Research

Overview

The Chandrani Lab focuses on computational biology and bioinformatics research to advance our understanding of cancer biology. We develop and apply cutting-edge computational methods to analyze large-scale genomic and clinical data, with the goal of improving cancer diagnosis, prognosis, and treatment.

Research Areas

Cancer Genomics & Precision Medicine

We perform comprehensive genomic profiling of various cancer types to identify actionable alterations that can guide treatment decisions. Our work on EGFR mutations, ALK fusions, and other driver alterations in lung cancer has directly impacted clinical practice in India.

Key achievements:

  • Development of ClinOme, a precision medicine solution that has been successfully technology-transferred
  • Genomic characterization of over 3,000 cancer patients across multiple tumor types
  • Identification of novel therapeutic targets and biomarkers for treatment response

Integrative Multi-Omics Analysis

We integrate data from multiple molecular layers (genomics, transcriptomics, proteomics) to gain comprehensive insights into cancer biology. Our approaches help identify:

  • Molecular subtypes of cancers with distinct clinical outcomes
  • Mechanisms of drug resistance
  • Novel therapeutic vulnerabilities

Bioinformatics Pipeline Development

We develop robust, clinically-validated bioinformatics pipelines for:

  • Next-generation sequencing (NGS) data analysis
  • Variant calling and annotation
  • Tumor mutation burden assessment
  • Fusion detection from RNA-seq data
  • Liquid biopsy analysis using cell-free DNA

Tumor Microenvironment & Host Factors

Beyond tumor-intrinsic alterations, we investigate:

  • Microbiome associations with cancer (e.g., Fusobacterium in tongue cancer)
  • Immune microenvironment profiling
  • Host germline variants influencing cancer susceptibility and treatment response

Recent Publications

Induction of cancer stem cells from mouse fibroblasts

Shabrish S, Naorem LD, Mohanty S, Kumar R, Lopes R, Akhter N, Khare NK, Joshi R, Sawant R, Raghuram GV, Jadhav V, Shinde S, Chandrani P, Mittra I

Sci Rep (2025)
Paper

Comprehensive Genomic Profiling of Anaplastic Thyroid Cancer Identifies Alterations in THRA, a Potential Modifier of Cellular Plasticity

Trivedi V, Noronha V, Bal M, Chandrani P, Poojary D, Saldanha E, Choughule A, Pange P, Gupta V, Menon N, Patil V, Shah M, Chaturvedi P, Prabhash K, Dutt A

JCO Glob Oncol (2025)
Paper

Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing

Behel V, Hait S, Noronha V, Chowdhury A, Chandrani P, Patil V, Menon N, Mishra R, Bawaskar B, Dahimbekar G, Shah M, Kaushal R, Veldore V, Goswami H, Bharde A, Khandare J, Shafi G, Choughule A, Tyagi N, Desai S, Prabhash K, Dutt A

NPJ Syst Biol Appl (2025)
Paper

Genomic Profiling of Driver Gene Alterations in Patients With Non-Small Cell Lung Cancer, Patterns of Treatment and Impact on Survival Outcomes: A Single Center Experience of More Than 1200 Patients

Shah M, Noronha V, Patil V, Singh AK, Menon N, Goud S, Shah S, More S, Kapoor A, Mishra BK, Chandrani P, Chougule A, Gupta V, Pange P, Shetty O, Pai T, Kaushal R, Yadav S, Basu M, Vora D, Vaidyanathan A, Kumar P, Jacob R, Shah A, Pradhan RR, Samaddar D, Shenoy V, Singh B, Puviarasan R, Bagra S, Desai R, Saldanha E, Poojary D, Pathak A, Ray S, Bhardwaj H, Shetty U, Iyer R, Das R, Mer N, Shah H, Kaushal Y, Singh A, Panmand H, Gosavi G, Ubharay A, Iyer A, Turel U, Shetake A, Maske K, Janu A, Purandare N, Pawar A, Mandhania M, Prabhash K

Clin Lung Cancer (2025)
Paper

Genomic Characterization of Papillary Thyroid Cancer Reveals Germline Mutations Associated With Congenital Hypothyroidism

Trivedi V, Kore H, Poojary D, Noronha V, Bal M, Chandrani P, Choughule A, Pange P, Gupta V, Menon N, Patil V, Shah M, Chaturvedi P, Prabhash K, Dutt A

JCO Glob Oncol (2025)
Paper

The impact of co-occurring tumor suppressor mutations with mEGFR as early indicators of relapse in lung cancer

Hait S, Noronha V, Chowdhury A, Chaudhary A, Bawaskar B, Dahimbekar G, Ahmad S, Joshi A, Patil V, Menon N, Shah M, Kaushal R, Choughule A, Bharde A, Khandare J, Shafi G, Lakhwani D, Desai S, Chandrani P, Prabhash K, Dutt A

ESMO Open (2025)
Paper

Clinical characteristics and first-line palliative treatment patterns in 3,414 patients with advanced lung cancer in India

Trikha M, Noronha V, Shah M, Patil V, Menon N, Singh A, Chandrani P, Shetty O, Kaushal RK, Pai T, Janu A, Purandare N, Prabhash K

Ecancermedicalscience (2025)
Paper

Deep Diving Into the Fusion Across Cancer Types in the Indian Population From Formalin-Fixed Paraffin-Embedded RNA-Exome Data: A Road to Discovering Novel Rearrangements With Clinical Relevance

Khuntia SP, Mukherjee N, Javle V, Tanwar NA, Sreekanthreddy P, Varghese L, Gowda P, Kottlahouse A, Chandrani P, Choughule A, Pange P, Gupta V, Noronha V, Patil VM, Pramanik R, Kumar S, Nayak SP, Babu S, Shetty R, Kantharaju M, Chinder PS, Korlimarla A, Srinath BS, Prabhash K, Periyasamy G, Rishi KD, Goswami HM, Veldore VH

JCO Glob Oncol (2024)
Paper

Uniqueness of lung cancer in Southeast Asia

Noronha V, Budukh A, Chaturvedi P, Anne S, Punjabi A, Bhaskar M, Sahoo TP, Menon N, Shah M, Batra U, Nathany S, Kumar R, Shetty O, Ghodke TP, Mahajan A, Chakrabarty N, Hait S, Tripathi SC, Chougule A, Chandrani P, Tripathi VK, Jiwnani S, Tibdewal A, Maheshwari G, Kothari R, Patil VM, Bhat RS, Khanderia M, Mahajan V, Prakash R, Sharma S, Jabbar AA, Yadav BK, Uddin AFMK, Dutt A, Prabhash K

Lancet Reg Health Southeast Asia (2024)
Paper

RET Alterations Differentiate Molecular Profile of Medullary Thyroid Cancer

Prabhash K, Saldanha E, Patil V, Bal M, Reddy PS, Sanjeev A, Kumar R, Poojary D, Noronha V, Menon N, Mittal N, Trivedi V, Nambiar K, Mishra R, Tanwar N, Malhotra R, Pange P, Gupta V, Veldore VH, Chougule A, Chaturvedi P, Dutt A, Chandrani P

JCO Precis Oncol (2024)
Paper

View All Publications

Collaborations

We actively collaborate with clinicians, pathologists, and researchers at:

  • Tata Memorial Centre
  • Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
  • National and international cancer research institutions

Funding & Support

Our research is supported by:

  • Department of Atomic Energy (DAE), Government of India
  • Tata Memorial Centre
  • Collaborative research grants

Contact

Interested in collaborating or learning more about our research?

Location: KS-121, ACTREC Tata Memorial Centre Kharghar, Navi Mumbai India

For research inquiries, please contact us through our application form.