Research

I am currently an Assistant Professor and Independent Group Leader at Tata Memorial Centre, Navi Mumbai, India, where I head the Medical Oncology Molecular Laboratory. I joined Tata Memorial Centre in October 2019 and secured an independent faculty position with PhD guideship in June 2021.

Comprehensive Genomic Profiling and Cancer Genomics Research

My research focuses on cancer genomics, computational biology, and therapeutic applications. I lead a comprehensive genomic profiling project of solid tumors in collaboration with 4baseCare (Bengaluru, India) and Illumina (California, USA), having completed sequencing of 1500 whole exome and transcriptome samples. I have established a novel hypothesis on microchromosome-mediated oncogenesis and initiated experimental validation efforts.

I have secured competitive funding from DST-SERC and DBT (Government of India) as PI and co-PI for multiple projects. My research has established national and international collaborations with institutions including the National Centre for Biological Sciences, University of Michigan, National Institute of Research in Reproductive Health, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), and Flinders University.

During my PhD at ACTREC (2011-2017) under Dr. Amit Dutt, I made key contributions including: (1) discovery and characterization of novel oncogene FGFR3 in lung adenocarcinoma, (2) development of integrative genomics approaches for small sample sizes, and (3) creation of HPVDetector, a computational tool for analyzing HPV infection and integration. I also developed ClinOme during my postdoctoral research, a computational tool for therapeutic inference from cancer genomics data that has been licensed to a commercial entity, and played a pivotal role in establishing a Molecular Tumor Board at Tata Memorial Centre.

