CAGI 5 Launches!

Dear CAGI Participant,

CAGI 5 has launched! Eight challenges have been released, and more challenges to follow. One has closed already but many more are open thought December to February.

* CAGI 5 challenges released:

Nonsynonymous variants
+CALM1: Predict the effect of protein variants in a yeast growth assay. Closing date: 20 December 2017
+Frataxin: Predict the impact of variants of Frataxin protein on thermodynamic stability. Closing date: 7 February 2017
+TPMT and p10: Predict the effect of variants on TPMT and p10 protein stability. Closing date: 1 December 2017
+Annotate the whole genome: Predict impact of all nonsynonymous variants in the genome. Ongoing challenge – Closing date: 8 February 2018
+PCM1: Predict the effect of missense mutations within the PCM1 gene on zebrafish development. Closing date: 5 February 2018

+ MaPSy: Identify causal variants and estimate their effects on splicing in a Massively Parallel Splicing Assay. . Closing date: 12 February 2018

*Challenges to be released soon:

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

+ Vex-seq: Predict the change in splicing from reference exons from data originated from a high-throughput assay.

Clinical sequences
+ SickKids clinical genomes: Predict patients’ clinical descriptions and pathogenic variants from their genome sequences

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

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:

* CAGI 5 conference:

Based on current logistics it seems likely that will either be either 23-25 March 2018, 24-26 March 2018, 25-27 April 2018, 27-29 April 2018 or 28-30 April 2018 in the San Francisco Bay Area. An NHGRI R13 grant will help support travel and participation in the meeting for junior investigators.

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

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