Informatics

The Informatics Program develops new algorithms, software, databases, visualization tools and other necessary components to interpret the large and complex datasets being generated by OICR’s cancer research programs. Our resources and expertise are shared with the Ontario cancer research community, with the goal of accelerating cancer research and bringing treatments to the clinic faster.

Our mission is to advance the knowledge and treatment of cancer through computational biology.

Our research objectives are to:

  • Gain new and deeper understanding of cancer biology through the application of computational and data-intensive techniques;
  • Develop information systems that apply this understanding to cancer clinical care;
  • Harmonize and disseminate large cancer-related data sets;
  • Train the next generation of computational biologists to work on cancer-related problems;
  • Foster efficiency, communication and collaboration within and among Informatics, OICR and the wider community.

Program Director

Dr. Lincoln Stein
Program Director and Principal Investigator, Informatics Program
Interim Scientific Director, Ontario Institute for Cancer Research

Principal Investigators and Directors

Program expertise and capabilities

Principal investigators and senior scientists in the Informatics Program have a broad set of research interests and expertise, ranging from open research and reproducibility, to software development for big data, algorithm development for long-read sequences, biomarker discovery, viral detection, and population-based genomics approaches to cancer, as well as pathway and network analysis. While the Informatics Program’s research activities and expertise focus on cancer, they also have broader application in genomic research.

Projects

The Informatics Program is involved in a wide variety of research projects. The Program plays both leadership and collaborative, scientific roles in many cancer research projects, with a strong mandate to output to the scientific community open-source and open-access data, tools and resources.

Projects under and related to our ICGCmed Strategic Initiative include:

  • The International Cancer Genome Consortium (ICGC), where Informatics houses the ICGC Secretariat and designed, built and maintains the ICGC Data Coordination Centre (ICGC DCC), a portal providing tools for visualizing, querying and downloading the data released by ICGC consortium members;
  • Genomic Data Commons, a unified data repository supporting the data sharing of several cancer genome programs at the NCI, including The Cancer Genome Atlas (TCGA);
  • The Cancer Genome Collaboratory is a unique compute cloud-based biomedical research resource designed to make the extensive genomic holdings of the ICGC project available in convenient form to the cancer research community. Researchers can create a project and request an account on the compute cloud;
  • Dockstore, developed by the Cancer Genome Collaboratory, is an open platform for sharing Docker-based tools described with the Common Workflow Language used by the Global Alliance for Genomics and Health (GA4GH).

Projects under and related to our Big Data Analytics Strategic Initiative include:

  • Canadian Prostate Cancer Genome Network (CPC-GENE), a project aimed at understanding the prostate cancer genome to better predict treatment failure for intermediate risk prostate cancers;
  • PRONTO, a pan-Canada research project to rapidly develop novel diagnostic markers for early prostate cancer;
  • Canadian Data Integration Centre (CDIC), which supports large scale genomics projects on population-wide and clinical cohorts, and provides analytical and bioinformatics support through access to the software and analytic systems needed to collect and harmonize diverse health and lifestyle data, analyze it and electronically publish the results. Researchers can request access and services for their project needs;
  • ICGC-TCGA DREAM Somatic Mutation Calling Challenge, which provides global coordination of benchmarking algorithms for analyzing cancer genomes.

As well, we also maintain active research efforts in many seminal, open-source, open-access community resources including:

  • Reactome: an open, curated knowledgebase of biological pathways in humans;
  • WormBase: an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans;
  • MISO: an open-source laboratory information management system (LIMS) for small-to-large scale sequencing centres developed in collaboration with Earlham Institute;
  • GMOD:the Generic Model Organism Database project is a collection of open source software tools for managing, visualizing, storing, and disseminating genetic and genomic data.

Data, Software and Tools

  • Nanopolish: A nanopore consensus algorithm using a signal-level hidden Markov model;
  • SGA: a String Graph Assembler for de novo genome assembly. SGA is very memory efficient. This efficiency is achieved by using a compressed representation of DNA sequence reads;
  • ICGC software stack including the Data Portal;
  • PCAWG data: over 2,400 consistently analyzed genomes corresponding to over 1,100 unique ICGC donors;
  • CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes;
  • ObiBa: Open source software for BioBanks;
  • VennDiagram: A set of R functions to generate high resolution Venn and Euler plots;
  • SeqControl : A set of Perl and R scripts for assessing the quality of sequencing data;
  • S22S: A random forest classifier that acts to identify somatic SNVs in a reference-free context;
  • ISOWN: Identification of Somatic mutations Without Normal tissues software is a supervised machine learning algorithm for predicting somatic mutations from tumour-only samples;
  • BAMQL : A query language for filtering SAM/BAM reads.

Opportunities to collaborate

The Informatics Program is open to and encourages research collaborations. Please contact any of the Principal Investigators or visit the OICR Collaborative Research Resources section for more information on how the Informatics Program can assist you.

News

Find out more about what’s happening in Informatics at OICR News.

Contact

Informatics Program Manager
Dr. Michelle Brazas
michelle.brazas@oicr.on.ca
Telephone: 416-673-8502
Mobile: 416-357-6687