Publications

• 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 (2025). Induction of cancer stem cells from mouse fibroblastsSci Rep.PMID: 40664734.[publication]
• 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 (2025). Comprehensive Genomic Profiling of Anaplastic Thyroid Cancer Identifies Alterations in THRA, a Potential Modifier of Cellular PlasticityJCO Glob Oncol.PMID: 40674659.[publication]
• 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 (2025). Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencingNPJ Syst Biol Appl.PMID: 40483308.[publication]
• 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 (2025). 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 PatientsClin Lung Cancer.PMID: 40050197.[publication]
• 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 (2025). Genomic Characterization of Papillary Thyroid Cancer Reveals Germline Mutations Associated With Congenital HypothyroidismJCO Glob Oncol.PMID: 40440572.[publication]
• 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 (2025). The impact of co-occurring tumor suppressor mutations with mEGFR as early indicators of relapse in lung cancerESMO Open.PMID: 40088801.[publication]
• 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 (2025). Clinical characteristics and first-line palliative treatment patterns in 3,414 patients with advanced lung cancer in IndiaEcancermedicalscience.PMID: 40492223.[publication]
• 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 (2024). 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 RelevanceJCO Glob Oncol.PMID: 39571115.[publication]
• 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 (2024). Uniqueness of lung cancer in Southeast AsiaLancet Reg Health Southeast Asia.PMID: 39157507.[publication]
• 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 (2024). RET Alterations Differentiate Molecular Profile of Medullary Thyroid CancerJCO Precis Oncol.PMID: 38754058.[publication]
• Noronha V, Sarkar L, Patil V, Menon N, Shah M, Pawar A, Chowdhury OR, Shetty O, Chougule A, Chandrani P, Kaushal R, Pai T, Janu A, Chakrabarty N, Prabhash K (2024). Clinical characteristics, outcomes and prognostic factors in KRAS mutant lung cancers: experience from a tertiary care cancer center in IndiaEcancermedicalscience.PMID: 38439805.[publication]
• Gardi N, Chaubal R, Parab P, Pachakar S, Kulkarni S, Shet T, Joshi S, Kembhavi Y, Chandrani P, Quist J, Kowtal P, Grigoriadis A, Sarin R, Govindarajan R, Gupta S (2024). Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast CancerCancer Res Commun.PMID: 38315150.[publication]
• Shah M, Noronha V, Patil V, Menon N, Singh AK, Shah A, Kumar P, Roychoudhary O, Peelay Z, Janu A, Purandare N, Chakrabarty N, Patil V, Kaushal R, Shetty O, Pai T, Chandrani P, Chougule A, Prabhash K (2024). The Role of Systemic Therapy in Patients with Advanced Non-small Cell Lung Cancer and a Poor Eastern Cooperative Oncology Group Performance StatusClin Oncol (R Coll Radiol).PMID: 38097463.[publication]
• Sambath J, Noronha V, Manda SS, Mishra R, Chandrani P, Patil V, Menon N, Chougule A, Ramachandran V, Limaye S, Kuriakose MA, Banavali SD, Kumar P, Prabhash K (2024). Whole exome sequencing uncovers HRAS mutations as potential mediators of resistance to metronomic chemotherapyGene.PMID: 37918550.[publication]
• Trivedi V, Noronha V, Sreekanthreddy P, Desai S, Poojary D, Varghese L, Gowda P, Butle A, Mishra R, Bal M, Mittal N, Rane S, Kane S, Basu S, Patil V, Menon N, Singh AK, Chaturvedi P, Chandrani P, Choughule A, Veldore V, Prabhash K, Dutt A (2023). Association of Cutibacterium acnes with human thyroid cancerFront Endocrinol (Lausanne).PMID: 38027096.[publication]
• Chougule A, Chandrani P, Noronha V, Pange P, Kale S, Nikam A, Nambiar K, Marchande D, Durve A, Gupta V, Jagtap V, Tiwrekar P, Menon N, Joshi A, Kaushal R, Pai T, Patil VM, Dutt A, Banavali SD, Prabhash K (2023). Real-World Evidence of EGFR Targeted Therapy in NSCLC- A Brief Report of Decade Long Single Center ExperienceJTO Clin Res Rep.PMID: 38033811.[publication]
• Tanwar NA, Malhotra R, Satheesh AP, Khuntia SP, Sreekanthreddy P, Varghese L, Kolla S, 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, Rishi KD, Goswami HM, Veldore VH (2023). Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From IndiaJCO Glob Oncol.PMID: 38085046.[publication]
