Challenge updates: PGP, Crohn's, eQTL; server security

Dear CAGI Participant,

This newsletter provides updates on the PGP, Crohn's exomes, and eQTL-causal SNPs challenges, and information on an intrusion of the CAGI server.

PGP challenge updates:
https://genomeinterpretation.org/content/4-PGP
On 12 October, we released 145 matched genomes & profiles as training data. On 26 October, we increased the number of challenge genomes from 13 to 23, and we decreased the number of challenge profiles from 228 to 101 to match the ratio of profiles to genomes in the PGP challenge in CAGI 2013.

Crohn's exomes challenge update:
https://genomeinterpretation.org/content/4-crohns-exomes
On 23 October, we released age of disease onset data for the Crohn's disease challenges in CAGIs 2011 and 2013 for use in training.

eQTL-causal SNPs challenge update:
https://genomeinterpretation.org/content/4-eQTL-causal_SNPs
The challenge submission deadline has been extended to 10 December 2015. On 30 October, we corrected the numbers of variants and eQTLs in the datasets.

Additional challenges will be released soon. Because challenges are under development, we cannot guarantee the release of each challenge. The current likelihood of release is indicated: + low, ++ moderate, and +++ high likelihood. Estimated closing dates for these challenges are in mid-December.
https://genomeinterpretation.org/content/developing-challenges-4

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

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

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

Research Exomes: predict phenotypes and mutations
++ Exomes, RNA-seq profiles, and microbomes from pre-diabetes patients and healthy individuals (provided by Mike Snyder, Stanford University). Challenge: predict each individualÕs fasting glucose level, glucose metabolic rate, and insulin response.

+++ Bipolar exomes (data provided by Peter Zandi, James B. Potash, and Richard McCombie). Challenge: distinguish between 1,000 exomes of bipolar disorder patients and healthy individuals.

Also, we wanted to make you aware of an intrusion of the server running the CAGI website on Saturday, 15 August, for approximately 30 minutes. Our investigation showed that the attacker installed software in an attempt to gain access to other systems. Logs show this server had no large data transfers to any unknown systems during the affected period. Therefore the CAGI challenges and registration data appear secure.

In an abundance of caution, we have deployed a rebuilt server. As a further precaution, you might wish to change your password using the "Request new password" button in the upper right corner of the home page. Although we deem it extremely unlikely that data were compromised, we wanted to report this incident to you.