Genetic characterization of Lynch syndrome germline variants in a LATAM cohort using a customized NGS gene panel

Abstract

Introduction: Lynch Syndrome accounts for 1-7% of all colorectal cancers and is caused by germline mutations in DNA mismatch repair (MMR) genes. Timely molecular diagnosis is crucial for effective genetic counseling and management. Among understudied Latin American populations, Uruguay's genetic admixture provides an opportunity to identify novel Lynch Syndrome related variants.

Methods: This study analyzed 70 unrelated Uruguayan colorectal cancer patients meeting Lynch Syndrome clinical criteria to identify carriers of pathogenic variants. A customized Next-Generation Sequencing (NGS) panel was developed and sequenced on the Ion Torrent platform to analyze nine genes: MLH1, MSH2, MSH6, EPCAM, FAN1, MUTYH, PMS1, PMS2, and APC. Copy number variations and large EPCAM deletions are not detected by the assay. Gene variants were prioritized based on allelic frequency, in silico predictions, pathogenicity records, and ACMG guidelines. The performance of this custom NGS panel was evaluated for in-house applications, and its limitations were thoroughly assessed.

Results and discussion: The custom NGS panel demonstrated effectiveness for scalable in-house testing despite minor disclosed sequence coverage limitations. Pathogenic and likely pathogenic variants were identified in 25 patients, including four novel Lynch Syndrome-associated variants. In four patients, a rare ambiguously classified gene variant co-occurs with a known pathogenic variant in another gene. The mutation profile correlated with clinical parameters such as age of diagnosis, diagnosis criteria, tumor location, and microsatellite instability (MSI).

Conclusion: This is the most comprehensive genetic study to date on a Uruguayan Lynch syndrome cohort. The mutational landscape aligns with findings in other populations while highlighting novel variants of clinical relevance. These findings highlight the value of customized panels for improving genetic screening in small-scale healthcare facilities.

Keywords: LATAM; Lynch Syndrome; NGS; colorectal cancer; germline cancer predisposition; novel variants.

Figure 1

Patient 9-gene panel Sequencing results. (A–D) Sequencing metrics per sample. (A) Mapped Reads, (B) Mean Depth (dotted line indicates 50x depth), (C) Reads Mapped on ROI (D) Uniformities. (E–H) Sequence metrics per amplicon. (E) Normalized reads per amplicon ordered by the average depth. (F) Detailed view of the first 8 amplicons shown in (E). (G) Amplicon performance per size (Slope: -4.74, Spearman’s correlation coefficient: - 0.38, p<0.0001). (H) Normalized reads per amplicon pool. The amplicon number difference (116 vs 113) was corrected by normalizing the number of reads to 114.5 amplicons per pool. (I) Base coverage analysis: The percentage of bases read more than 50x is plotted against the total mapped reads for each patient. Mean and standard deviations are plotted in all charts. Supplementary Table 3 contains raw data.

Figure 2

Clinically relevant Variants identified. (A) Summary of the variant classification results. *Gene variants coexisting with PV/LP (pathogenic/likely pathogenic variants) in a different gene. (B) Distribution of mutation types into MS (missense), NS (nonsense), FS (frameshift), S (splicing) and I (intronic). (C) Distribution of mutations in the analyzed genes.

Figure 3

Association between mutations and clinical characteristics of the cohort. Comparison of several aspects among the patients who tested positive for a relevant variant detected (in black), including VUS, likely pathogenic and pathogenic variants, or negative for these variants (in gray). (A) Diagnosis Age. (B) Fulfillment of Amsterdam Criteria or Bethesda Guidelines. (C) MSI status (D) Tumor Location. Abbreviations used are CL, colon left; CR, colon right; CNA, colon not assigned; R, rectum; O, other.