You're Invited: Graph-genomes and global data sharing for epigenomic data

Speaker Name: 
Dr. Guillaume Bourque
Speaker Title: 
Professor and Director of Bioinformatics
Speaker Organization: 
McGill University & Genome Quebec Innovation Center
Start Time: 
Thursday, December 12, 2019 - 11:30am
End Time: 
Thursday, December 12, 2019 - 12:30pm
Location: 
PSB - 305

Abstract:

Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesized that using a generic reference could lead to incorrectly mapped reads and bias downstream results. Using a benchmark dataset we show that accounting for genetic variation using a modified reference genome (MPG) or a denovo assembled genome (DPG) can alter ChIP-seq peak calls by either creating new personal peaks or by the loss of reference peaks. We also show that using a graph personalized genome (GPG), represents a reasonable compromise between MPGs and DPGs. We next apply this approach to a number of additional samples to identify novel peaks. In the second part of the presentation, I will talk about the International Human Epigenome Consortium (IHEC) and its link to the Global Alliance for Genomics and Health (GA4GH). One of the main issues for researchers interested in IHEC datasets is that obtaining the raw sequence files, often stored at controlled access repositories and bound by different access agreements, can be challenging. In this context, I will present a new GA4GH Driver Project called EpiShare that aims at facilitating epigenomic data discovery and analysis, while addressing the ethical and privacy aspects associated with data sharing.

 

Bio:

Guillaume started at McGill in 2010 after spending 6 years at the Genome of Institute of Singapore. He’s a Professor in the Department of Human Genetics and the Director of Bioinformatics at the McGill Genome Center. He also leads the Canadian Center for Computational Genomics (C3G) and the McGill initiative for Computational Medicine (MiCM).

He was fortunate to do his PhD in Applied Mathematics at the University of Southern California under Pavel Pevzner and his postdoc with David Sankoff at the Université de Montréal, two pioneers in Computational Biology.

 

Host: Benedict Paten, UC Santa Cruz Genomics Institute,  Baskin School of Engineering

 

To accommodate a disability, please contact Ben Coffey at the UC Santa Cruz Genomics Institute (becoffey@ucsc.edu, 831-459-1477).

Event Type: 
Event