CAGI2 Challenge

The second round of CAGI was completed in 2011, with 11 challenges provided to predictors. The experiment yielded a total of 117 predictions from 21 groups from 18 countries, with 55 people attending the December 2011 meeting. Experimental results for the following CAGI 2011 challenges have been published: Mouse exomes challenge: Fairfield et al., Mutation discovery in mice by whole exome sequencing. Genome Biology 2011, 12:R86. doi:10.1186/gb-2011-12-9-r86

Cancer cell lines challenge: Heiser LM et al., Subtype and pathway specific responses to anticancer compounds in breast cancer. doi: 10.1073/pnas.1018854108. CBS challenge: Mayfield JA, et al. Surrogate genetics and metabolic profiling for characterization of human disease alleles. Genetics. 2012, 190(4):1309-23. doi:10.1534/genetics.111.137471. CAGI was presented at ISMB/EECB 2011 in a special session in July, covered in GenomeWeb and in a special session at the Pacific Symposium on Biocomputing in January 2012.


The flagship manuscript describing the meeting as well as a collection of papers describing the predictions and challenges is currently underway.

Key Dates

23 Jun 2011: Initial Datasets posted on the CAGI website

31 Aug - 11 Oct 2011: Prediction submission deadline depends on the dataset. The deadline is always 3PM EDT (Eastern time in the USA).

  • 31 August - Mouse exomes
  • 30 September - Cancer cell lines
  • 3 October - CBS
  • 4 October - MR-1, SCN5A
  • 5 October - p53
  • 6 October - Asthma
  • 7 October - RAD50
  • 21 October - riskSNPs
  • 26 October - Crohn's disease
  • 31 October - PGP

15 Oct 2011: Registration for CAGI 2011 Conference opens

9 - 10 December 2011: Two-day CAGI 2011 Conference at the University of California, San Francisco Mission Bay campus

Challenges

The following challenges were launched:

  • 1. Discordant monozygotic twins – identify the twin with asthma
  • 2. Breast cancer cell line pharmacogenomics dataset
  • 3. Cystathionine beta-Synthase (CBS) single amino acid mutations observed in patients
  • 4. Distinguish between exomes of Crohn's disease patients and healthy individuals
  • 5. Mouse exomes dataset – predict the causative mutation of a given phenotype
  • 6. The fitness of tagged transposon insertions in Shewanella oneidensis strain MR-1 under stress conditions
  • 7. Single amino-acid changes in the human p53 core domain that can restore activity of inactive p53 found in human cancers
  • 8. Personal genome project (PGP) - Predict individuals' phenotypes
  • 9. RAD50 variants in breast cancer patients and controls
  • 10. Novel NaV1.5 channel mutations associated with Brugada syndrome
  • 11. Identify the splicing impact of variation(Withdrawn)
  • 12. Molecular Mechanisms underlying associations between genetic variation and disease risk


Results

Personally identifiable data is restricted according to dataset requirements permanently. All datasets remain embargoed until published or otherwise released by providers. CAGI results are embargoed until 1 Jan 2012. CAGI 2011 Assessment results are available here for registered users.

Risk SNP Results

Personally identifiable data is restricted according to dataset requirements permanently. For results see here.


Organizers and Support

Organizers

Steven E. Brenner, CAGI Chair, University of California, Berkeley

John Moult, CAGI Chair, IBBR, University of Maryland

Susanna Repo, CAGI Organizer, University of California, Berkeley

Data Providers

Adam Arkin, University of California, Berkeley

George Church, Harvard Medical School

Andre Franke, Christian–Albrechts–Universität zu Kiel

Joe W. Gray, Lawrence Berkeley National Laboratory

Rick Lathrop and the p53 "cancer rescue" team, University of California, Irvine

John Moult and Lipika R. Pal, University of Maryland

Jasper Rine, University of California, Berkeley

Jeremy Sanford, University of California, Santa Cruz

Nicole Schmitt, University of Copenhagen

Jay Shendure, University of Washington

Michael Snyder, Stanford University

Sean Tavtigian, University of Utah

Confirmed Assessors

Rui Chen, Stanford University

Iddo Friedberg, Miami University

Gad Getz, Broad Institute

Sean Mooney, Buck Institute

Alexander A. Morgan, Stanford University

Artem Sokolov, University of California, Santa Cruz

Josh Stuart, University of California, Santa Cruz

Sean Tavtigian, University of Utah

Confirmed CAGI Advisory Board

Russ Altman, Stanford University

George Church, Harvard Medical School

Tim Hubbard, Wellcome Trust Sanger Institute

Scott Kahn, Illumina Inc.

Sean Mooney, Buck Institute

Pauline Ng, Genome Institute of Singapore

Confirmed CAGI Scientific Council

Patricia Babbitt, University of California, San Francisco

Atul Butte, Stanford University

Garry Cutting, Johns Hopkins University School of Medicine

Laura Elnitski, NIH/NHGRI

Reece Hart, Locus Development

Rachel Karchin, Johns Hopkins University

Robert Nussbaum, University of California, San Francisco

Michael Snyder, Stanford University

Shamil Sunyaev, Harvard Medical School

Joris Veltman, Radboud University Nijmegen

Liping Wei, Peking University

CAGI Assessors, ex officio

CAGI Advisory Board members, ex officio

Website Development and Administration

Maya Zuhl, IBBR, University of Maryland

Sri Jyothsna Yeleswarapu, Tata Consultancy Services

Support

The CAGI experiment website development has been supported in part by Tata Consultancy Services.

Funding for the CAGI 2011 Conference was made possible (in part) by 1R13HG006650-01 from the National Human Genome Research Institute. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

Susanna Repo has been supported by Marie Curie International Outgoing Fellowship PIOF-QA-2009-237751.

CAGI 2011 Conference Slides and Videos

Slides and videos of the meeting presentations are available below. To view the videos, you need to have Quicktime installed on your computer. If you are using Windows, please go here to download the software: http://www.apple.com/quicktime/download/. On Macs, the software is already installed. Conference slides and videos are available only to logged in users. Please log in, in order to view the videos.