CAGI publication plans; conference slides and video now available

Dear CAGI community,

The CAGI 4 conference was held 25-27 March 2016 in San Francisco. Presentations by data providers, assessors, and predictors, and discussion sessions, are now available as slides and video to registered users:
https://genomeinterpretation.org/content/4-Conference-program
You are encouraged to use the remixable slides in your own presentation per the items provided.

Flagship manuscript

We are now preparing a CAGI "flagship" manuscript. We propose that the >250 participants in the four CAGI experiments be recognized by banner authorship as "CAGI Participants" and searchable in PubMed as "investigator name". The manuscript will address all of CAGI for 2010-2016. Rather than presenting details of every challenge, we are organizing the manuscript around key theme lessons learned. Some themes include:
* Top missense prediction methods are highly statistically significant, but individual variant accuracy is limited.
* Missense methods tend to correlate better with each other than with experiments.
* Structure-based missense methods excel in a few cases.
* Predictors were able to identify causal variants that were overlooked by the clinical laboratory.
* Predicting complex traits from exomes is fraught.
* Bespoke approaches often enhance performance.
* Clinical implications.
* Creating a good challenge that provides a reliable gold standard is difficult.
Feedback and suggestions for additional themes are welcome.

Assessor and predictor manuscripts

We are also organizing a series of manuscripts for special issues of Human Mutation (HuMu) and the Annals of Human Genetics (Annals). All CAGI assessors and predictors are encouraged to submit manuscripts on their approaches and results in the four CAGI experiments held to date. HuMu has a longer format and may be appropriate for most assessment manuscripts and prediction reports that encompass multiple challenges or provide substantial insights; Annals may be appropriate for shorter reports such as predictions with an established method.

Manuscripts are to be submitted directly to the journals through the normal process. In your cover letter, please reference the "CAGI special issue." The submission deadline is 30 July 2016. Manuscripts that are not accepted for publication in HuMu can be considered for publication in Annals without resubmission or re-review. Papers accepted for the special issues will appear online without delay in advance of the publication in print, which is planned for Spring 2017.

If you are interested in submitting a manuscript for one of the special issues, please contact us now for further information.

With all best regards,

Roger, John, and Steven