The CAGI Special Issue in Human Mutation and CAGI 5

Dear CAGI Participant,

We are very pleased to announce that CAGI 5 will launch very soon rolling out an initial half-dozen challenges, and more challenges to follow. Please help us select dates for the CAGI 5 conference in the Google form below. Also in this newsletter, we are thrilled to let you know that the CAGI special issue in Human Mutation is now published. Finally, please meet with us at a gathering at ASHG in Orlando (FL) on Wednesday 19 October from 12:30pm-1:30pm.

*Initial challenges to be released for CAGI 5
We currently anticipate releasing imminently the following challenges:

Nonsynonymous variants
+CALM1: Predict the effect of protein variants in a yeast growth assay.
+Frataxin: Predict the impact of variants of Frataxin protein on thermodynamic stability.
+TPMT and p10: Predict the effect of variants on TPMT and p10 protein stability. 
+Annotate the whole genome: Predict impact of all nonsynonymous variants in the genome.
+PCM1: Predict the effect of missense mutations within the PCM1 gene on zebrafish development.

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

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

*CAGI conference
The CAGI 5 conference is likely to be either 23-25 March 2018 or 24-26 March 2018 in the San Francisco Bay Area.
Please help us choose your preferred dates at:
https://goo.gl/forms/16uYRh0crMGlE1YX2

*CAGI at ASHG
We will be holding an informal CAGI gathering at ASHG in Orlando on Wednesday 19 October from 12:30pm-1:30pm. Please join us!

Please write us at cagi@genomeinterpretation.org to let us know if you will be at ASHG. Let us know if you can join the gathering, and we will let you know the location once ASHG starts. Alternatively we can meet with you separately.

There will also be a CAGI talk on Saturday at 10:30-10:45 am, in Room 220F, Level 2 (Session #98. Improved Interpretation of Missense Variants). Please come and meet with Gaia then.

We are currently recruiting predictors for CAGI 5 and new data providers for CAGI 6. We would greatly appreciate sharing any ideas for contacts or recommendations of predictors we should reach out to, or people who could contribute CAGI challenge datasets.

*CAGI Special Issue in Human Mutation
The CAGI special issue of Human Mutation is published:
http://onlinelibrary.wiley.com/doi/10.1002/humu.2017.38.issue-9/issuetoc

All 23 articles are available free online without a subscription. We thank all assessors, predictors, and data providers who worked on the contributions and congratulate them on publication. While the print issue is now complete, we continue to accept additional manuscripts that will be added to the CAGI online special collection at Human Mutation and Annals of Human genetics.

We are now returning our attention to the CAGI "flagship" manuscript. As noted before, we propose that all >250 participants in the four CAGI experiments be recognized as authors. If the journal prohibits this, then there will be a single banner authorship, and everyone will be listed as banner authors.

Please distribute widely and follow our Twitter feed @CAGInews and the https://genomeinterpretation.org web site for updates.