Workshop on Genomic Applications in Healthcare & Translational Research
December 10-23, 2017
The aim of this intensive workshop is to introduce highly talented Indian students to the emerging area of genomics and enable them to explore the power and excitement of Next Generation Sequencing technologies to address clinically relevant research questions. The workshop will train participants on the experimental aspects of genomic sequencing and computational analysis of sequencing data through didactic and research lectures and hands-on sessions.
Day 1 | Sunday, December 10
Registration
4:00-7:00 pm – Registration open
7:00 pm – Dinner
Day 2 | Monday, December 11
Introductory Genomics
9:30-9:35 am – Opening Remarks
N.Yathindra, Director – IBAB, Bangalore
9:30-10:05 am – Inaugural Address
Kiran Mazumdar Shaw, Chairperson and MD, Biocon Ltd, Bangalore
10:05-10:30 pm – Tea Break
10:30-11:30 pm – Plenary Lecture: Helicobacter pylori and Humans: an ancient association
D.N.Rao, Indian Institute of Science, Bangalore
11:30-12:30 pm – Didactic Lecture: Structural and Functional organisation of the genome – transcription and regulation of gene expression
S.S. Shivakumara, IBAB, Bangalore
12:30-1:30 pm – Lunch
1:30-2:30 pm – Didactic Lecture: Genomics in Medicine and Healthcare
Cynthia Morton, Harvard Medical School, Boston
2:30-4:00 pm – Hands-on Session: Linux for Genomics
Subhashini Srinivasan, IBAB; Jian Carrot Zhang, Broad Institute, Boston
Teaching Assistants: Sagar Desai/Suvratha J, IBAB
4:00-4:30 pm – Tea Break
4:30-6:30 pm – Hands-on Session: Genome Informatics Tools – UCSC Browser, Databases, Interpretation of Genomic Data
Subhashini Srinivasan, IBAB; Jian Carrot Zhang, Broad Institute, Boston
Teaching Assistants: Sagar Desai/Suvratha J, IBAB
6:30-7:30 pm – Discussions and interactions with faculty
Cynthia Morton, Jian Carrot Zhang, Subha Srinivasan
7:30 pm – Dinner
Day 3 | Tuesday, December 12
Cancer Genomics
9:00- 10:00 am – Didactic Lecture: The NGS Revolution and Making Sense of the Cancer Genome Data
Amit Dutt, ACTREC Mumbai
10:00-11:00 am – Application Talk: From Genome Wide Association Studies (GWAS) to Therapy in Uterine Leiomyomata
Cynthia Morton
11:00-11:30 am – Tea Break
11:30 am -1:15 pm – Hands-on Session: NGS data formats, indexing of reference genome, NGS reads alignment to a reference genome (cover file formats, hg19, BWA, and Bowtie)
Amit Dutt, Cythia Morton
TAs: Pratik Chandrani; Sanket Desai, ACTREC, Mumbai; Sagar Desai, Suvratha J, IBAB
1:15-2:00 pm – Lunch
2:00-4:00 pm – Hands-on Session: Preparation and pre-processing of NGS reads alignment data for variant calling (Sam tools, Picard tools, GATK pre-processing steps)
Cynthia Morton, Amit Dutt
TAs: Pratik Chandrani; Sanket Desai, ACTREC, Mumbai; Sagar Desai, Suvratha J, IBAB
4:00-4:30 pm – Tea Break
4:30-6:00 pm – Hands-on Session: Preparation and pre-processing of NGS reads alignment data for variant calling (Sam tools, Picard tools, GATK pre-processing steps)
Cynthia Morton, Amit Dutt
TAs: Pratik Chandrani; Sanket Desai, ACTREC, Mumbai; Sagar Desai, Suvratha J, IBAB
6:00-7:00 pm – Discussion in groups and brain storming sessions with faculty
Cynthia Morton, Amit Dutt, Jian Carrot Zhang
