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A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies
Zilin Li, Xihao Li, Hufeng Zhou, Sheila M. Gaynor, Margaret Sunitha Selvaraj, Theodore Arapoglou, Corbin Quick, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K. Arnett, Paul L. Auer, Lawrence F. Bielak, Joshua C. Bis, Thomas W. Blackwell, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jennifer A. Brody, Brian E. Cade, Matthew P. Conomos, Adolfo Correa, L. Adrienne Cupples, Joanne E. Curran, Paul S. de Vries, Ravindranath Duggirala, Nora Franceschini, Barry I. Freedman, Harald H.H. Göring, Xiuqing Guo, Rita R. Kalyani, Charles Kooperberg, Brian G. Kral, Leslie A. Lange, Bridget M. Lin, Ani Manichaikul, Alisa K. Manning, Lisa W. Martin, Rasika A. Mathias, James B. Meigs, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Take Naseri, Jeffrey R. O’Connell, Patricia A. Peyser, Bruce M. Psaty, Laura M. Raffield, Susan Redline, Alex P. Reiner, Muagututi‘a Sefuiva Reupena, Kenneth Rice, Stephen S. Rich, Jennifer A. Smith, Kent D. Taylor, Margaret A. Taub, Ramachandran S. Vasan, Daniel E. Weeks, James G. Wilson, Lisa R. Yanek, Wei Zhao, Namiko Abe, Gonçalo R. Abecasis, François Aguet, Christine M. Albert, Laura Almasy, Álvaro Alonso, Seth A. Ament, Peter Anderson, Pramod Anugu, Deborah Applebaum‐Bowden, Kristin Ardlie, Dan E. Arking, Allison E. Ashley‐Koch, Stella Aslibekyan, Tim Assimes, Dimitrios Avramopoulos, Najib Ayas, Adithya Balasubramanian, John Barnard, Kathleen C. Barnes, R. Graham Barr, Emily Barron‐Casella, Lucas Barwick, Terri H. Beaty, Gerald J. Beck, Diane M. Becker, Lewis C. Becker, Rebecca Beer, Amber L. Beitelshees, Emelia J. Benjamin, Takis Benos, Marcos Bezerra, Nathan R. Blue, Russell P. Bowler, Ulrich Broeckel, Jai Broome, Deborah Brown, Karen Bunting, Esteban G. Burchard, Carlos D. Bustamante, Erin Buth, Jonathan Cardwell, Vincent J. Carey, Julie Carrier, April P. Carson, Cara L. Carty, Richard Casaburi, Juan P. Romero, James F. Casella, Peter J. Castaldi, Mark Chaffin, Christy Chang, Yi‐Cheng Chang, Daniel I. Chasman, Sameer Chavan, Bo-Juen Chen, Wei‐Min Chen, Yii‐Der Ida Chen, Michael Cho, Seung Hoan Choi, Lee‐Ming Chuang, Mina K. Chung, Ren‐Hua Chung, Clary B. Clish, Suzy Comhair, Elaine Cornell, Carolyn Crandall, James D. Crapo, Jeffrey L. Curtis, Brian Custer, Coleen Damcott, Dawood Darbar, Sean P. David, Colleen Davis, Michelle Daya, Mariza de Andrade, Lisa de las Fuentes, Michael R. DeBaun, Ranjan Deka, Dawn L. DeMeo, Scott E. Devine, Huyen Dinh, HarshaVardhan Doddapaneni, Qing Duan, Shannon Dugan‐Perez, Jon Peter Durda, Susan K. Dutcher, Charles B. Eaton, Lynette Ekunwe, Adel Boueiz, Patrick T. Ellinor, Leslie S. Emery, Serpil C. Erzurum, Charles R. Farber, Jesse Farek, Tasha E. Fingerlin, Matthew Flickinger, Myriam Fornage, Chris Frazar, Mao Fu, Stephanie M. Fullerton, Lucinda Fulton, Stacey Gabriel, Weiniu Gan, Shanshan Gao, Yan Gao, Margery Gass, Heather Geiger, Bruce D. Gelb, Mark W. Geraci, Søren Germer, Robert E. Gerszten, Auyon Ghosh, Richard A. Gibbs, Chris Gignoux, Mark T. Gladwin, David C. Glahn, Stephanie M. Gogarten, Da‐Wei Gong, Sharon Graw, Kathryn J. Gray, Daniel Grine, Colin Gross, C. Charles Gu, Yue Guan, Namrata Gupta, Michael E. Hall, Yi Han, Patrick J. Hanly, Daniel Harris, Nicola L. Hawley, Jiang He, Ben Heavner, Susan R. Heckbert, Ryan