CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Jain, Shantanu and Bakolitsa, Constantina and Brenner, Steven E. and Radivojac, Predrag and Moult, John and Repo, Susanna and Hoskins, Roger A. and Andreoletti, Gaia and Barsky, Daniel and Chellapan, Ajithavalli and Chu, Hoyin and Dabbiru, Navya and Kollipara, Naveen K. and Ly, Melissa and Neumann, Andrew J. and Pal, Lipika R. and Odell, Eric and Pandey, Gaurav and Peters-Petrulewicz, Robin C. and Srinivasan, Rajgopal and Yee, Stephen F. and Yeleswarapu, Sri Jyothsna and Zuhl, Maya and Adebali, Ogün and Patra, Ayoti and Beer, Michael A. and Hosur, Raghavendra and Peng, Jian and Bernard, Brady M. and Berry, Michael and Dong, Shengcheng and Boyle, Alan P. and Adhikari, Aashish and Chen, Jingqi and Hu, Zhiqiang and Wang, Robert and Wang, Yaqiong and Miller, Maximilian and Wang, Yanran and Bromberg, Yana and Turina, Paola and Capriotti, Emidio and Han, James J. and Ozturk, Kivilcim and Carter, Hannah and Babbi, Giulia and Bovo, Samuele and Di Lena, Pietro and Martelli, Pier Luigi and Savojardo, Castrense and Casadio, Rita and Cline, Melissa S. and De Baets, Greet and Bonache, Sandra and Díez, Orland and Gutiérrez-Enríquez, Sara and Fernández, Alejandro and Montalban, Gemma and Ootes, Lars and Özkan, Selen and Padilla, Natàlia and Riera, Casandra and De la Cruz, Xavier and Diekhans, Mark and Huwe, Peter J. and Wei, Qiong and Xu, Qifang and Dunbrack, Roland L. and Gotea, Valer and Elnitski, Laura and Margolin, Gennady and Fariselli, Piero and Kulakovskiy, Ivan V. and Makeev, Vsevolod J. and Penzar, Dmitry D. and Vorontsov, Ilya E. and Favorov, Alexander V. and Forman, Julia R. and Hasenahuer, Marcia and Fornasari, Maria S. and Parisi, Gustavo and Avsec, Ziga and Çelik, Muhammed H. and Nguyen, Thi Yen Duong and Gagneur, Julien and Shi, Fang Yuan and Edwards, Matthew D. and Guo, Yuchun and Tian, Kevin and Zeng, Haoyang and Gifford, David K. and Göke, Jonathan and Zaucha, Jan and Gough, Julian and Ritchie, Graham R.S. and Frankish, Adam and Mudge, Jonathan M. and Harrow, Jennifer and Young, Erin L. and Yu, Yao and Huff, Chad D. and Murakami, Katsuhiko and Nagai, Yoko and Imanishi, Tadashi and Mungall, Christopher J. and Jacobsen, Julius O.B. and Kim, Dongsup and Jeong, Chan Seok and Jones, David T. and Li, Mulin Jun and Guthrie, Violeta Beleva and Bhattacharya, Rohit and Chen, Yun Ching and Douville, Christopher and Fan, Jean and Kim, Dewey and Masica, David and Niknafs, Noushin and Sengupta, Sohini and Tokheim, Collin and Turner, Tychele N. and Yeo, Hui Ting Grace and Karchin, Rachel and Shin, Sunyoung and Welch, Rene and Keles, Sunduz and Li, Yue and Kellis, Manolis and Corbi-Verge, Carles and Strokach, Alexey V. and Kim, Philip M. and Klein, Teri E. and Mohan, Rahul and Sinnott-Armstrong, Nicholas A. and Wainberg, Michael and Kundaje, Anshul and Gonzaludo, Nina and Mak, Angel C.Y. and Chhibber, Aparna and Lam, Hugo Y.K. and Dahary, Dvir and Fishilevich, Simon and