Detection of hotspot mutations in oral cancer through Ion AmpliSeq™ cancer hotspot panel v.2.0: A circulating DNA fragmentomics approach in the Northeast Indian population.

UNLABELLED

Oral Squamous Cell Carcinoma (OSCC) is the most commonly diagnosed cancer worldwide, with 90-95% of cases reported to be SCC. The present study aimed to investigate the presence of circulating cell-free tumor DNA (cftDNA) in the patient's plasma with OSCC and determine the feasibility of liquid biopsies in genomic profiling using deep sequencing-based approach. Mutation analysis of cfDNA will help evaluate the molecular and clinical impacts of the identified somatic alterations during primary staging.

METHODS

Paired samples from 11 OSCC patients, including cfDNA, tumor tissue, and blood, were submitted for deep sequencing of 50 genes by next-generation sequencing using the Ion Ampliseq Cancer Hotspot Panel v2.

RESULTS

We found higher mutational load in cfDNA than in tumor tissue samples, suggesting the potential of cfDNA as a liquid biopsy for monitoring therapeutic responses. The TP53 p.Pro72Arg variant was identified in all the samples, indicating its potential as a diagnostic marker. Molecular dynamics simulations of the p53 protein showed higher fluctuations in the mutant form, potentially affecting protein function. The RB1 p.Ile680Thr pathogenic variant was found in 64% of oral squamous cell carcinoma samples. Recurrently mutated genes, including TP53, KDR, APC, RB1, MET, PIK3CA, CDKN2A, RET, and EGFR, were identified in both tumor tissue and cfDNA samples.

CONCLUSION

The detection of tumor imprints and heterogeneity in cfDNA samples highlights the potential of liquid biopsy as a valuable tool for monitoring therapeutic responses in OSCC. The identification of recurrently mutated genes and pathogenic variants provides insights into potential therapeutic targets.