D. Hernandez, David M. Herrington, Craig P. Hersh, Bertha Hidalgo, James E. Hixson, Brian D. Hobbs, John E. Hokanson, Elliott Hong, Karin F. Hoth, Chao A. Hsiung, Jianhong Hu, Yi‐Jen Hung, Haley Huston, Chii Min Hwu, Marguerite R. Irvin, Rebecca D. Jackson, Deepti Jain, Cashell E. Jaquish, Jill M. Johnsen, Andrew M. Johnson, Craig Johnson, Rich Johnston, Kimberly Jones, Hyun Min Kang, Robert C. Kaplan, Sharon L. R. Kardia, Shannon Kelly, Eimear E. Kenny, Michael D. Kessler, Alyna Khan, Ziad Khan, Wonji Kim, John Kimoff, Gregory L. Kinney, Barbara A. Konkle, Holly Kramer, Christoph Lange, Ethan M. Lange, Cathy C. Laurie, Cecelia Laurie, Meryl S. LeBoff, Jiwon Lee, Wen‐Jane Lee, Jonathon LeFaive, David Levine, Joshua P. Lewis, Xiaohui Li, Yun Li, Henry J. Lin, Honghuang Lin, Simin Liu, Yongmei Liu, Yu Liu, Ruth J. F. Loos, Steven A. Lubitz, Kathryn L. Lunetta, James Luo, Ulysses J. Magalang, Michael C. Mahaney, Barry J. Make, JoAnn E. Manson, Melissa Marton, Susan Mathai, Susanne May, Patrick F. McArdle, Merry‐Lynn McDonald, Sean McFarland, Daniel McGoldrick, Caitlin McHugh, Becky McNeil, Hao Mei, Vipin K. Menon, Luisa Mestroni, Ginger Metcalf, Deborah A. Meyers, Emmanuel Mignot, Julie Mikulla, Yuan‐I Min, Mollie Minear, Ryan L. Minster, Matt Moll, Zeineen Momin, Courtney G. Montgomery, Donna M. Muzny, Josyf C. Mychaleckyj, Girish N. Nadkarni, Rakhi P. Naik, Sergeï Nekhai, Sarah C. Nelson, Bonnie Neltner, Caitlin Nessner, Deborah A. Nickerson, Osuji Nkechinyere, Kari E. North, Tim O’Connor, Heather M. Ochs‐Balcom, Geoffrey Okwuonu, Allan I Pack, David T. Paik, James S. Pankow, George Papanicolaou, Juan M. Peralta, Marco Perez, James A. Perry, Ulrike Peters, Lawrence S. Phillips, Jacob Pleiness, Toni I. Pollin, Wendy S. Post, Julia Powers Becker, Meher Preethi Boorgula, Michael Preuß, Pankaj Qasba, Dandi Qiao, Zhaohui Qin, Nicholas Rafaels, Mahitha Rajendran, D. C. Rao, Laura J. Rasmussen‐Torvik, Aakrosh Ratan, Robert M. Reed, Catherine Reeves, Elizabeth A. Regan, Rébecca Robillard, Nicolas Robine, Dan M. Roden, Carolina Roselli, Ingo Ruczinski, Alexi Runnels, Pamela Russell, Sarah Ruuska, Kathleen A. Ryan, Éster Cerdeira Sabino, Danish Saleheen, Shabnam Salimi, Sejal Salvi, Steven L. Salzberg, Kevin Sandow, Vijay G. Sankaran, Jireh Santibanez, Karen Schwander, David Schwartz, Frank C. Sciurba, Christine E. Seidman, Jonathan G. Seidman, Frédéric Sériès, Vivien Sheehan, Stephanie L. Sherman, Amol C. Shetty, Aniket Shetty, Wayne Hui-Heng Sheu, M. Benjamin Shoemaker, B. Silver, Edwin K. Silverman, Robert Skomro, Albert V. Smith, J. G. Smith, Nicholas L. Smith, Tanja Smith, Sylvia Smoller, Beverly Snively, M Snyder, Tamar Sofer, Nona Sotoodehnia, Adrienne M. Stilp, Garrett Storm, Elizabeth A. Streeten, Jessica Lasky‐Su, Jody Sylvia, Adam A. Szpiro, Daniel Taliun, Hua Tang, Matthew R.G. Taylor, Simeon I. Taylor, Marilyn J. Telen, Timothy A. Thornton, Machiko Threlkeld, Lesley Tinker, David Tirschwell, Sarah A. Tishkoff, Hemant K. Tiwari, Catherine Tong, Russell P. Tracy, Michael Y. Tsai, Dhananjay Vaidya, David Van Den Berg, Peter VandeHaar, Scott Vrieze, Tarik Walker, Robert B. Wallace, Avram Walts, Fei Fei Wang, Heming Wang, Jiongming Wang, Karol E. Watson, Jennifer Watt, Joshua Weinstock, Bruce S. Weir, Scott T. Weiss, Lu‐Chen Weng, Jennifer Wessel, Kayleen Williams, L. Keoki Williams, Carla