Welcome to the CAGI experiment!

CAGI prediction season is now open

The Fourth Critical Assessment of Genome Interpretation (CAGI) prediction season has opened. On 3 August 2015 we released the first three challenges. Additional challenges will roll out soon. A preview of the challenges under consideration and development is available in the recent newsletter.

Please distribute this information widely and follow our Twitter feed @CAGInews and the web site for updates. For more information on the CAGI experiment, see the Overview.

The challenge season will extend through early December, with the first challenges closing beginning in mid-November. The CAGI meeting will occur around March 2016.

Challenges released:

  • Nonsynonymous variants and targeted assays
    • NAGLU (closes 8 December 2015):
      Predict the effect of naturally occurring missense mutations on cellular enzymatic activity
    • NPM-ALK (challenge closed):
      The Nucleophosmin - Anaplastic Lymphoma Kinase fusion protein (NPM-ALK): predict the effect of mutations in the kinase domain on kinase activity and Hsp90 binding affinity
    • SUMO ligase (challenge closed):
      Human SUMO ligase (UBE2l): predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay
    • Pyruvate kinase (closes 11 January 2015):
      Liver pyruvate kinase (L-PYK): predict the effects of missense mutations on kinase activity and allosteric regulation
  • Regulatory variants and gene expression
    • eQTL causal SNPs (closes 10 December 2015):
      Identify regulatory sequences and eQTL-causal variants, and estimate their effects on activation of transcription in a massively parallel reporter assay
  • Research trial exomes, complex disease
    • Crohn's exomes (closes 9 December 2015):
      Distinguish between exomes of Crohn's disease patients and healthy individuals
    • Warfarin exomes (closes 8 December 2015):
      Estimate patients’ therapeutic warfarin doses from their exome sequence
    • Bipolar exomes (closes 7 January 2016):
      Distinguish between exomes of bipolar disorder patients and unaffected individuals
  • Clinical sequences
    • Hopkins clinical panel (closes 18 January 2016):
      Predict patients’ clinical descriptions and pathogenic variants from gene panel sequences
  • Personal genomes and trait profiles
    • PGP (closes 7 December 2015):
      The Personal genome project (PGP): predict individuals' phenotypes