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Comprehensive Genomic Characterization of 1,200 Samples across 25 Cancer Types of Indian Ethnicity
CC BY 4.0 · Indian J Med Paediatr Oncol 2024; 45(S 01): S1-S16
DOI: DOI: 10.1055/s-0044-1788213
*Corresponding author: (e-mail: pratikchandrani@gmail.com).
Abstract
Background: Large-scale genomic projects have greatly aided in characterizing the genomic alterations in cancers. These studies have catalogued novel biomarkers and driver genes, opening new paths for targeted therapeutics. However, the ethnic diversity is poorly represented in these genomic projects.
Materials and Methods: In this study, we attempted genomic characterization of 1,200 Indian patient samples across 25 cancer types using whole exome and whole transcriptome sequencing. We developed integrated genomics analysis pipeline to tackle the lack of genomics data of Indian origin. We further validated our analysis methods against TCGA dataset.
Results: From the integrated genomics analysis, we have provided the first landscape of cancer driver alterations, therapeutic targets, microsatellite instability (MSI), tumor mutation burden (TMB), and molecular subtypes from the Indian cancer cohort. Interestingly, we report about 1,100 novel deleterious mutations from the Indian population with huge potential for further therapeutic development. We further report enigmatic associations between genotypes and phenotypes providing interesting biological opportunities to study further.
Conclusion: In summary, this study provides the first comprehensive genomic characterization of different cancer types in the Indian cohort emphasizing the potential for further ethnic-specific biological studies and clinical trials.
Publication History
Article published online:
08 July 2024
© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India
*Corresponding author: (e-mail: pratikchandrani@gmail.com).
Abstract
Background: Large-scale genomic projects have greatly aided in characterizing the genomic alterations in cancers. These studies have catalogued novel biomarkers and driver genes, opening new paths for targeted therapeutics. However, the ethnic diversity is poorly represented in these genomic projects.
Materials and Methods: In this study, we attempted genomic characterization of 1,200 Indian patient samples across 25 cancer types using whole exome and whole transcriptome sequencing. We developed integrated genomics analysis pipeline to tackle the lack of genomics data of Indian origin. We further validated our analysis methods against TCGA dataset.
Results: From the integrated genomics analysis, we have provided the first landscape of cancer driver alterations, therapeutic targets, microsatellite instability (MSI), tumor mutation burden (TMB), and molecular subtypes from the Indian cancer cohort. Interestingly, we report about 1,100 novel deleterious mutations from the Indian population with huge potential for further therapeutic development. We further report enigmatic associations between genotypes and phenotypes providing interesting biological opportunities to study further.
Conclusion: In summary, this study provides the first comprehensive genomic characterization of different cancer types in the Indian cohort emphasizing the potential for further ethnic-specific biological studies and clinical trials.
No conflict of interest has been declared by the author(s).
Publication History
Article published online:
08 July 2024
© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India