Bipolar exomes; deadline extensions; publication plans

Dear CAGI Participant,

This newsletter announces the release of a new challenge, Bipolar exomes; the extension of the prediction submission deadlines for the NAGLU, Crohn's exomes, and Warfarin exomes challenges; deadlines updates; and publication plans for CAGI 4.

* New challenge released 4 November 2015:
Bipolar exomes: Distinguish between exomes of bipolar disorder patients and unaffected individuals. Challenge closes 7 January 2016.
https://genomeinterpretation.org/content/4-bipolar-exomes

* Prediction submission deadlines have been extended for three challenges:

NAGLU: N-acetyl-glucosaminidase (NAGLU): predict the effect of naturally occurring missense mutations on cellular enzymatic activity. Challenge now closes 8 December 2015.
https://genomeinterpretation.org/content/4-NAGLU

Warfarin exomes: Estimate patientsÕ therapeutic warfarin doses from their exome sequences. Challenge now closes 8 December 2015.
https://genomeinterpretation.org/content/4-Warfarin_exomes

Crohn's exomes: Distinguish between exomes of Crohn's disease patients and healthy individuals. Challenge now closes 9 December 2015.
https://genomeinterpretation.org/content/4-crohns-exomes

* Challenge submission deadline close time
These are the final changes to prediction submission deadlines for released challenges. Most challenge close at 9:00 PM PST (Pacific Standard Time) on the specified date; see individual pages for precise times.

* Prediction submissions for two challenges are approaching soon:

NPM-ALK: The Nucleophosmin - Anaplastic Lymphoma Kinase fusion protein: predict the effect of mutations in the kinase domain on kinase activity and Hsp90 binding affinity. Challenge closes 9 November 2015.
https://genomeinterpretation.org/content/4-NPM-ALK

SUMO ligase: Human SUMO ligase (UBE2l): predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay. Challenge closes 18 November 2015. The experimental distribution of growth scores has been provided.
https://genomeinterpretation.org/content/4-SUMO_ligase

* Data for one challenge has been updated:

eQTL-causal SNPs: Identify regulatory sequences and eQTL-causal variants, and estimate their effects on activation of transcription in a massively parallel reporter assay. The sample dataset has been updated with edits to two variants.
https://genomeinterpretation.org/content/4-eQTL-causal_SNPs

* Publication plans for CAGI 4
We are in communication with editors at three journals about a virtual collection of publications on the CAGI 4 experiment. We plan a flagship paper reporting an overview of the challenges and general results, for which all CAGI participants will be listed as authors or in banner authorship. This is to be written within 6 weeks after the CAGI conference in late March 2016.

We will also have a series of papers from assessors and predictors on the detailed results of individual challenges or sets of related challenges. The timeline for submission of papers will be 3 to 6 months following the CAGI conference. The papers would be available free online, with the option to pay for full open access. Papers on individual challenges are to be organized primarily by the assessors and predictors, with support from the organizers as needed.

We are also working on publications from previous CAGI experiments, a matter of great concern to us.

* Rapid updates
There will be more news as challenges come to a close, not all of which will be in a newsletter, to avoid filling your inbox. All changes are highlighted on the challenge webpages. Please watch our twitter feed @CAGInews for udpates.