New computational tools to aid in analyzing 3D genomic data

Source: McGill Reporter
Major federal and provincial investments in genomics research were announced this week following three recent Genome Canada competitions. The announcement, made at University of Guelph, includes over $10 million in funding to seven projects led by McGill researchers. Here’s a quick look at one of those projects. (A complete list follows.)

Since the sequencing of the human genome at the beginning of the millennium, scientists have made great strides in understanding the role genes play in our identity, differences among individuals and our susceptibility to diseases such as cancer. Bioinformatics and computational tools are critical in visualizing and analyzing genetic data, but they fall short when it comes to three-dimensional analysis of how DNA is folded onto itself to fit into the nucleus, known as its chromatin architecture. This 3D structure defines the genome’s normal function during early cell differentiation and development and is known to drive many developmental disabilities as well as cancer. There is a pressing need for a new generation of computational tools that integrates our knowledge of these 3D states, to help researchers make optimal use of the rapidly increasing amounts of data produced by modern DNA sequencing.

A team led by McGill professors Mathieu Blanchette, Jacek Majewski and, Jérome Waldispühl will create and release improved computational and statistical tools for analyzing 3D data in their native 3D context. Their new tools will be integrated with the team’s 3D visualization platform that will help scientists explore the data, build new hypotheses and test them in rigorous statistical frameworks. The results of this project will be made widely available through open-source software that will enable statistically robust analysis of individual and groups of 3D genomic data; provide a virtual reality-based 3D genome browser supporting integrated visualization of genomic data; and include a toolset for integrative mining of genomic and epigenomic data in their 3D genome context. A lay version of the visualization platform will also be used for community outreach through exhibits in schools and museums.

Complete list of McGill projects:

1. 2017 Bioinformatics and Computational Biology (B/CB) Competition Results

(Multi-sector stream projects)

  • Bioinformatics tools for integrative 3D epigenomics

    Project leaders: Mathieu Blanchette, Jacek Majewski, Jérome Waldispühl, McGill University

    Genome Centre: Génome Québec

    Total funding: $1,122,405

  • Epigenomics Secure Data Sharing Platform for Integrative Analyses (EpiShare)

    Project leaders: Guillaume Bourque, Yann Joly, McGill University

    Genome Centre: Génome Québec

    Total Funding: $1,000,000

  • Precision Medicine in Cellular Epigenomics

    Project leaders: Celia Greenwood, Lady Davis Institute for Medical Research; Karim Oualkacha,

    Université du Québec à Montréal

    Genome Centre: Génome Québec

    Total funding: $660,512

  • An integrative platform for metabolomics and systems biology

    Project leaders: Jianguo Xia, Guillaume Bourque, McGill University; Pierre-Étienne Jacques,

    Université de Sherbrooke

    Genome Centre: Génome Québec

    Total funding: $1,094,607

  • Development and Validation of a Web-Based Platform for Environmental Omics andToxicology

    Project leaders: Jianguo Xia, Niladri Basu, McGill University

    Genome Centre: Génome Québec

    Total funding: $1,047,507

2. 2017 Disruptive Innovation in Genomics Competition For Phase 1 Projects Advancing to Phase 2

  • Digital Omics of Single Exosomes

    Project leader: David Juncker, McGill University

    Genome Centre: Génome Québec

    Total funding: $2 million

  • The RNA Zipcode Discovery Pipeline: Emerging tools for therapeutic targeting at subcellular resolution

    Project leaders: Eric Lécuyer, Institut de recherche clinique de Montréal (IRCM); Mathieu

    Blanchette, Jérôme Waldispühl, McGill University

    Genome Centre: Génome Québec

    Total funding: $3.2 million



February 8, 2019