Lancet, Doron and Lee, Insuk and Bachman, Benjamin and Katsonis, Panagiotis and Lua, Rhonald C. and Wilson, Stephen J. and Lichtarge, Olivier and Bhat, Rajendra R. and Sundaram, Laksshman and Viswanath, Vivek and Bellazzi, Riccardo and Nicora, Giovanna and Rizzo, Ettore and Limongelli, Ivan and Mezlini, Aziz M. and Chang, Ray and Kim, Serra and Lai, Carmen and O’Connor, Robert and Topper, Scott and van den Akker, Jeroen and Zhou, Alicia Y. and Zimmer, Anjali D. and Mishne, Gilad and Bergquist, Timothy R. and Breese, Marcus R. and Guerrero, Rafael F. and Jiang, Yuxiang and Kiga, Nikki and Li, Biao and Mort, Matthew and Pagel, Kymberleigh A. and Pejaver, Vikas and Stamboulian, Moses H. and Thusberg, Janita and Mooney, Sean D. and Teerakulkittipong, Nuttinee and Cao, Chen and Kundu, Kunal and Yin, Yizhou and Yu, Chen Hsin and Kleyman, Michael and Lin, Chiao Feng and Stackpole, Mary and Mount, Stephen M. and Eraslan, Gökcen and Mueller, Nikola S. and Naito, Tatsuhiko and Rao, Aliz R. and Azaria, Johnathan R. and Brodie, Aharon and Ofran, Yanay and Garg, Aditi and Pal, Debnath and Hawkins-Hooker, Alex and Kenlay, Henry and Reid, John and Mucaki, Eliseos J. and Rogan, Peter K. and Schwarz, Jana M. and Searls, David B. and Lee, Gyu Rie and Seok, Chaok and Krämer, Andreas and Shah, Sohela and Huang, Cheng Lai V. and Kirsch, Jack F. and Shatsky, Maxim and Cao, Yue and Chen, Haoran and Karimi, Mostafa and Moronfoye, Oluwaseyi and Sun, Yuanfei and Shen, Yang and Shigeta, Ron and Ford, Colby T. and Nodzak, Conor and Uppal, Aneeta and Shi, Xinghua and Joseph, Thomas and Kotte, Sujatha and Rana, Sadhna and Rao, Aditya and Saipradeep, V. G. and Sivadasan, Naveen and Sunderam, Uma and Stanke, Mario and Su, Andrew and Adzhubey, Ivan and Jordan, Daniel M. and Sunyaev, Shamil and Rousseau, Frederic and Schymkowitz, Joost and Van Durme, Joost and Tavtigian, Sean V. and Carraro, Marco and Giollo, Manuel and Tosatto, Silvio C.E. and Adato, Orit and Carmel, Liran and Cohen, Noa E. and Fenesh, Tzila and Holtzer, Tamar and Juven-Gershon, Tamar and Unger, Ron and Niroula, Abhishek and Olatubosun, Ayodeji and Väliaho, Jouni and Yang, Yang and Vihinen, Mauno and Wahl, Mary E. and Chang, Billy and Chong, Ka Chun and Hu, Inchi and Sun, Rui and Wu, William Ka Kei and Xia, Xiaoxuan and Zee, Benny C. and Wang, Maggie H. and Wang, Meng and Wu, Chunlei and Lu, Yutong and Chen, Ken and Yang, Yuedong and Yates, Christopher M. and Kreimer, Anat and Yan, Zhongxia and Yosef, Nir and Zhao, Huying and Wei, Zhipeng and Yao, Zhaomin and Zhou, Fengfeng and Folkman, Lukas and Zhou, Yaoqi and Daneshjou, Roxana and Altman, Russ B. and Inoue, Fumitaka and Ahituv, Nadav and Arkin, Adam P. and Lovisa, Federica and Bonvini, Paolo and Bowdin, Sarah and Gianni, Stefano and Mantuano, Elide and Minicozzi, Velia and Novak, Leonore and Pasquo, Alessandra and Pastore, Annalisa and Petrosino, Maria and Puglisi, Rita and Toto, Angelo and Veneziano, Liana and Chiaraluce, Roberta