Venue: ACTREC-TMC KS Conference Rm. 9:00 am 8:00 pm. Hands on Cancer Bioinformatics for NGS Data Analysis: a Primer for Clinicians

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3 DAY 0 (11 th January 2019) Venue: ACTREC-TMC KS Conference Rm 9:00 am 8:00 pm Hands on Cancer Bioinformatics for NGS Data Analysis: a Primer for Clinicians Despite wider acceptance of comprehensive profiling of cancer patient using next-generation sequencing for clinical application, the hurdle of genomic analysis for clinical utilization remains one of the major blockage for the clinicians.this one-day workshop is primarily aimed to introdue key applications of cancer genomics, along with the analytical methods used in identification of clinically relevant mutations and disease sub-type specific gene expression patterns. Further, participants will be also introduced to a complementary application of NGS datasets for the discovery of pathogens. In particular, the participants would be introduce ClinOme an easy to use clinical cancer genomics analysis and reporting tool for identification of therapeutically relevant genomics alterations and pathogenic infections. ClinOme integrates standard line of treatment recommendation and clinical annotations from various sources and provides a comprehensive genetic diagnosis report from next generation sequencing data. This easy to use graphical user interface widens the utility of ClinOme for biologists and clinicians without computational expertise. This one-day cancer informatics hands-on workshop would emphasize on the following: 1. Whole transcriptome analysis to identify molecular sub-classes of different tumor types Quantification of transcripts from RNA-seq data using alignment and/or quasi-alignment based methods Processing, normalization of gene/ transcript counts and its use to identify differentially expressed genes Clustering of samples for identification of disease sub-type classes from expression datasets 2. Clinome: an automated computational tool to identify clinically relevant therapeutic alterations Generation of variants from the whole genome, exome and targeted sequencing data (primary, secondary, tertiary analysis of DNA sequencing data) Filtration and annotation of variants with germline variant databases, like TMC-SNPdb, ExAC and dbsnp Clinically relevant variant calling and automated clinical report generation 3. Discovery and tumor association of pathogens associated with cancer using NGS datasets Computational subtraction methods and HPV identification using HPVDetector Cancer associated pathogen discovery using Cancer Pathogen Detector Application of pathogen discovery to complement traditional genomic analysis The 20 selected participants would require bringing their own laptop. The minimum recommended specifications are as follows: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, and a recent version of Windows, Mac OS X or Linux operating systems.

4 DAY 1 (12 th January 2019) Venue: ACTREC-TMC KS Auditorium AM Registration AM Chairperson AM 10:00-10:45 AM Welcome by Prof. Sudeep Gupta, Director, ACTREC-TMC/ Introduction to MPAI by Prof. B. R. Das, President, MPAI Plenary Session Prof. RA Badwe, Director, TMC, Mumbai Plenary Lecture by Prof. Indraneel Mittra, Dr. Ernest Borges Chair in Translational Research, TMC, Mumbai "On the Futility of Killing Cancer Cells to Cure Cancer" Plenary Lecture by Prof. Lalit Kumar, AIIMS, New Delhi 10: AM Tea/Coffee Break/Poster installation Session I: Clinical and Biological Aspects of Solid Tumors (each talk for : PM minutes) Chairpersons Deepak K Mishra, TMC, Kolkata; Anant Ramaswamy, TMH-TMC, Mumbai Kumar Prabhash, TMH-TMC, Mumbai Shantanu Chowdhury, IGIB, New Delhi Telomerase Reactivation - the 'Achilles Heel' of Aggressive Cancers - and the Promise of Non-duplex DNA Structure as Drug Targets Mohan Menon, Sir H. N. R. F. Hospital, Mumbai Speakers Sorab Dalal, ACTREC-TMC, Mumbai " LCN2: A Potential Therapeutic Target in Multiple Tumor Types" Ullas Batra, RGCI, New Delhi Pritha Ray, ACTREC-TMC, Mumbai Amrita Roy, Biotechne " Introduction of a Novel RNA ISH Assay for HR-HPV E6/7 mrna" 1: PM Lunch Break with Poster Presentation :00 PM Panel Discussion: Molecular Diagnostics in Oncology Moderator B. R. Das Panelists: Sarjana Dutt, Neeraj Arora, Helen Fernandes, Margaret Gulley, Ram Prasad, Vanita Noronha, Vaijyanti Gupta 03: PM Session II: Haemato Oncology (each talk for minutes) Chairpersons Shubada Kane, Nanavati Hospital, Mumbai; MB Agarwal, B.H.I.M.S, Mumbai Gurvinder Kaur, AIIMS, New Delhi CLL mirnome Shilpee Dutt, ACTREC-TMC, Mumbai Nikhil Patkar, ACTREC-TMC, Mumbai Minimal Residual Disease Assessment using Ultradeep Next Generation Sequencing Speakers Deepak K Mishra, TMC, Kolkata Hemant Malhotra, SRCC, Jaipur " Molecular Monitoring in CML: Principals & Pitfalls" Syed Hasan, ACTREC-TMC, Mumbai 05: PM Tea/Coffee Break with Poster Presentation Session III: The Broad Landscape of Clinical Diagnosis in Human Diseases (each 05: PM talk for minutes) Chairpersons Sagarika Damle, KC College, Mumbai; Vikas Ostwal, TMH-TMC, Mumbai Speakers Anuradha Choughule, TMH-TMC, Mumbai

