A Pilot Study Based on the Correlation Between Whole Exome and Transcriptome Reveals Potent Variants in the Indian Population of Cervical Cancer

• Published in: Indian journal of microbiology 2024-09, Vol.64 (3), p.1222-1245
• Main Authors: Duppala, Santosh Kumari, Poleboyina, Pavan Kumar, Kour, Bhumandeep, Bale, Govardhan, Vyas, Ashish, Pawar, Smita C., Suravajhala, Prashanth N., Vuree, Sugunakar
• Format: Article
• Language: English
• Subjects: Bioinformatics; Biomedical and Life Sciences; Cancer; Cervical cancer; Chromosome 7; Diagnostic systems; Gene mapping; Gene polymorphism; Life Sciences; Malignancy; Medical Microbiology; Medical prognosis; Microbiology; Mutation; Original Article; Pharmacology; Phenotypes; Polymorphism; Population studies; Prognosis; Quality of life; Survival; Transcriptomes; Tumors; Whole genome sequencing
• ISSN: 0046-8991; 0973-7715
• DOI: 10.1007/s12088-024-01295-6

Cervical malignancy (CC) is the 2nd most prevalent malignancy among females, leading to cancer mortality. Primary detection of CC tumors results in an improved prognosis. CC is a malignant gynecological tumor, with few treatment options. New diagnostic and therapeutic agents are required to expand patient survival and quality of life. If CC tumors can be found at an early stage, the prognosis is much brighter. New diagnostic and therapeutic agents are needed to increase patient survival and quality of life. In this work, we performed whole-exome sequencing utilizing V5 (Illumina platform) 10 samples, 5 control and 5 CC tumour tissue, and we compared the results with transcriptome studies. KMT2C variations were shown to be among the most vicious in this analysis. From an Indian viewpoint, we found a plethora of SNVs and mutations, including those with known, unknown, and possible effects on health. Based on our findings, we know that the KMT2C gene is on chr. Seven and in exon 8, all three recognized variants are missense, synonymous, coding synonymous, non-coding variants, and GnomAD MAF (− 0.05). The variation at position (7:152265091, T > A, SNV 62478356) in KMT2C is unique, potent, and pathogenic. The missense coding transcript CIQTNF maps to chromosome 7 and displays T > C SNV. In addition, we performed single strand conformational polymorphism analysis on 64 samples and further confirmed them using Sanger sequencing to understand and verify the mutations. KMT2C shows a log FC value of − 1.16. Understanding emerging harmful mutations from an Indian viewpoint is facilitated by our bioinformatics-based, extensive correlation studies of WES analysis. Potentially harmful and new mutations were found in our preliminary analysis; among these ten top mutated genes, KMT2C and CIQTNF were altered in ten cases of CC with an Indian phenotype.