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INTIGRATED CANCER GENOMICS LAB

The goal of Dutt laboratory is to understand the somatic genetics of human cancer and help develop the next generation of effective targeted therapies to improve treatment of cancer patients. The group specifically focuses on the genomic features of genetic alterations underlying oncogenesis and cancer progression in the lung, breast, cervical, gallbladder, head and neck, and others cancers. The efforts involve using advanced sequencing methodologies followed by functional validation to study the implications of genetic alterations in identifying novel cancer dependencies, therapeutic strategies, and biomarkers.

Computational Cancer Genomics:

Using computational approaches we analyze genome wide alterations underlying the cancer genome such as point mutations, complex structural alterations, and aberrant transcript fusion and expression. We develop robust in-house automated computational pipelines and analytical tools to analyze the high throughput datasets generated by whole exome, transcriptome and genome sequencing such as Waterhose, ClinOme, Cancer Pathogen Detector, TMC-SNPdb - the first Indian germline SNPdb, HPVDetector, DepRanker, RVD , COVID qPCR Analyzer , Infectious Pathogen Detector and others. We recently developed TMC-SNPdb 2.0 database an updated version of TMC-SNPdb

Tools :

We have developed a computational pipeline, HPVDetector to detect the presence of HPV DNA sequences in human clinical cancer samples. Next we used a similar aproach to detect the presence of non-typhoidal Salmonella in gallbladder cancer. We are currently expanding our endeavor to explore the presence of several other pathogen sequences in the human cancer genome using Cancer Pathogen Detector (CPD), an improved version of the computation pipeline. Simultaneouly, we are in process to deploy the CPD application as a “Container” onto the host cloud system (like CGC) using Docker system.

Functional Genomics:

The genome-discovery efforts made in the laboratory are paired with functional validation using biochemical, molecular, cell based experimental approaches, and transgenic mouse models. We perturb the candidate target genes using CRISPR-Cas system and perform genome wide pooled shRNA screen using tumor derived cell lines to complement and validate our findings from genomic approaches. Specifically, the lab focusses on EGFR, FGFR and NOTCH family pathways.

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