SNP analysis of nasopharyngeal carcinoma (NPC) associated genetic loci in LMP1 signalling pathway genes in tribal populations from North-Eastern India using computational methods

Rákkutatás · Nasopharyngeal carcinoma

We identified that one of the case-control variations might be associated with the risk factor for NPC in the NFKBIA region (NM_020529.3:c.336 + 104T > C) (ACMG criterion PP3).

Background: Nasopharyngeal carcinoma (NPC) is a rare head and neck cancer with distinct racial and geographic characteristics. Genome-wide association studies suggest that NPC and the LMP1 signalling pathway may share disease processes. To better understand the LMP1 signalling pathway, we examined polymorphisms in the genes CHUK, PIK3CA, NFKBIA, TRAF3 and MAP2K4, which are associated with the risk of NPC. Methods: Whole exome sequencing (WES) was performed on 15 samples (9 cases and 6 controls) from three North-East tribal groups using the Ion Proton platform. Variants passing quality control in Haploview were subjected to in‑silico functional prediction. Results: Twenty‑two variants passed quality filtering. One case‑control variant in the NFKBIA region (c.336+104T>C) was predicted to be damaging (ACMG criterion PP3) and is a high‑priority candidate for further validation. Conclusion: These data indicate that high‑risk Epstein‑Barr virus (EBV) and genes from the LMP‑1 signalling pathway may act synergistically to increase NPC risk. Given the limited sample size and exploratory nature of the analyses, the findings should be regarded as hypothesis‑generating; larger, independent cohorts and functional validation are required.

The identification of a potentially pathogenic NFKBIA variant in a high‑risk tribal population highlights a specific genetic factor that could inform future risk screening and targeted interventions for nasopharyngeal carcinoma.

Bizonyítékszint: Sejtvonalas. Laboratóriumi sejtekben vizsgálták.

Eredeti forrás

Kapcsolódó jelek