Targeted Resequencing of DNA Repair Genes in Familial Colorectal Cancer: Insights from a Custom 56-Gene Panel

Background Germline mutations in high-penetrance genes contribute to the development of colorectal cancer with a >1% familial risk. The proband with a family history of cancer was at an increased risk for colorectal cancer development. However, data on the germline mutational landscape in non-Western populations, particularly in India, remain limited. Objective This study aimed to investigate the prevalence of germline mutations in individuals fulfilling clinical criteria for suspected Lynch Syndrome (LS) or familial adenomatous polyposis (FAP) using a targeted multigene next-generation sequencing (NGS) approach. Method Mutation analysis was performed for 110 suspected Lynch syndrome and 12 familial adenomatous polyposis (FAP) and attenuated FAP (AFAP) patients. Sanger sequencing was employed to validate pathogenic, likely pathogenic, and novel variants. Results Pathogenic mutations were identified in 20% of suspected Lynch syndrome cases and 66% of FAP cases, indicating a stronger genetic contribution in FAP. Notably, this is the first study to report a FANCD2 mutation in FAP. Most LS-associated mutations occurred in mismatch repair genes ( MLH1, MSH2, MSH6 ), while APC and MUTYH mutations predominated in FAP. Four novel mutations were identified: MLH1 c.676delC, MLH1 c.378delC, MDC1 c.2839C>T , and RAD52 c.1215delG . Functional prediction of 100 VUS revealed several potentially disruptive variants, notably BLM P866L , which showed significant loss of protein–protein interactions. A pathogenic FANCD2 mutation was identified in one FAP family, suggesting a broader spectrum of contributing genes. Conclusion This study demonstrates the utility of multigene NGS panels in detecting clinically actionable germline mutations in suspected hereditary CRC cases in an Indian population. The identification of novel and ethnically distinct variants highlights the need for population-specific genetic databases and reinforces the role of genetic screening and counseling in cancer prevention and early diagnosis.