Click to Subscribe & Stay Informed via Email!

Subscribe Here!

Subscribe and stay informed about our latest news and events!
  • Please List your Professional Affiliation

B4 Genomics Workshop Schedule

B4_header
 

 

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 AnalysisWhole 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 AnalysisWhole 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