[BBC] Fwd: CASP: CAGI community experiment

[Sanne Abeln]

The Critical Assessment of Genome Interpretation (CAGI) is a community

experiment to assess computational methods for predicting the

phenotypic impacts of genomic variation.  The current CAGI experiment

has eight open challenges, available on the CAGI website:

  https://genomeinterpretation.org/



In the CAGI experiment, participants are provided genetic variants and

make predictions of resulting phenotypes.  Independent assessors then

evaluate these predictions against experimental characterizations.

The primary goals of the experiment are to establish the current

state of the art, identify bottlenecks in genome interpretation,

inform critical areas of future research, and connect researchers

from diverse disciplines whose expertise is essential for advancing

methods for interpreting genomic variation.



The deadline for current CAGI predictions is 28 March 2013.

Anonymous submissions, with limitations, are allowed this year.

  https://genomeinterpretation.org/content/anonymity-policy

We encourage use of both established methods and experimental

approaches, and we welcome predictors of all backgrounds.



The current CAGI experiment will culminate in a conference in Berlin,

on 17-18 July 2013, immediately before the ISMB SIGs.  An NHGRI R13

grant will help support travel and participation in the meeting.

  https://genomeinterpretation.org/content/cagi-2012-conference



Previous CAGI experiments have highlighted striking breakthroughs

as well as disappointing failures.  Publications from the previous

CAGI are underway; slides and posters presentations about CAGI may

be found at:

  https://genomeinterpretation.org/content/cagi-presentations

The results from the current CAGI challenge will be published as well.



The currently open CAGI challenges are:



+ Seventy-seven PGP genomes (provided by George Church).

  Challenge: Predict clinical phenotypes from genome data, and match

  individuals to their health records.

  https://genomeinterpretation.org/content/PGP2012



+ Exomes of Crohn's disease patients and healthy individuals (provided

  by Andre Franke).  Challenge: predict which individuals have Crohn's.

  https://genomeinterpretation.org/content/new-crohns-dataset



+ Exomes from two families with lipid metabolism disorders (provided

  by John Kane and Pui-Yan Kwok). Challenge: predict lipid profiles

  and a causative variant.

  https://genomeinterpretation.org/content/FCH

  https://genomeinterpretation.org/content/HA



+ Variants in DNA double-strand break repair genes (provided by Sean

  Tavtigan).  Challenge: predict probability of each variant occurring

  in a breast cancer case versus healthy control.

  https://genomeinterpretation.org/content/MRN



+ Mutations in p53 gene exons affecting mRNA splicing (provided by

  Jeremy Sanford).  Challenge: predict how variants impact splicing.

  https://genomeinterpretation.org/content/Splicing-2012



+ Variants of a p16 tumor suppressor protein (provided by Silvio

  Tosatto). Challenge: predict how well variants inhibit cell

  proliferation.

  https://genomeinterpretation.org/content/p16_2012



+ Shewanella oneidensis MR-1 gene disruptions (provided by Adam Arkin).

  Challenge: Predict impact of microbial gene disruptions on cell

  growth under stress conditions

  https://genomeinterpretation.org/content/MR-1_2012



+ riskSNPs disease-associated loci (provided by John Moult). Challenge:

  identify potential causative SNPs.

  https://genomeinterpretation.org/content/risksnps2012



We are also soliciting challenges for the next CAGI. Please contact us

at cagi at genomeinterpretation.org with proposals for suitable datasets.



In order to access the current challenges and submit predictions for CAGI,

please register at https://genomeinterpretation.org/.



Registered users also have access to presentations from the previous

CAGI conferences, as well as posters and talk slides that summarize

the results.





Sincerely,



  Daniel Barsky, CAGI 2012 Organizer

  Steven E. Brenner, CAGI Chair

  John Moult, CAGI Chair



  cagi at genomeinterpretation.org