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Monday, September 19, 2011

Announcing Critical Assessment of Genome Interpretation & Prediction season open

The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to assess computational methods for predicting the phenotypic impacts of genomic variation. The CAGI 2011 experiment is now well underway with 11 datasets available at the CAGI website: http://genomeinterpretation.org/. Remaining deadlines to submit predictions start September 30, 2011 and continue until 31 October.

In the CAGI experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and make predictions of resulting molecular, cellular, or organismal phenotype. These predictions are evaluated against experimental characterizations, and independent assessors perform evaluations. The CAGI Conference 2011 will be held 9 - 10 December at UCSF Mission Bay campus to disseminate results, assess our collective ability to make accurate and meaningful phenotypic predictions, and better understand progress in the field. From this experiment, we expect to identify bottlenecks in genome interpretation, inform critical areas of future research, and connect researchers from diverse disciplines whose expertise is essential to methods for genome interpretation.

The CAGI 2011 challenges include:
• Disease-associated variants of a human metabolic enzyme.
• Variants from the resequencing of breast cancer patients and control subjects.
• Disease-associated variants of a human sodium channel.
• Genome and RNA-seq data from identical twins with discordant disease.
• Multiple genomics data for cancer cell lines, with differential response to drugs.
• Exomes of Crohn's disease patients and healthy individuals.
• Double mutants of p53 to identify mutations that restore the activity of inactive p53.
• Predicting the medical phenotypes of individuals with genome data.
• Microbial dataset measuring the effect of gene disruptions under stress conditions.
• The riskSNPs dataset to identify potential causative SNPs from lists of candidates in the disease-associated loci for seven complex trait diseases.
The CAGI submission deadline for the mouse exomes challenge already passed, but we are accepting submissions for archival purposes.

The first CAGI experiment, called pre-pro-CAGI, was organized in 2010. Assessors are preparing a manuscript to discuss these results. While the identities of the prediction methods have been embargoed for this "training" CAGI, we will de-anonymize methods from predictors who give us the permission to do so and future CAGI experiments will be more open. The next CAGI experiment is anticipated for 2013.

In order to access the challenges, download datasets, and submit predictions to CAGI 2011, please go to the website http://genomeinterpretation.org and register. For more information, contact the organizers at cagi@genomeinterpretation.org.

We are grateful to the following:

Data providers:
Adam Arkin, George Church, Andre Franke, Joe W. Gray, Rick Lathrop, Jasper Rine, Jeremy Sanford, Nicole Schmitt, Jay Shendure, Michael Snyder, and Sean Tavtigian.

Confirmed Assessors:
Rui Chen, Iddo Friedberg, Gad Getz, Sean Mooney, Pauline Ng, and Sean Tavtigian.

Confirmed CAGI Advisory Board:
Russ Altman, George Church, Tim Hubbard, Scott Kahn, and Sean Mooney.

Confirmed CAGI Scientific Council:
Patricia Babbitt, Atul Butte, Garry Cutting, Rachel Karchin, Robert Nussbaum, Michael Snyder, and Liping Wei.

URL: http://genomeinterpretation.org

Contact Person: Susanna Repo (srepo@compbio.berkeley.edu)