CAGI 5 updates

Dear CAGI Participant,

CAGI 5 has launched with 14 challenges. Two have now closed already but many more are open through late April. The CAGI conference will be held this Summer, possibly early July. We are currently finalizing options and venues. There will be some support for trainees.

* CAGI 5 challenges open:

* Nonsynonymous variants
+Frataxin: Predict the impact of variants of Frataxin protein on thermodynamic stability. Closing date: 18 April 2018
+Annotate the whole genome: Predict impact of all nonsynonymous variants in the genome. Ongoing challenge. Closing date: 30 April 2018
+PCM1: Predict the effect of missense mutations within the PCM1 gene on zebrafish development. Closing date: 19 April 2018
+ GAA: The challenge is to predict the fractional enzyme activity of each mutant protein compared to the wild-type enzyme. Closing date: 17 April 2018

* Splicing
+MaPSy: Identify causal variants and estimate their effects on splicing in a Massively Parallel Splicing Assay. Closing date: 30 April 2018
+Vex-seq: Predict the change in splicing from reference exons from data originated from a high-throughput assay. Closing date: 25 April 2018

* Regulatory variants
+Expression variants: Predict effects of non-coding variants in disease associated promoter and enhancer elements in a massivly parallel reported assay. Closing date: 26 April 2018

* Clinical sequences
+SickKids clinical genomes: Predict patients' clinical descriptions and pathogenic variants from their genome sequences. Closing date: 19 April 2018
+Intellectual Disability: Predict patients' range of neurodevelopmental presentations (ID, autism, epilepsy, etc...) and report the causative variants. Closing date: 23 April 2018

* Research exomes, complex disease
+Clotting disorders: Distinguish between exomes of individuals who have developed clotting disorder and which did not. Closing date: 16 April 2018

* Germline cancer variants:
+ENIGMA: Predict the probability that variants in BRCA1 and BRCA2 evaluated by the ENIGMA consortium are pathogenic. Closing date: 24 April 2018
+CHEK2: Predict the probability of an individual with a given mutation being in the case (breast cancer) or control (healthy). Closing date: 17 April 2018

We encourage the use of both established methods and experimental approaches, and we welcome predictors of all backgrounds.

Publications of results from the experiment are planned and encouraged. The previous CAGI special issue is at:

Please contact us if there is any way we can facilitate your participation.
We look forward to an exciting and productive CAGI, and we hope that you will participate in making it a great success!

With all best regards,

Gaia, Steven, and John

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