were classified as pathogenic or likely pathogenic (in 12 participants), including variants in genes involved in the Wnt/β-catenin signaling pathway, such as ST7 L, A1CF, and DKK4, and variants in DNA-repair genes, such as NTHL1, PNKP, and PMS2, as well as a variant found at the FRK gene identified in a patient with classic polyposis at age 19 and with a family history of polyps.

Conclusion: This study identified novel genes potentially associated with polyposis in patients lacking germline pathogenic variants in the APC and MUTYH genes. These findings support the use of next-generation sequencing for screening, expanding the scope of polyposis-related variants beyond these two genes.

Keywords: Colorectal cancer; Exome sequencing; Familial adenomatous polyposis; Hereditary colorectal cancer; Polyposis; Polyposis predisposition genes.

Figure 1

Representative plot of variants identified in patients with polyposis. All genes harboring pathogenic (V) or likely pathogenic (IV) variants are shown (genes at the top). Genes harboring only variants of uncertain significance are shown if they have an indel, nonsense, or missense variant with a high pathogenic score (high variants of uncertain significance). ACMG: American College of Medical Genetics and Genomics.