• Das L, Shekhar S, Chandrani P, Varma AK (2023). In silico structural analysis of secretory clusterin to assess pathogenicity of mutations identified in the evolutionarily conserved regionsJ Biomol Struct Dyn.PMID: 34821197.[publication]
• Yadav N, Sunder R, Desai S, Dharavath B, Chandrani P, Godbole M, Dutt A (2022). Progesterone modulates the DSCAM-AS1/miR-130a/ESR1 axis to suppress cell invasion and migration in breast cancerBreast Cancer Res.PMID: 36578092.[publication]
• George IA, Sathe G, Ghose V, Chougule A, Chandrani P, Patil V, Noronha V, Venkataramanan R, Limaye S, Pandey A, Prabhash K, Kumar P (2022). Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancerFront Cell Dev Biol.PMID: 36393868.[publication]
• Sahu A, Kose K, Kraehenbuehl L, Byers C, Holland A, Tembo T, Santella A, Alfonso A, Li M, Cordova M, Gill M, Fox C, Gonzalez S, Kumar P, Wang AW, Kurtansky N, Chandrani P, Yin S, Mehta P, Navarrete-Dechent C, Peterson G, King K, Dusza S, Yang N, Liu S, Phillips W, Guitera P, Rossi A, Halpern A, Deng L, Pulitzer M, Marghoob A, Chen CJ, Merghoub T, Rajadhyaksha M (2022). In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy responseNat Commun.PMID: 36085288.[publication]
• Noronha V, Chougule A, Chandrani P, Kaushal RK, Patil VM, Menon N, Kapoor A, Chopade S, Singh A, Shetty O, Dutt A, Banavali S, Prabhash K (2022). Lung cancer with dual EGFR and ALK driver alterations at baseline: a retrospective observational cohort studyActa Oncol.PMID: 35972844.[publication]
• Behel V, Noronha V, Choughule A, Shetty O, Chandrani P, Kapoor A, Bondili SK, Bajpai J, Kumar R, Pai T, Bal M, Gurav M, Bapat P, Mittal N, Menon S, Patil V, Menon N, Dutt A, Prabhash K (2022). Impact of Molecular Tumor Board on the Clinical Management of Patients With CancerJCO Glob Oncol.PMID: 35802838.[publication]
• Behel V, Chougule A, Noronha V, Patil VM, Menon N, Singh A, Chopade S, Kumar R, Shah S, More S, Banavali SD, Chandrani P, Prabhash K (2022). Clinical Utility of Liquid Biopsy (Cell-free DNA) Based EGFR Mutation Detection Post treatment Initiation as a Disease Monitoring Tool in Patients With Advanced EGFR-mutant NSCLCClin Lung Cancer.PMID: 35649817.[publication]
• Chougule A, Jagtap V, Nikam A, Kale S, Nambiar K, Bagayatkar P, Chandrani P, Kaushal R, Noronha V, Patil V, Banavali S, Prabhash K (2022). Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in DiagnosticsDiagnostics (Basel).PMID: 35626446.[publication]
• Panda GS, Noronha V, Shah D, John G, Chougule A, Patil V, Kumar R, Menon N, Singh A, Chandrani P, Mahajan A, Prabhash K (2022). Treatment pattern and outcomes in de novo T790M-mutated non-small cell lung cancerEcancermedicalscience.PMID: 35919239.[publication]
• Desai S, Dharavath B, Manavalan S, Rane A, Redhu AK, Sunder R, Butle A, Mishra R, Joshi A, Togar T, Apte S, Bala P, Chandrani P, Chopra S, Bashyam MD, Banerjee A, Prabhash K, Nair S, Dutt A (2022). Fusobacterium nucleatum is associated with inflammation and poor survival in early-stage HPV-negative tongue cancerNAR Cancer.PMID: 35252868.[publication]
• Agrawal AK, Noronha V, Patil V, Menon N, Kapoor A, Chougule A, Chandrani P, Prabhash K (2022). Systemic Therapy in Thyroid CancerIndian J Surg Oncol.PMID: 35462658.[publication]
• Roychowdhury A, Jondhale M, Saldanha E, Ghosh D, Kumar Panda C, Chandrani P, Mukherjee N (2021). Landscape of toll-like receptors expression in tumor microenvironment of triple negative breast cancer (TNBC): Distinct roles of TLR4 and TLR8Gene.PMID: 34022297.[publication]
• Joshi A, Mishra R, Desai S, Chandrani P, Kore H, Sunder R, Hait S, Iyer P, Trivedi V, Choughule A, Noronha V, Joshi A, Patil V, Menon N, Kumar R, Prabhash K, Dutt A (2021). Molecular characterization of lung squamous cell carcinoma tumors reveals therapeutically relevant alterationsOncotarget.PMID: 33796225.[publication]
• Salunkhe S, Mishra SV, Ghorai A, Hole A, Chandrani P, Dutt A, Chilakapati M, Dutt S (2020). Metabolic rewiring in drug resistant cells exhibit higher OXPHOS and fatty acids as preferred major source to cellular energeticsBiochim Biophys Acta Bioenerg.PMID: 32858000.[publication]
• Arora R, Choi JE, Harms PW, Chandrani P (2020). Merkel Cell Polyomavirus in Merkel Cell Carcinoma: Integration Sites and Involvement of the KMT2D Tumor Suppressor GeneViruses.PMID: 32878339.[publication]
