CAGI 5 Launches; Your name in Human Mutation; new Data Use Agreement

Dear CAGI Participant,

CAGI 5 will launch very soon with an initial 6 challenges, and more challenges to follow; details are below. Also in this newsletter, we have updates on the CAGI special issue of Human Mutation and the new Data Usage Agreement.

*CAGI Special Issue in Human Mutation*
The CAGI special issue of Human Mutation will be printed in August 2017 with 22 articles, and many papers are already online. We thank all assessors, predictors, and data providers who worked on the contributions and congratulate them on publication. While the printed issue is now finished, we continue to accept additional manuscripts that will be added to the CAGI online special collection at Human Mutation and Annals of Human genetics.

The full list of manuscripts is at:
https://genomeinterpretation.org/content/CAGI_publications

The short introduction to the CAGI special issue in Human Mutation recognizes every CAGI participant in the acknowledgments. Please find the short introduction at:
https://genomeinterpretation.org/content/cagi-special-issue-introduction

Please let us know immediately of any errors or omissions as we only have a day or two to make corrections.

The list of names in the acknowledgment are:

Predictors: Allison Abad, Ogun Adebali, Ivan Adzhubey, Talal Amin, Johnathan R. Azaria, Giulia Babbi, Eraan Bachar, Benjamin Bachman, Minkyung Baek, Greet De Baets, Michael Beer, Violeta Beleva-Guthrie, Bonnie Berger, Brady Bernard, Rajendra Bhat, Rohit Bhattacharya, Samuele Bovo, Marcus Breese, Aharon S. Brodie, Yana Bromberg, Binghuang Cai, Colin Campbell, Chen Cao, Emidio Capriotti, Marco Carraro, Rita Casadio, Billy H. W. Chang, Shann-Ching Chen, Yun-Ching Chen, Chien-Yuan Chen, Melissa Cline, Andrea Corredor, Carla Davis, Mark Diekhans, Rezarta I. Dogan, Christopher Douville, Ian Driver, Roland Dunbrack, Joost van Durme, Andrea Eakin, Matthew Edwards, Gokcen Eraslan, Hai Fang, Carlo Ferrari, Anna Flynn, Lukas Folkman, Colby T. Ford, Adam Frankish, Zaneta Franklin, Yao Fu, Alessandra Gasparini, Tom Gaunt, David Gifford, Manuel Giollo, Nina Gonzaludo, Valer Gotea, Julian Gough, Yuchun Guo, Jennifer Harrow, Marcia Hasenahuer, Lim Heo, Ramin Homayouni, Raghavendra Hosur, Cheng L. V. Huang, Peter Huwe, Sohyun Hwang, Tadashi Imanishi, Jules Jacobsen, Chan-Seok Jeong, Yuxiang Jiang, David T. Jones, Daniel Jordan, Beomchang Kang, Rachel Karchin, Panagiotis Katsonis, Sunduz Keles, Manolis Kellis, Nikki Kiga, Dongsup Kim, Eiru Kim, Jack F. Kirsch, Michael Kleyman, Andreas Kraemer, Anshul Kundaje, Kunal Kundu, Pui-Yan Kwok, Ernest Lam, Dae Lee, Gyu R. Lee, Insuk Lee, Pietro Di Lena, Emanuela Leonardi, Andy Li, Jun Li, Yue Li, Biao Li, Olivier Lichtarge, Chiao-Feng Lin, Rhonald C. Lua, Angel Mak, Pier L. Martelli, David Masica, Zev Medoff, Aziz M. Mezlini, Rahul Mohan, Alexander M. Monzon, Sean D. Mooney, Matthew Mort, John Moult, Steve Mount, Eliseos Mucaki, Jonathan Mudge, Nikola Mueller, Chris Mungall, Katsuhiko Murakami, Yoko Nagai, Noushin Niknafs, Abhishek Niroula, Conor M. L. Nodzak, Yanay Ofran, Ayodeji Olatubosun, Kymberleigh Pagel, Lipika R. Pal, Taeyong Park, Nathaniel Pearson, Vikas Pejaver, Jian Peng, Alexandra Piryatinska, Catherine Plotts, Predrag Radivojac, Aditya R. Rao, Aliz Rao, Graham Ritchie, Peter Rogan, Frederic Rousseau, Jana M. Schwarz, Joost Schymkowitz, Chaok Seok, George Shackelford, Sohela Shah, Maxim Shatsky, Ron Shigeta, Hashem A. Shihab, Jung E. Shim, Junha Shin, Sunyoung Shin, Ilya Shmulevich, Bradford R. Silver, Nasa Sinnott-Armstrong, Ben Smithers, Yesim A. Son, Mario Stanke, Nathan Stitziel, Andrew Su, Laksshman Sundaram, Paul Tang, Nuttinee Teerakulkittipong, Natalie Thurlby, Janita Thusberg, Kevin Tian, Collin Tokheim, Silvio C. E. Tosatto, Yemliha Tuncel, Tychele Turner, Ron S. Unger, Aneeta Uppal, Gurkan Ustunkar, Jouni Valiaho, Mauno Vihinen, Mary Wahl, Michael Wainberg, Meng Wang, Maggie Wang, Yanran Wang, Xinyuan Wang, Li-San Wang, Liping Wei, Qiong Wei, Rene Welch, Stephen Wilson, Chunlei Wu, Lijing Xu, Qifang Xu, Yuedong Yang, Christopher Yates, Yizhou Yin, Chen-Hsin Yu, Dejian Yuan, Jan Zaucha, Haoyang Zeng, and Maya Zuhl