Day 4 | Wednesday, December 13
Cancer Genomics
9:00-10:00 am – Didactic Lecture: Genome-Driven Medicine in Oncology
Amit Dutt, ACTREC Mumbai
10:00-10:30 am – Tea Break
10:30-11:30 am – Hands-on Session: Variant calling (SNVs and Indels) and annotation (GATK variant calling, Oncotator/Annovar, cancer specific analysis)
Cynthia Morton, Amit Dutt
TAs: Pratik Chandrani; Sanket Desai, ACTREC, Mumbai; Pushpinder Singh, IBAB
11:30 am-12:30 pm – Hands-on Session: Functional prediction and prioritization of variants, cancer driven alterations, identification and copy-number variation analysis from exome data (dbNSFP, Control-FREEC)
Amit Dutt, Jian Carrot Zhang
TAs: Pratik Chandrani; Sanket Desai, ACTREC, Mumbai; Pushpinder Singh, IBAB
12:30-1:30 pm – Lunch
1:30-4:00 pm – Hands-on Session: DNA and RNA extraction and quantification, quality control
Bibha Choundhary, IBAB
TAs: Jinsha K, Snehal Nirgude, Samatmika Ravi, Sooran Nambisan, IBAB
4:00-4:30 pm – Tea Break
4:30-6:00 pm – Hands-on Session: DNA and RNA extraction and quantification, quality control
Bibha Coundhary, IBAB
TAs: Jinsha K, Snehal Nirgude, Samatmika Ravi, Sooran Nambisan, IBAB
6:00-7:00 pm – Application Talk: Informing Clinical Interpretations of Structural Chromosome Rearrangements: Implementing Evolving Knowledge from Chromatin
Cynthia Morton, Harvard Medical School
7:30 pm – Dinner
Day 5 | Thursday, December 14
Clinical Genomics
8:30-9:30 am – Didactic Lecture: Strategies for developing successful gene expression biomarkers
Marc Lenburg, Professor of Medicine, Division of Computational Biomedicine, Boston University
9:30-10:30 am – Application Talk: Strategies for developing successful gene expression biomarkers – Computational tools for Clinical Genomics
Marc Lenburg, Boston University
10:30-11:00 am – Tea Break
11:00 am-12:00 pm – Application Talk: SEQaBOO: Towards a Clinical Genomic Future in Newborn Hearing Screening
Cynthia Morton, Harvard Medical School
12:00-12:30 pm – Address by the Principal Secretary, Government of Karnataka
Shri Gaurav Gupa, IAS, Principal Secretary, Department of IT, BT, S&T, Government of Karnataka
12:30-1:00 pm – Media Interaction
1:00-1:45 pm – Lunch
1:45-4:00 pm – Hands-on Session: Library preparation for sequencing
Bibha Choudhary, IBAB
TAs: Samatmika Ravi, Pushpinder Singh, Snehal Nirgude, Meghana Jinsha K
4:00-4:30 pm – Tea Break
4:30-6:00 pm – Hands-on Session: Library preparation for sequencing
Bibha Choudhary, IBAB
TAs: Samatmika Ravi, Pushpinder Singh, Snehal Nirgude, Meghana Jinsha K
6:00-7:00 pm – Hands-on Session: Identification of context specific gene expression signatures
Subhashini Srinivasan, Marc Lenburg, and Jian Carrot Zhang
TAs: Suvratha J, Sagar Desai
7:30 pm – Dinner
Day 6 | Friday, December 15
Genomics of Non-Coding RNA
9:00-10:00 am – Plenary Lecture: Burden of recessive diseases in South Asia: population and genomic perspectives
K. Thangaraj, CCMB, Hyderabad
10:00-11:00 am – Plenary Lecture: Epigenetics: Long non coding RNA- New player in gene regulation
Mrs. Rao, JNCASR, Bangalore
11:00-11:30 am – Tea Break
11:30 am-1:30 pm – Didactic Lecture: Genomics of small RNAs
Dasaradhi Palakodeti, InStem, Bangalore
12:30-1:30 – Lunch