• Salunkhe S, Chandran N, Chandrani P, Dutt A, Dutt S (2020). CytoPred: 7-gene pair metric for AML cytogenetic risk predictionBrief Bioinform.PMID: 30380003.[publication]
• Sikder S, Kumari S, Kumar M, Sen S, Singhal NB, Chellappan S, Godbole M, Chandrani P, Dutt A, Gopinath KS, Kundu TK (2019). Chromatin protein PC4 is downregulated in breast cancer to promote disease progression: Implications of miR-29aOncotarget.PMID: 31839879.[publication]
• Arora R, Rekhi B, Chandrani P, Krishna S, Dutt A (2019). Merkel cell polyomavirus is implicated in a subset of Merkel cell carcinomas, in the Indian subcontinentMicrob Pathog.PMID: 31600537.[publication]
• Iyer P, Shrikhande SV, Ranjan M, Joshi A, Gardi N, Prasad R, Dharavath B, Thorat R, Salunkhe S, Sahoo B, Chandrani P, Kore H, Mohanty B, Chaudhari V, Choughule A, Kawle D, Chaudhari P, Ingle A, Banavali S, Gera P, Ramadwar MR, Prabhash K, Barreto SG, Dutt S, Dutt A (2019). ERBB2 and KRAS alterations mediate response to EGFR inhibitors in early stage gallbladder cancerInt J Cancer.PMID: 30304546.[publication]
• Godbole M, Togar T, Patel K, Dharavath B, Yadav N, Janjuha S, Gardi N, Tiwary K, Terwadkar P, Desai S, Prasad R, Dhamne H, Karve K, Salunkhe S, Kawle D, Chandrani P, Dutt S, Gupta S, Badwe RA, Dutt A (2018). Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1-NDRG1 axis in both PR-positive and -negative breast cancer cellsJ Biol Chem.PMID: 30337371.[publication]
• Godbole M, Chandrani P, Gardi N, Dhamne H, Patel K, Yadav N, Gupta S, Badwe R, Dutt A (2017). miR-129-2 mediates down-regulation of progesterone receptor in response to progesterone in breast cancer cellsCancer Biol Ther.PMID: 28876975.[publication]
• Upadhyay P, Gardi N, Desai S, Chandrani P, Joshi A, Dharavath B, Arora P, Bal M, Nair S, Dutt A (2017). Genomic characterization of tobacco/nut chewing HPV-negative early stage tongue tumors identify MMP10 asa candidate to predict metastasesOral Oncol.PMID: 28939077.[publication]
• Chandrani P, Prabhash K, Prasad R, Sethunath V, Ranjan M, Iyer P, Aich J, Dhamne H, Iyer DN, Upadhyay P, Mohanty B, Chandna P, Kumar R, Joshi A, Noronha V, Patil V, Ramaswamy A, Karpe A, Thorat R, Chaudhari P, Ingle A, Choughule A, Dutt A (2017). Drug-sensitive FGFR3 mutations in lung adenocarcinomaAnn Oncol.PMID: 27998968.[publication]
• Upadhyay P, Nair S, Kaur E, Aich J, Dani P, Sethunath V, Gardi N, Chandrani P, Godbole M, Sonawane K, Prasad R, Kannan S, Agarwal B, Kane S, Gupta S, Dutt S, Dutt A (2016). Notch pathway activation is essential for maintenance of stem-like cells in early tongue cancerOncotarget.PMID: 27391340.[publication]
• Upadhyay P, Gardi N, Desai S, Sahoo B, Singh A, Togar T, Iyer P, Prasad R, Chandrani P, Gupta S, Dutt A (2016). TMC-SNPdb: an Indian germline variant database derived from whole exome sequencesDatabase (Oxford).PMID: 27402678.[publication]
• Iyer P, Barreto SG, Sahoo B, Chandrani P, Ramadwar MR, Shrikhande SV, Dutt A (2016). Non-typhoidal Salmonella DNA traces in gallbladder cancerInfect Agent Cancer.PMID: 26941832.[publication]
• Chandrani P, Upadhyay P, Iyer P, Tanna M, Shetty M, Raghuram GV, Oak N, Singh A, Chaubal R, Ramteke M, Gupta S, Dutt A (2015). Integrated genomics approach to identify biologically relevant alterations in fewer samplesBMC Genomics.PMID: 26572163.[publication]
• Chandrani P, Kulkarni V, Iyer P, Upadhyay P, Chaubal R, Das P, Mulherkar R, Singh R, Dutt A (2015). NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genomeBr J Cancer.PMID: 25973533.[publication]
• Choughule A, Sharma R, Trivedi V, Thavamani A, Noronha V, Joshi A, Desai S, Chandrani P, Sundaram P, Utture S, Jambhekar N, Gupta S, Aich J, Prabhash K, Dutt A (2014). Coexistence of KRAS mutation with mutant but not wild-type EGFR predicts response to tyrosine-kinase inhibitors in human lung cancerBr J Cancer.PMID: 25117816.[publication]
• Chougule A, Prabhash K, Noronha V, Joshi A, Thavamani A, Chandrani P, Upadhyay P, Utture S, Desai S, Jambhekar N, Dutt A (2013). Frequency of EGFR mutations in 907 lung adenocarcioma patients of Indian ethnicityPLoS One.PMID: 24124538.[publication]

The full list of my publications is available on my Google Scholar profile.