New challenges released: Hopkins clinical panel and Pyruvate kinase

Dear CAGI Participant,

* New challenges
This newsletter announces the release of two new CAGI 4 challenges that expand the scope of CAGI.

The Hopkins clinical panel challenge provides real clinical gene panel sequences from a diagnostic laboratory used in medical evaluation of patients. Predictors will aim to determine patientsÕ disease and causal variants.

Hopkins clinical panel (released 18 November 2015):
Predict patientsÕ clinical descriptions and pathogenic variants from gene panel sequences. Challenge closes 18 January 2016.
https://genomeinterpretation.org/content/4-Hopkins_clinical_panel

In addition to enzyme activity, the Pyruvate kinase challenge asks for prediction of the effect of non-synonymous variants on allosteric regulation.

Pyruvate kinase (released 11 November 2015):
Liver pyruvate kinase (L-PYK): predict the effects of missense mutations on kinase activity and allosteric regulation. Challenge closes 11 January 2016.
https://genomeinterpretation.org/content/4-Pyruvate_kinase

* Challenges to be released
Two additional challenges are being developed and will be released soon. Because challenges are currently under development, we cannot guarantee the release of each challenge.

SickKids clinical genomes: Genome sequences from sick children (provided by M. Stephen Meyn, Hospital for Sick Children). Challenge: match patientsÕ genomes to their clinical descriptions and predict causal variants.

Splice acceptors: High-throughput splicing assay (data provided by William Fairbrother, Brown University). Challenge: predict the effect on splicing of naturally occurring intronic variants near 3Õ splice sites.

* Deadlines
Prediction submission deadlines for five challenges are approaching.

NAGLU: Predict the effect of naturally occurring missense mutations on cellular enzymatic activity. Challenge closes 8 December 2015.
https://genomeinterpretation.org/content/4-NAGLU

eQTL causal SNPs: Identify regulatory sequences and eQTL-causal variants, and estimate their effects on activation of transcription in a massively parallel reporter assay. Challenge closes 10 December 2015.
https://genomeinterpretation.org/content/4-eQTL-causal_SNPs

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

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

PGP: The Personal genome project: predict individuals' phenotypes. Challenge closes 7 December 2015.
https://genomeinterpretation.org/content/4-PGP

We remind you to check the website and follow us @CAGInews for more updates.