Nonsynonymous variants and targeted assays
Predict the effect of naturally occurring missense mutations on cellular enzymatic activity
Data provided by: Jonathan H. LeBowitz, Wyatt T. Clark, G. Karen Yu, BioMarin Pharmaceutical, Inc.
The Nucleophosmin - Anaplastic Lymphoma Kinase fusion protein (NPM-ALK): predict the effect of mutations in the kinase domain on kinase activity and Hsp90 binding affinity.
Data provided by: Paolo Bonvini and Federica Lovisa, Padua Children's Hospital
3. SUMO ligase
Human SUMO ligase (UBE2l): predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay.
Liver pyruvate kinase (L-PYK): predict the effects of missense mutations on kinase activity and allosteric regulation.
Data provided by: Aron Fenton, University of Kansas Medical Center
Regulatory variants and gene expression
Identify regulatory sequences and eQTL-causal variants, and estimate their effects on activation of transcription in a massively parallel reporter assay.
Data provided by: Ryan Tewhey and Pardis Sabeti, Broad Institute
Research trial exomes, complex disease
Distinguish between exomes of Crohn's disease patients and healthy individuals.
Data provided by: Prof. Dr. Andre Franke & Dr Britt-Sabina Petersen, Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Germany
Estimate patients’ therapeutic warfarin doses from their exome sequence.
Data provided by: Roxana Daneshjou and Russ Altman, Stanford University School of Medicine
Distinguish between exomes of bipolar disorder patients and unaffected individuals.
Data provided by: Mehdi Pirooznia and Peter Zandi, The Johns Hopkins University; Richard McCombie, Cold Spring Harbor Laboratory; James B. Potash, University of Iowa
Predict patients’ clinical descriptions and pathogenic variants from gene panel sequences.
Data provided by: Bethany Buckley, Molly Sheridan, and Garry R. Cutting, The Johns Hopkins University
Predict patients’ clinical descriptions and pathogenic variants from their genome sequences.
Data provided by: Stephen Meyn & colleagues, SickKids
Personal genomes and trait profiles
The Personal genome project (PGP): predict individuals' phenotypes.
Data provided by: George Church and colleagues, Harvard Medical School
Prediction season: through January 2016. During this period, challenges will typically close 2 to 3 months following their release date. A specific close date is posted on each challenge web page.
Assessment season: December 2015 to February 2016.
Conference: 25-27 March 2016 in Genentech Hall on the UCSF Mission Bay campus in San Francisco, California. Further details will be provided as plans develop.
The CAGI 4 (2016) predictors were: 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, Maya Zuhl Data Providers: Russ Altman, Adam P. Arkin, Madeleine P. Ball, Jason Bobe, Paolo Bonvini, Bethany Buckley, George Church, Garry R. Cutting, Emma D’Andrea, 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, Peter Zandi.
The CAGI 4 Conference took place 25-27 March 2016 at UCSF Mission Bay, San Francisco, CA. This year's The CAGI 4 results are now posted. The conference program page contains the full set of slides that were presented at the meeting. The abstract book contains abstracts describing the prediction methods. Each challenge page has the slides for talks given for that challenge as well as the challenge's answer key, assessor summary, and predictions.
The CAGI prediction season concluded in November 2015 and the assessment phase concluded inFebruary 2016. There were a total of 174 predictions submitted from 38 groups. Predictors hailed from 13 countries representing academics, research institutes, and industry.
Bipolar exomes: 29 submissions.
Crohn's exomes: 46 submissions.
eQTL causal SNPs: 22 submissions.
NAGLU: 18 submissions.
NPM-ALK: 4 submissions.
PGP: 5 submissions.
SickKids clinical genomes: 4 submissions.
SUMO ligase: 16 submissions.
Warfarin exomes: 9 submissions.
Hopkins clinical panel: 16 submissions.
Pyruvate kinase: 5 submissions.