5 Helen Fernandes, Columbia University, New York Sangeeta Desai, TMH-TMC, Mumbai Moushumi Suryavanshi, RGCI, Delhi Relevance of BRCA testing in womens cancers Abhijit De, ACTREC-TMC, Mumbai Neeraj Arora, TMC, Kolkata " Implementing NGS to the Clinics: Tata Medical Centre Experience" RV Shaji, CMC, Vellore " Application of NGS in Inherited Haematological Diseases" Premas/Illumina Talk 6:45-7:30 PM MPAI general body meeting (Conference Room) 08:15 PM onwards Gala Dinner

6 DAY 2 (13 th January 2019) Venue: ACTREC-TMC KS Auditorium Chairpersons Debjani Dasgupta, D.Y. Patil University, Mumbai AM Proffered papers/ oral presentation by young investigators (5 talks) Plenary Session Chairpersons Unnati Padalia, K.J. Somaiyya College, Mumbai; Amit Joshi, TMH-TMC, Mumbai AM Plenary lecture by Prof. Tapas Kundu, CSIR-CDRI, Lucknow AM Plenary lecture by Prof. David I Smith, Mayo Clinic, USA " How DNA Sequencing will Completely Transform Pathology?" AM Tea/Coffee Break with Poster Presentation PM Session IV: Translational Cancer Research (each talk for minutes) Archana Rath, Mumbai University; Karuna Gokarn, St. Xaviers College, Mumbai Chairpersons Dhanalaxmi Shetty, ACTREC-TMC, Mumbai; Murali Bashyam, CDFD, Hyderabad " Translational Colorectal Cancer Research: Identifying Novel Genes and Pathways in Rectal Cancer" Sagar Sengupta, NII, Delhi; Enhancement of c-jun Oncoprotein Degradation - A Mechanism of Tumour Suppression Bushra Ateeq, IIT Kanpur Speakers Bharat Rekhi, ACTREC-TMC, Mumbai Impact of Molecular Advances in the Diagnosis and Management of Musculoskeletal Tumors Vikram Gota, ACTREC-TMC, Mumbai Amit Dutt, ACTREC-TMC, Mumbai " Translating Cancer Genomics to Medicine" PM Lunch Break with Poster Presentation Hereditary Cancer Clinic: An enlightening live show enactment by Rajiv Sarin and :30 PM group PM Session V: Genetic and Infectious Diseases (each talk for minutes) Chairpersons Usha Dave, MILS International, Mumbai; RamPrasad, Medgenome Amit Singh, IISc, Bangalore Margaret Gulley, UNC School of Medicine, USA " Genomic Tests for Gastric Adenocarcinoma: Human, Epstein-Barr Virus and Helicobacter Targets" Rajiv Sarin, ACTREC-TMC, Mumbai Speakers Reena Das, PGI, Chandigarh " Newer Diagnostic Approaches in Hereditary Hemolytic Anemias" Rohini Kelkar, TMH-TMC, Mumbai Rajesh Dikshit, CCE, Mumbai 05: PM Valedictory Function