Preprint Communication Version 1 Preserved in Portico This version is not peer-reviewed

Exome Sequencing reveals characteristic KMT2C mutations in the Indian Phenotype of Cervical Cancer

Version 1 : Received: 21 November 2022 / Approved: 23 November 2022 / Online: 23 November 2022 (07:42:19 CET)

How to cite: Duppala, S.K.; Kour, B.; Shukla, N.; Dhakane, M.A.; Mishra, A.K.; Digumarti, R.; Pawar, S.C.; Suravajhala, P.N.; Vuree, S. Exome Sequencing reveals characteristic KMT2C mutations in the Indian Phenotype of Cervical Cancer. Preprints 2022, 2022110440. https://doi.org/10.20944/preprints202211.0440.v1 Duppala, S.K.; Kour, B.; Shukla, N.; Dhakane, M.A.; Mishra, A.K.; Digumarti, R.; Pawar, S.C.; Suravajhala, P.N.; Vuree, S. Exome Sequencing reveals characteristic KMT2C mutations in the Indian Phenotype of Cervical Cancer. Preprints 2022, 2022110440. https://doi.org/10.20944/preprints202211.0440.v1

Abstract

We attempted to understand the cervical cancer patient samples through Whole Exome Sequencing. We derived the variants from raw reads via our in-house benchmarked pipeline and validated the variants by IGV. This is the first cervical cancer exome data from the Indian cohort. Background: Cervical cancer (CC) is caused mainly by persistent infections of high-risk HPV, reduced parity, and factors like a decrease in average socioeconomic levels. We keep this because no cervical cancer exome data is available from the Indian cohort. Methods: The CC patient clinical samples were initially subjected to preparation using Qiagen DNA extraction, quantified, and the library preparation using the Agilent target enrichment system. Further, exome capture by Illumina platform (100X), quality check, alignment, and variant calling followed by the downstream analysis and finally visualized by IGV. Results: We observed a large number of SNVs or mutations from an Indian perspective, such as KMT2C, OR4M1, PDPR2P, EPHB1, FAS, OPCML, MGST1, C1QTNF9, HS6ST3, OR4K2, PRPSAP2, KCNJ12, FIGNL1, SFXN1, BAGE2, ARVCF, NAMPT variants of significance, unknown significance and possibly significant are reported. Conclusion: For the first time, KMT2C is observed as a novel potent mutation and pathogenic, showing the variant position at (7:152265091, T>A, SNV 62478356) from the Indian context in CC. Further, we visualized and validated the mutations using the Integrative Genomic Viewer (IGV) browser. Finally, we discuss the inherent challenges through KMT2C mutations.

Keywords

Cervical cancer; Functional genomics; Bioinformatics; Next Generation Sequencing; Exome

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

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