Origin of the Indian Cancer Genome Atlas

The growing burden of cancer and the existing knowledge gap in India highlight the need for a multidisciplinary translational cancer research hub that can bring clinicians, researchers, and patients together on a common platform. The current state-of-the-art facilities for cancer management are fruits of translational research in the Western world, where several NGOs, government organizations, and bio-medical research fraternity actively collaborate to reduce the cancer burden in their populations. Unfortunately, efforts of such magnitude have been missing in India.

Prashanti Cancer Care Mission1 (PCCM), a non-profit organization that provides affordable medical care and rehabilitation to breast cancer patients, collaborated with Indian Institute of Science Education and Research (IISER), Pune2 to establish the Center for Translational Cancer Research3 (CTCR) in 2017. The CSR seed funding received from Bajaj Auto Ltd.5 was instrumental in building the infrastructure as well as manpower needed at CTCR and facilitated the establishment of tissue and data biobank for building a retrospective cohort of breast cancer patients treated at PCCM.

During one of PCCM’s capacity building initiatives for oncoplastic surgery techniques6, Professor Sunil Badve (Emory University School of Medicine), an esteemed surgical pathologist with expertise in breast cancer, Dr. C. B. Koppiker (Managing Trustee and Head PCCM, Pune) along with Professor L. S. Shashidhara from IISER Pune, Dr. Anand Deshpande from Persistent Systems4 had a collective vision to establish  a cancer atlas for the Indian subcontinent which can help understand different cancer profiles and identify targeted therapies.

For initiating a pan-India consortium to corroborate heterogeneity within cancer profiles with respect to Indian context, it was essential to learn and adapt from previously successful program like The Cancer genome Atlas (TCGA), a landmark cancer genomics collaboration between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) that has molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.

Professor Sunil Badve was instrumental in bringing CTCR and Persistent Systems in contact with the TCGA team led by Dr. JC Zenklusen (Director, TCGA), leading them to organize the first TCGA conference and workshop in India in 2019. The Wellcome Trust – DBT India Alliance, a major biomedical funding agency in India partnered in this important conference, highlighting the significance given by the Indian community for a TCGA India initiative.

The first TCGA India conference, an in-person meeting was organized in IISER Pune with the theme “Multi-omics Studies in Cancer: Learnings from The Cancer Genome Atlas (TCGA)”.Dr. Jean Claude Zenklusen (Director, TCGA) along with a team of TCGA domain experts served as conference faculty besides other distinguished cancer researchers from India and abroad.

Over 350 delegates comprising of onco-clinicians, basic researchers, bioinformaticians, geneticists, translational researchers, big-data scientists, bioethicists, and regulatory experts attended the event. In addition to discussing the global trends in multi-omics research, the conference proceedings were focused on the need for understanding the molecular profiles of Indian cancers in view of increasing cancer burden, unique clinico-pathological profiles, and intrinsic population diversity.

The scientific discussions and brainstorming at the first TCGA India conference, culminated on the need for developing a national mission program for multi-omics profiling of Indian cancers. Based on this consensus and several rounds of subsequent discussion with Dr. Zenklusen (Director TCGA), Professor Sunil Badve and the CTCR (composed of PCCM and IISER Pune) with the Persistent Systems proposed setting up Indian Cancer Genome Atlas (ICGA) with the support from US-NCI-TCGA as a knowledge partner.

PCCM team was also one of the main organizer with the support from CTCR and other partner organizations for delivering the highly successful second TCGA India virtual conference with the theme ‘Towards Team Science for Multi-omics Studies in South Asia’ in 2020 (Editorial in Ecancermedicalscience) as well as the third ICGA Conference with the theme ‘Biobanking to Omics: Collecting the Global Experience’ (Proceedings in JCO Global Oncology) in 2022.