and Ball, Mad P. and Bobe, Jason R. and Church, George M. and Consalvi, Valerio and Cooper, David N. and Buckley, Bethany A. and Sheridan, Molly B. and Cutting, Garry R. and Scaini, Maria Chiara and Cygan, Kamil J. and Fredericks, Alger M. and Glidden, David T. and Neil, Christopher and Rhine, Christy L. and Fairbrother, William G. and Alontaga, Aileen Y. and Fenton, Aron W. and Matreyek, Kenneth A. and Starita, Lea M. and Fowler, Douglas M. and Löscher, Britt Sabina and Franke, Andre and Adamson, Scott I. and Graveley, Brenton R. and Gray, Joe W. and Malloy, Mary J. and Kane, John P. and Kousi, Maria and Katsanis, Nicholas and Schubach, Max and Kircher, Martin and Mak, Angel C.Y. and Tang, Paul L.F. and Kwok, Pui Yan and Lathrop, Richard H. and Clark, Wyatt T. and Yu, Guoying K. and LeBowitz, Jonathan H. and Benedicenti, Francesco and Bettella, Elisa and Bigoni, Stefania and Cesca, Federica and Mammi, Isabella and Marino-Buslje, Cristina and Milani, Donatella and Peron, Angela and Polli, Roberta and Sartori, Stefano and Stanzial, Franco and Toldo, Irene and Turolla, Licia and Aspromonte, Maria C. and Bellini, Mariagrazia and Leonardi, Emanuela and Liu, Xiaoming and Marshall, Christian and McCombie, W. Richard and Elefanti, Lisa and Menin, Chiara and Meyn, M. Stephen and Murgia, Alessandra and Nadeau, Kari C.Y. and Neuhausen, Susan L. and Nussbaum, Robert L. and Pirooznia, Mehdi and Potash, James B. and Dimster-Denk, Dago F. and Rine, Jasper D. and Sanford, Jeremy R. and Snyder, Michael and Cote, Atina G. and Sun, Song and Verby, Marta W. and Weile, Jochen and Roth, Frederick P. and Tewhey, Ryan and Sabeti, Pardis C. and Campagna, Joan and Refaat, Marwan M. and Wojciak, Julianne and Grubb, Soren and Schmitt, Nicole and Shendure, Jay and Spurdle, Amanda B. and Stavropoulos, Dimitri J. and Walton, Nephi A. and Zandi, Peter P. and Ziv, Elad and Burke, Wylie and Chen, Flavia and Carr, Lawrence R. and Martinez, Selena and Paik, Jodi and Harris-Wai, Julie and Yarborough, Mark and Fullerton, Stephanie M. and Koenig, Barbara A. and McInnes, Gregory and Shigaki, Dustin and Chandonia, John Marc and Furutsuki, Mabel and Kasak, Laura and Yu, Changhua and Chen, Rui and Friedberg, Iddo and Getz, Gad A. and Cong, Qian and Kinch, Lisa N. and Zhang, Jing and Grishin, Nick V. and Voskanian, Alin and Kann, Maricel G. and Tran, Elizabeth and Ioannidis, Nilah M. and Hunter, Jesse M. and Udani, Rupa and Cai, Binghuang and Morgan, Alexander A. and Sokolov, Artem and Stuart, Joshua M. and Minervini, Giovanni and Monzon, Alexander M. and Batzoglou, Serafim and Butte, Atul J. and Greenblatt, Marc S. and Hart, Reece K. and Hernandez, Ryan and Hubbard, Tim J.P. and Kahn, Scott and O’Donnell-Luria, Anne and Ng, Pauline C. and Shon, John and Veltman, Joris and Zook, Justin M. (2024) CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25 (1). ISSN 1474-7596 (Print) 1474-760X (Online)

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