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Journal of Cancer Research and Clinical Oncology

Published in:

20-03-2023 | NSCLC | Research

Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience

Authors: Mamta Gurav, Sridhar Epari, Prachi Gogte, Trupti Pai, Gauri Deshpande, Nupur Karnik, Omshree Shetty, Sangeeta Desai

Published in: Journal of Cancer Research and Clinical Oncology | Issue 10/2023

Abstract

Purpose

Molecular Profiling of solid tumours is extensively used for prognostic, theranostic, and risk prediction. Next generation sequencing (NGS) has emerged as powerful method for molecular profiling. The present study was performed to identify molecular alterations present in solid tumours in Indian tertiary cancer centre.

Methods

Study included 1140 formalin Fixed paraffin embedded samples. NGS was performed using two targeted gene panels viz. Ampliseq Focus panel and Sophia Solid Tumor Plus Solution. Data was analyzed using Illumina’s Local Run Manager and SOPHiA DDM software. Variant interpretation and annotations were done as per AMP/ACMG guidelines.

Results

Total 896 cases were subjected to NGS after excluding cases with suboptimal nucleic acid quality/quantity. DNA alterations were detected in 64.9% and RNA fusions in 6.9% cases. Among detected variants, 86.7% were clinically relevant aberrations. Mutation frequency among different solid tumours was 70.8%, 67.4%, 64.4% in non-small cell lung (NSCLC), lung squamous cell carcinomas and head neck tumours respectively. EGFR, KRAS, BRAF, ALK and ROS1were commonly altered in NSCLC. Gastrointestinal tumours showed mutations in 63.6% with predominant alterations in pancreatic (88.2%), GIST (87.5%), colorectal (78.7%), cholangiocarcinoma (52.9%), neuroendocrine (45.5%), gall bladder (36.7%) and gastric adenocarcinomas (16.7%). The key genes affected were KRAS, NRAS, BRAF and PIK3CA. NGS evaluation identified co-occurring alterations in 37.7% cases otherwise missed by conventional assays. Resistance mutations were detected in progressive lung tumours (39.5%) against EGFR TKIs and ALK/ROS inhibitors.

Conclusion

This is the largest Indian study on molecular profiling of solid tumours providing extensive information about mutational signatures using NGS.

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Title: Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience
Authors: Mamta Gurav
Sridhar Epari
Prachi Gogte
Trupti Pai
Gauri Deshpande
Nupur Karnik
Omshree Shetty
Sangeeta Desai
Publication date: 20-03-2023
Publisher: Springer Berlin Heidelberg
Keywords: NSCLC
NSCLC
Published in: Journal of Cancer Research and Clinical Oncology / Issue 10/2023
Print ISSN: 0171-5216
Electronic ISSN: 1432-1335
DOI: https://doi.org/10.1007/s00432-023-04693-3

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