Wilson, Lara Winterkorn, Quenna Wong, Joseph Wu, Huichun Xu, Ivana V. Yang, Ketian Yu, Seyedeh M. Zekavat, Yingze Zhang, Snow Xueyan Zhao, Xiaofeng Zhu, Elad Ziv, Michael C. Zody, Sebastian Zoellner, Elizabeth J. Atkinson, Christie M. Ballantyne, Wei Bao, Romit Bhattacharya, Larry Bielak, Corneliu Bodea, Sarah E. Calvo, Jenna C. Carlson, I‐Shou Chang, So Mi Cho, Ana F. Diallo, Ron Do, Jacqueline S. Dron, Amanda Elliott, Hilary K. Finucane, Caitlin Floyd, Andrea Ganna, Sarah E. Graham, Mary E. Haas, Bernhard Haring, Scott Heemann, Blanca E. Himes, Gail P. Jarvik, Jicai Jiang, Roby Joehanes, Paule V. Joseph, Goo Jun, Masahiro Kanai, Sekar Kathiresan, Amit V. Khera, Sumeet A. Khetarpal, Derek Klarin, Satoshi Koyama, Rozenn N. Lemaître, Changwei Li, Yingchang Lu, Ravi Mathur, Stephen T. McGarvey, John C. McLenithan, Amy Miller, Vamsi K. Mootha, Andrew E. Moran, Tetsushi Nakao, Jeff O’Connell, Christopher J. O’Donnell, Kaavya Paruchuri, Aniruddh P. Patel, Gina M. Peloso, Mary Pettinger, James P. Pirruccello, Samantha L. Rosenthal, Jerome I. Rotter, Shamil Sunyaev, Ida Surakka, Carole Sztalryd, Mark Trinder, Md Mesbah Uddin, Sarah Urbut, Eric Van Buren, Marie Verbanck, Ann Von Holle, Yuxuan Wang, Kerri L. Wiggins, John T. Wilkins, Cristen J. Willer, Brooke N. Wolford, Zhi Yu, Norann A. Zaghloul, Jingwen Zhang, Ying Zhou, Pradeep Natarajan, Xihong Lin
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.
Bibliographic record
VenueNature Methods · 2022
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenetic Associations and Epidemiology
Canadian institutionsUniversity of SaskatchewanUniversité LavalUniversity of OttawaMcGill UniversityUniversity of CalgaryProvidence Health Care
FundersNational Institute on Minority Health and Health DisparitiesNational Center for Advancing Translational SciencesNational Institute of Environmental Health SciencesNational Institute of Neurological Disorders and StrokeNational Institute of General Medical SciencesNational Cancer InstituteNational Human Genome Research InstituteNational Institute of Mental HealthNational Heart, Lung, and Blood InstituteNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institute of Arthritis and Musculoskeletal and Skin DiseasesNational Center for Research ResourcesNational Institute of Allergy and Infectious DiseasesUniversität des SaarlandesNational Institutes of HealthRegeneron PharmaceuticalsNational Institute on AgingQuest DiagnosticsNational Institute on Drug AbuseUniversity of PennsylvaniaBoston Scientific CorporationYale UniversityEli Lilly and CompanyAstraZenecaAmgen
KeywordsComputational biologyGenomeBiologyAnnotationGeneWhole genome sequencingDNA sequencingGeneticsGenome projectGenetic associationGene AnnotationHuman genomeSingle-nucleotide polymorphismGenotype
Abstract
No abstract in any covered source. Its absence is recorded, not treated as a negative.
No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.004
metaresearch head score (Gemma)0.007
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.778
Threshold uncertainty score0.817
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.007 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.059
GPT teacher head0.428
Teacher spread0.369 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itQuick stats
Citations109
Published2022
Admission routes1
Has abstractno