New CAGI challenges released; close dates

Dear CAGI participant,

Three new challenges were released today:
https://genomeinterpretation.org/content/challenges-4

More challenges will be released over the next few weeks:
https://genomeinterpretation.org/content/developing-challenges-4

All released challenges now have posted close dates, with the first close on 9 November 2015.

Challenges released today:

* PGP: predict individuals' phenotypes from their genomes

* SUMO ligase: predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay

* eQTL-causal SNPs: identify regulatory sequences and eQTL-causal variants, and estimate their effects on activation of transcription in a massively parallel reporter assay

Additional challenges being developed with the likelihood of release is indicated: + low, ++ moderate, and +++ high likelihood:

Protein-Coding Variants
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+++ Pyruvate kinase mutations cause hereditary non-spherocytic hemolytic anemia (data provided by Aron Fenton, The University of Kansas Medical School). Challenge: predict the effects of single-amino-acid mutations on enzyme activity, and allosteric activation and inhibition in cell extracts.

Splicing Variants
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+++ Pre-mRNA splicing (data provided by William Fairbrother, Brown University). Challenge: predict the effect of naturally occuring intronic variants near 3’ splice sites of medically actionable genes in a high-throughput splicing assay.

Clinical Sequences
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+ Genome sequences and microarrays from sick children (provided by M. Stephen Meyn, Hospital for Sick Children). Challenge: match patients’ genomes to their clinical descriptions and predict causal pathogenic variants.

++ Clinical gene panel sequences (provided by Garry Cutting Johns Hopkins). Challenge: match the patients’ gene panel sequences to their clinical descriptions and predict the causal pathogenic variants.

Research Exomes
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+ Exomes, RNA-seq profiles, and microbomes from pre-diabetes patients and healthy individuals (provided by Mike Snyder, Stanford University). Challenge: predict each individual’s fasting glucose level, glucose metabolic rate, and insulin response.
+ Exomes of bipolar disorder patients and healthy individuals (provided
by Peter Zandi, James B. Potash, and Richard McCombie). Challenge: predict which individuals have bipolar disorder.

These challenges are anticipated to have close dates in early December.

We are currently exploring CAGI meeting dates in late March. Most likely the meeting will be 18-19 March in the San Francisco Bay Area.

Please distribute widely and follow our Twitter feed @CAGInews and the web site for updates.