1:30-2:30 pm – Didactic Lecture: Long non-coding RNAs and functional relevance of non-coding genome
Rakesh Mishra CCMB, Hyderabad
2:30-4:00 pm – Hands-on Session: Identification of non-coding RNAs from sequencing data -Quantification, target screening for microRNAs
Dasaradhi Palakodeti, InStem, Bangalore
TAs: Vairavan L, InStem, Bangalore; Sagar Desai, IBAB, Bangalore
4:00-4:30 pm – Tea break
4:30-6:00 pm – Hands – on Session : Identification of non-conventional small RNAs: tRNA derived fragments in the genome
Dasaradhi Palakodeti, InStem, Bangalore
TAs: Vairavan L, InStem, Bangalore; Sagar Desai, Suvratha J, IBAB, Bangalore
Dasaradhi Palakodeti, InStem, Bangalore
TAs: Vairavan L, InStem, Bangalore; Sagar Desai, IBAB, Bangalore
6:00-7:00 pm – Hands-on Session: Library preparation for sequencing
Bibha Choudhary, IBAB
TAs: Samatmika Ravi, Pushpinder Singh, Snehal Nirgude, Meghana, Jinsha K
7:30 pm – Dinner
Day 7 | Saturday, December 16
Off-site Discussions (Arranged by IBAB)
Day 8 | Sunday, December 17
Break
Day 9 | Monday, December 18
Epigenomics
9:00-10:00 am – Didactic Lecture: Understanding the Epigenome – implications on disease onset and progression
M. Vijayalakshmi, IBAB
10:00-10:30 am – Tea Break
10:30 am-12:30 pm – Hands-on Session: Analysis of ChIP- seq data and data from Bisulphite sequencing
Vijayalakshmi, Subashini Srinivasan, IBAB
TAs: Vairavan, InStem, Bangalore; Pushpinder Singh, IBAB, Bangalore
12:30-1:30 pm – Lunch
1:30-2:30 pm – Application Talk: The definition of epigenetics revisited: mRNA modifications and cancer stem cells
Kumaravel Somasundaram, IISc, Bangalore
2:30-4:00 pm – Hands-on Session: Library preparation for sequencing
Bibha Choudhary, IBAB
TAs: Meghana, Pushpinder, Jinsha, Snehal, Samathmika Ravi
4:00-4:30 pm – Tea Break
4:30-7:30 pm – Hands-on Session: Library preparation for sequencing
Bibha Choudhary, IBAB
TAs: Meghana, Pushpinder, Jinsha, Snehal, Samathmika Ravi
7:30 pm – Dinner
Day 10 | Tuesday, December 19
Microbial Genomics
8:30-10:00 am – Hands-on Session: Clonal cluster generation
Bibha Choudhary, Srikanth Reddy, IBAB
10:00-11:00 am – Didactic Lecture: evolution of the bacterial genome
Aswin Sai Narain Seshasayee, NCBS-TIFR, Bangalore
11:00-11:30 am – Tea Break
11:30 am 12:30 pm – Didactic Lecture : Understanding bacterial physiology through genomics
Aswin Sai Narain Seshasayee, NCBS-TIFR, Bangalore
12:30-1:30 pm – Lunch
1:30-4:00 pm – Hands-on Session: Microbial genome assembly, analysis of metagenomics data
Subashini Sirinivasan, IBAB
TAs: Suvratha J, Pushpinder Singh IBAB
4:00-4:30 pm – Tea Break
4:30-7:30 pm – Hands-on Session: Sequencing on the Illumina Platform
Bibha Choudhary, Srikanth Reddy, IBAB
7:30 pm – Dinner
Day 11 | Wednesday, December 20
Genomics of Infectious Diseases
9:00-10:00 am – Didactic Lecture : Vinettes of Disease genetics and the environment I
Maha Farhat, Harvard Medical School, Boston
10:00-11:00 am – Didactic Lecture : Vinettes of Disease genetics and the environment II
Maha Farhat
11:00-11:30 am – Tea Break
11:30 am-12:30 pm – Didactic Lecture : Basic approaches in the analysis of pathogen sequence data collected from clinical studies
Maha Farhat
12:30-1:30 pm – Lunch
