Diagnostic Yield of Expanded Multigene Testing in Hereditary Polyposis Syndromes: Functional Characterization of Clinically Relevant Variants

Hereditary polyposis syndromes comprise a genetically heterogeneous group of disorders characterized by multiple gastrointestinal polyps and an increased risk of colorectal cancer (CRC). Although pathogenic variants in APC and MUTYH account for a substantial proportion of cases, the molecular basis remains unresolved in many patients, supporting the use of expanded multigene testing.

Fifty unrelated patients with suspected hereditary polyposis were analyzed using next-generation sequencing (NGS) and a 101-gene hereditary cancer panel. Variants were classified according to ACMG/AMP recommendations and disease-specific ClinGen specifications when available. Functional RNA analysis was performed for a selected splice-site variant.

Pathogenic or likely pathogenic variants were identified in 14/50 patients (overall detection rate: 28.0%), whereas variants in established polyposis-predisposition genes accounted for a diagnostic yield of 20.0% (10/50). Fourteen unique variants corresponding to 17 variant observations were identified across eight genes. APC and MUTYH accounted for 64.7% (11/17) of all variant observations. Variants were also detected in other polyposis-associated genes (SMAD4 and PTEN) and in four additional hereditary cancer predisposition genes (ATM, CDKN2A, CHEK2, and FANCM). Functional RNA studies demonstrated that the APC c.220+3A>T splice-site variant generates an aberrant transcript consistent with complete exon 3 skipping. In addition, the FANCM c.3911delA (p.Asn1304Ilefs*8) variant, not previously reported in ClinVar, was identified. Ten variants of uncertain significance were detected.

Expanded multigene panel testing identified pathogenic or likely pathogenic germline variants in 28.0% of patients with suspected hereditary polyposis, while established polyposis-predisposition genes accounted for a diagnostic yield of 20.0%. The marked molecular heterogeneity observed supports the value of comprehensive germline testing for molecular diagnosis and hereditary cancer risk characterization.