PCCM has acted as a convenor to bring together various key opinion leaders and organizations together on a common platform for discussion and thus laying the foundation for the establishment of ICGA Foundation. ICGA Foundation is a not-for-profit, public-private-philanthropic partnership registered as a section 8 company. Its vision is to establish a comprehensive open-source database of clinical and molecular profiles of cancers in India. The Centre for Scientific and Industrial Research (CSIR), Government of India, has funded multi-omics of ~1000 breast cancer patient samples. The demographic distribution and clinical features of breast cancer patients in India are significantly different compared to that of the world. The meta-analysis has also reported a higher proportion of TNBCs with younger age at incidence. Hence, a pilot study has begun with breast cancer patients to understand the cancer genomics that will help develop continent specific guidelines for cancer screening and management.

PCCM is in forefront to help ICGA consortium to make informed choices and will be readily supporting its endeavor including setting up of its biobanking facility. This massive effort will enable an understanding of the differences in molecular profiles of cancers relevant to the Indian scenario, thus facilitating the development of appropriate therapeutic regimens. For sample and data collection, ICGA has partnered with various hospitals across the country and with appropriate ethical approval the high-quality genomic data along with the clinical data is being collected to set up an open-sourced database accessible to the global scientific community.

1About Prashanti Cancer Care Mission (PCCM)

PCCM is a non-profit organization which is actively providing affordable medical care and rehabilitation to breast cancer patients in Pune and its surrounding areas. It has been instrumental in offering medical education, training, and research and has a growing cancer research department. PCCM is recognized by the Department of Scientific and Industrial Research (DSIR), Government of India with Scientific and Industrial Research Organization (SIRO) status. 6Simultaneous to its efforts in translational research, PCCM through its capacity building initiatives for oncoplastic surgery techniques, established the International School of Oncoplastic Surgery which runs a Master’s program in association with University of East Anglia, UK. https://www.prashanticancercare.org/

2About Indian Institute of Science Education and Research, Pune (IISER Pune)

IISER Pune is an autonomous institution of the Ministry of Education, Government of India. Established in 2006, it is dedicated to research and teaching in the basic sciences. In 2012, IISER Pune was declared as an Institute of National Importance by an Act of Parliament. https://www.iiserpune.ac.in/

3About Center for Translational Cancer Research (CTCR)

To strengthen the translational cancer research, PCCM collaborated with IISER Pune to establish the Center for Translational Cancer Research (CTCR) in 2017, a powerful model of public-private partnership through CSR seed funding from Bajaj Auto Ltd. CTCR aims to bring together clinicians and researchers to integrate cancer research, training, and education. PCCM pioneered the collaboration of a clinical practice with a government institute to conduct clinically relevant translational research to address clinical questions related to breast cancer prognosis and improve patient care. CTCR collaboration with IISER led to deeper insights into the molecular aspects of various breast cancer subtypes with a specific focus on TNBCs and it is anticipated that the activities of the Centre will have a direct positive impact on the national capacity for translational cancer research and, most importantly, on the effective management of cancer in India. http://ctcr.in/

4About Persistent Systems (PS)

Persistent Systems is an Indian multinational technology services company which was incorporated on 16 May 1990. Persistent Systems has been at the forefront in leveraging technology for advancement in research and innovation for the healthcare and life sciences domain. It builds software that drives the business of its customers; serving software product companies and enterprises with software at the core of their digital transformation https://www.persistent.com/

5About Bajaj Group and its CSR

For over a century, the Bajaj Group in its quest for nation building, has been proactively contributing through various public charitable trusts and has undertaken various philanthropic and social activities for economic development of communities which distinctly impacts the quality of life of the weaker sections of the society. The CSR seed funding received from Bajaj Auto Ltd. was instrumental in building the infrastructure and manpower needed at CTCR and facilitated the establishment of tissue and data biobank in 2018 for building a retrospective cohort of breast cancer patients that have been diagnosed and treated at PCCM. https://www.bajajauto.com/corporate/corporate-social-responsibility