1:30-3:00 pm – Application Talk : Whole genome sequencing for the understanding of antibiotic resistance and transmissibility of Mycobacterium tuberculosis
Maha Farhat
3:00-3:30 pm – Tea Break
3:30-6:00 pm – Hands-on Session: Microbial whole genome analysis including alignment assembly and variant calling
Maha Farhat
TAs: Suvrata JP, Sagar Desai
6:00-7:00 pm – Discussions and brain storming
Maha Farhat
7:30 pm – Dinner
Day 12 | Thursday, December 21
Genomics of Rare Diseases
9:00-10:00 am – Didactic Talk: Personal Genomes to Precision Medicine – 1
Vinod Scaria, IGIB, New Delhi
10:00-11:00 am – Personal Genomes to Precision Medicine – 2
Vinod Scaria, IGIB, New Delhi
11:00-11:30 am – Tea Break
11:30 am-12:30 pm – Discussion : GUaRDIAN project -genomics for Understanding Rare Diseases-Indian Alliance Network
Vinod Scaria, Bibha Choudhary, Subhashini Srinivasan
12:30-1:30 pm – Lunch
1:30-4:00 pm – Hands-on Session : Data Analysis – Whole Genome Sequencing
Subashini Sirinivasan, IBAB
TAs: Pushpinder Singh, Samathmika, Suvratha, IBAB
4:00-4:30 pm – Tea Break
4:30-6:30 pm – Hands -on Session : Data Analysis – Whole Genome Sequencing
Subhashini Srinivasan, Jian Carrot Zhang
TAs: Pushpinder Singh, Samathmika, Suvratha, IBAB
7:00 pm – Dinner
Day 13 | Friday, December 22
Precision Medicine
9:00-10:00 am – Didactic Talk: Integrating next-generation sequencing technologies into precision medicine
Jian Carrot Zhang, Broad Institute, Boston
10:00-11:00 am – Didactic Talk: Biomarker discovery, validation, and prioritization for translation
Subhashini Srinivasan, IBAB
11:00-11:30 am – Tea Break
11:30 am-1:00 pm – Kiran Mazumdar Shaw Lecture: Application of Integrative Sequencing for Precision Oncology
Arul Chinnaiyan, University of Michigan, Ann Arbor
1:00-2:00 pm – Lunch
2:00-4:00 pm – Brainstorming session with oncologists on genomics based diagnosis and therapy
Arul Chinnaiyan, University of Michigan, Ann Arbor and clinicians from across India, participants
4:00-4:30 pm – Lunch
4:30-7:00 pm – Hands-on Session: Prediction of drug resistance using genotypic data: Building a random forest predictive model using ‘R’
Maha Farhat
TAs: Sagar Desai, Suvratha J, IBAB
7:30 pm – Dinner
Day 14 | Saturday, December 23
Industry Interaction Day
10:00-10:20 am – Welcome and brief of the workshop
Vijayalakshmi M, IBAB
10:20 am-12:00 pm – Panel Discussion on ‘Genomics-Trends and Opportunities’
Chair : Arul Chinnaiyan, University of Michigan, Ann Arbor
Moderator : Amit Dutt, ACTREC, Mumbai
- Ramesh Hariharan, CEO,Strand Life Sciences, Bangalore
- Rajgopal Srinivasan, Head-Bio-IT, Tata Innovation Labs, Hyderabad
- Ajit Kamath, Executive Director, Mitra Biotech, Bangalore
- Ramprasad, CEO, MedGenome India, Bangalore
S.G.Senthilvel, SME & Solution Architect – Healthcare & Life Sciences at IBM India Pvt. Ltd.,Bangalore
12:00-12:30 pm – Discussion with participants
12:30-2:00 pm – Lunch
2:00-2:30 pm – Key Note Address
Representatives from DBT, GoI
2:30-4:00 pm – Discussions on the impact of B4 program: Moderated by Prof. Venkatesh Murthy, Chair of Molecular & Cellular Biology, Harvard University, Boston
Participants: B4 fellows, faculty from IISc & NCBS
4:00 pm – Vote of Thanks
N. Yathindra, IBAB