CAGI manuscripts update; welcome Gaia Andreolett

Dear CAGI participant,

In this newsletter we have updates on the assessor and predictor manuscripts for the CAGI collection and special issues of Human Mutation and the Annals of Human Genetics. We particularly encourage predictors to submit manuscripts--see details below.

We are pleased to welcome and introduce Gaia Andreoletti, who has joined us to lead future CAGI experiments. We also have updates on the flagship manuscript.

* CAGI paper collection
We strongly encourage all assessors and predictors to submit manuscripts to the CAGI collection in Human Mutation and Annals of Human Genetics. We are extending the deadline for manuscript submissions to 25 August 2016. If there are special circumstances that preclude submitting your manuscript by the deadline, please let us know and we’ll try to accommodate. Presently we have 17 manuscripts confirmed, listed below along with submission details below, as well as plans for several more.

* Welcome Gaia Andreoletti
We are delighted to introduce Gaia Andreoletti, who has joined us to lead the CAGI experiment as a postdoctoral fellow. Gaia has recently completed a Ph.D. in genomic medicine at the University of Southampton. As you may know, Roger is unable to continue as lead scientist and will leave us soon. Many of you met Gaia at the CAGI 4 conference. She and Roger are overlapping this week, so she will be able to hit the ground running. We look forward to initiating the CAGI 5 experiment with her. She can be reached as .

* Flagship manuscript and authorship
We continue to develop the flagship manuscript and welcome further input expanding the themes previously circulated. Based on feedback, we have revised the authorship plan: We will submit the manuscript with all interested CAGI participants as named authors; we estimate this will be ~270 authors. If the journal refuses, then we will propose a single banner author, such as “CAGI Participants,” with all authors (including organizers) named at the back of the paper and searchable in PubMed. (This plan could still change pending feedback from more authors and Journal policy.)

* CAGI papers collection logistics and details
There will be no publication charges for manuscripts accepted for the special issues of the two journals. There will be no page charges and no charges for color figures. All papers in the special issues will be free online. If you would like full open access to your paper (called OnlineOpen at Wiley), the fee for Human Mutation is $3,500. Wiley has also confirmed that preprints may be submitted to bioRxiv.

The editors have requested that submitting authors include “CAGI special issue” near the beginning of their cover letter. They also request that submitting authors recommend 5 or 6 potential referees, as these are difficult to recruit in the summer months.

Previously we did not correctly describe the procedure for resubmission of returned manuscripts. If a manuscript is deemed not to meet the criteria for acceptance at Human Mutation, the corresponding author will receive a rejection letter and the reviews. If the authors would like to submit the manuscript to the Annals of Human Genetics, then the reviews from Human Mutation may be included with the cover letter in the submission, and this may expedite a decision by the editors at the Annals.

Please let us know if you are planning to submit a manuscript and to which journal. We are tracking the manuscripts in preparation, so that the journal editors can prepare. Our current confirmed list includes 8 manuscripts on assessment of challenge results and 9 manuscripts from predictors:

Assessor manuscripts:
p16 challenge. Silvio C.E. Tosatto, et al.
NAGLU challenge. Wyatt T. Clark, et al.
SUMO ligase challenge. Nick Grishin, et al.
CBS challenges, Iddo Fridberg et al (tentative)
Predicting gene expression from DNA sequence in a massively parallel reporter assay: a comparative study, Anat Kreimier, Nir Yosef, et al.
Predicting disease and drug phenotypes from exome data, Roxana Daneshjou, Alexander A. Morgan, et al.
PGP challenges. Sean D. Mooney, et al.
Hopkins clinical panel challenge. John-Marc Chandonia, Shamil Sunyaev, et al.
SickKids clinical genomes challenge, M. Stephen Meyn, et al.

Predictor manuscripts:
Improving prediction performance: lessons learned from CAGI challenges. Abhishek Niroula and Mauno Vihinen.
eQTL-causal SNPs. Michael Beer
MutPred performance in nonsynonymous variant challenges. Predrag Radivoja, et al.
Evolutionary Action performance in nonsynonymous variant challenges. Olivier Lichtarge, et al.
Cautions in bipolar phenotype prediction using exome sequencing SNPs. Maggie Haitian Wang, Billy Chang, Rui Sun, Inchi Hu, Benny Zee.
Crohn’s exome challenges, Lipika R. Pal, John Moult, et al.
SickKids clinical genomes challenge, Lipika R. Pal, John Moult, et al.
Hopkins clinical panel challenge. Kunal Kundu, John Moult, et al.
NAGLU and SUMO ligase challenges, Yizhou Yin, John Moult, et al.
Bipolar exomes challenge. Laksshman Sundaram, Rajendra Rana Bhat, and Xiaolin Li.

With all best regards,

Gaia, Roger, John, and Steven