Data providers: Russ Altman, Adam P. Arkin, Madeleine P. Ball, Jason Bobe, Paolo Bonvini, Bethany Buckley, George Church, Garry R. Cutting, Emma DíAndrea, Lisa Elefanti, Aron W. Fenton, Andre Franke, Nina Gonzaludo, Joe W. Gray, Linnea Jannson, John P. Kane, Pui-Yan Kwok, Rick Lathrop, Jonathan H. LeBowitz, Federica Lovisa, Angel C. Y. Mak, Mary J. Malloy, Richard McCombie, Chiara Menin, M. Stephen Meyn, John Moult, Robert Nussbaum, Lipika R. Pal, Britt-Sabina Petersen, Mehdi Pirooznia, James B. Potash, Clive R. Pullinger, Jasper Rine, Frederick Roth, Pardis Sabeti, Jeremy Sanford, Maria C. Scaini, Nicole Schmitt, Jay Shendure, Molly Sheridan, Michael Snyder, Tim Sterne-Weiler, Paul L. F. Tang, Sean Tavtigian, Ryan Tewhey, Silvio C. E. Tosatto, Jochen Weile, G. Karen Yu, and Peter Zandi.

Assessors: Aashish Adhikari, Marco Carraro, John-Marc Chandonia, Rui Chen, Wyatt T. Clark, Roxana Daneshjou, Roland Dunbrack, Iddo Friedberg, Gad Getz, Nick Grishin, Rachel Karchin, Anat Kreimer, Stephen. Meyn, Sean D. Mooney, Alexander A. Morgan, John Moult, Robert Nussbaum, Jeremy Sanford, David B. Searls, Artem Sokolov, Josh Stuart, Shamil Sunyaev, Sean Tavtigian, Silvio C. E. Tosatto, Qifang Xu, and Nir Yosef.

Board members: Russ Altman, George Church, Tim Hubbard, Scott Kahn, Sean D. Mooney, Pauline Ng, Susanna Repo, and John Shon; our Scientific Council: Patricia Babbitt, Atul Butte, Garry R. Cutting, Laura Elnitski, Reece Hart, Ryan Hernandez, Rachel Karchin, Robert Nussbaum, Michael Snyder, Shamil Sunyaev, Joris Veltman, and Liping Wei.

CAGI Ethics Forum: Wylie Burke, Lawrence R Carr, Flavia Chen, Julie Harris-Wai, Kirsten Isgro, Barbara A. Koenig, Selena Martinez, Robert Nussbaum, and Mark Yarborough.

Organizers: John-Marc Chandonia, Ajithavalli Chellappan, Flavia Chen, Navya Dabbiru, Reece Hart, Melissa K. Ly, Andrew J. Neumann, Gaurav Pandey, Sadhna Rana, Rajgopal Srinivasan, Stephen Yee, Sri Jyothsna Yeleswarapu, and Maya Zuhl. We especially recognize Tata Consultancy Services, which has been a generous collaborator in organizing the CAGI experiment. We also acknowledge the efforts of Brenner and Moult lab researchers who contributed to CAGI.

Communicating editors: Rachel Karchin, Sean D. Mooney, Robert Nussbaum, Predrag Radivojac, Scott Kahn and Atul Butte.

Guest editors: Gaia Andreoletti, Steven E. Brenner and John Moult

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.

*Initial challenges to be released for CAGI 5*

Nonsynonymous variants and targeted assays
+CALM: Predict the effect of protein variants on competitive growth in a yeast assay.
+Frataxin: Predict the impact of different variants of Frataxin protein on its thermodynamic stability in terms of unfolding free energy.
+TPMT and p10: Predict the effect of variants on TPMT and p10 protein stability.†
+Annotate everything: Predict impact each coding single nucleotide variant from the genome. To be assessed against clinical data over time.

Regulatory variants
+Expression variants: Predict effects of non-coding variants in disease associated promoter and enhancer elements.

Research trial exomes, complex disease
+Clotting disorders: Distinguish between exomes of individuals who have developed clotting disorder and which did not

Challenges under development are listed at:
https://genomeinterpretation.org/content/developing-challenges-cagi-5

Some possible challenges include:
+ CHEK2: Predict the probability of an individual with a given mutation being in the case (breast cancer) or control (healthy).
+ Crohn's exomes: Distinguish between exomes of Crohn's disease patients and healthy individuals.
+ Splicing Variants: predict the effect of naturally occurring intronic variants near 3' splice sites of medically actionable genes in a high-throughput splicing assay.
+ PCM1: Predict the effect of missense mutations in†zebrafish.

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

*New Data Usage Agreement*
Our Ethics Forum has recommended clarifications to our Data Use Agreement (DUA), which we have adopted for all new participants. The new DUA will be released on Friday, 14 July 2017. We request that all current CAGI participants review the new agreement at:
https://genomeinterpretation.org/data-use-agreement-14-July-2017