Introduction:
Colorectal cancer (CRC) is one of the most common types of cancer and significantly contributes to cancer-associated morbidity and mortality. While genetic testing has been wildly integrated into clinical practice in Western countries, the genetic landscape of hereditary cancer syndrome associated with CRC in Southeast Asian patients, particularly among Thais, has not been well-established.

Methods:
In this single-center study at Siriraj Hospital, we collected and analyzed clinical and genomic data from Thai patients with CRC who underwent multiple gene panel testing (MGPT) from January 2016 to October 2024. The germline DNA was extracted from peripheral blood and enriched using a custom-made target enrichment library. DNA sequencing was performed by ion semiconductor and sequencing by synthesis. All identified single nucleotide variants and copy-number variants were confirmed with Sanger sequencing and multiplex ligation-dependent probe amplification respectively. The variants were analyzed, classified, and systematically verified following the 2015 ACMG-AMP standard and guidelines for the interpretation of sequence variants and 2020 ACMG-ClinGen technical standards for the interpretation and reporting of constitutional copy-number variants.

Results:
From 943 CRC patients who underwent MGPT, 206 pathogenic/likely pathogenic variants (P/LP) were identified in 243 individuals. The mean age of diagnosis was 47.1±14 years. Five hundred and thirty-six individuals (56.8%) were female. Mutations in mismatch repair genes contributing to Lynch syndrome (LS) were identified in 125 patients (51.4%). Among LS patients, 68 patients had P/LP variants in the MLH1(54.4%), followed by 35 patients in MSH2 (28%), 13 patients in PMS2(10.4%), 8 patients in MSH6 (6.4%), and one patient with a terminal deletion in EPCAM. APC P/LP variants were found in 52 patients (21.4%). Twenty-three patients (9.5%) had P/LP variants in other genes associated with polyposis syndromes (biallelic MUTYH, STK11, SMAD4, BMPR1A, biallelic MSH3, POLE, and PTEN). We also identified 43 patients with P/LP variants in other non-CRC cancer-predisposing genes (17.7%). In addition, two individuals carried double P/LP variants.

            In our cohort, 734 individuals met at least one NCCN criteria for genetic testing. The major indication was early-onset CRC (n=581). Among these, 213 (29%) patients had germline P/LP variants. In contrast, 30 out of 209 (13.7%) patients who did not meet NCCN criteria were tested positive. The positive rate of genetic testing increased when more criteria were fulfilled. The detection rate in CRC patients was 19.5%, 41.1%, and 77.1% if one, two, and at least three criteria were met, respectively.

            Among 125 LS patients with CRC, 69 were female. The mean age of CRC diagnosis was 46.2 ± 13.5 years. From 79 patients with eligible data, CRC involvement was mostly left-sided (n=40, 50.6%), followed by right-sided (n=30, 38%) and both sides of the colon (n=9, 11.4%). Twenty-three patients had multi-focal CRC. Among 188 individuals with available MMR status from histopathologic results, patients with MMR defect had a positive rate at 55%, compared to 9.6% in those with intact MMR.

            Among 52 patients with P/LP APC variants, 30 individuals were female. The mean age of CRC diagnosis was 38.7 ± 11.8 years. From 36 patients with eligible data, classic FAP (defined by at least 100 polyps on colonoscopic examination) was found in 32 individuals, whereas 4 patients were attenuated FAP (less than 100 polyps).

 

Conclusion:
This study revealed the genetic landscape of CRC among Thai patients. With MGPT, we demonstrated a high diagnostic rate for germline P/LP variants. This result emphasized the clinical significance of MGPT in identifying hereditary cancer predisposition syndrome in the Thai CRC populations.