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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Olivier Delaneau, Jonathan Marchini, Gil McVean, Peter Donnelly, Gerton Lunter, Simon Myers, Anjali Gupta Hinch, Zamin Iqbal, Iain Mathieson, Andy Rimmer, Dionysia K. Xifara, Angeliki Kerasidou, Claire Churchhouse, David Altshuler, Stacey Gabriel, Eric S. Lander, Namrata Gupta, Mark J. Daly, Mark A. DePristo, Eric Banks, Gaurav Bhatia, Mauricio O. Carneiro, Guillermo del Angel, Giulio Genovese, Robert E. Handsaker, Chris Hart, Steven A. McCarroll, James Nemesh, Ryan Poplin, S. F. Schaffner, Khalid Shakir, Pardis C. Sabeti, Sharon R. Grossman, Shervin Tabrizi, Ridhi Tariya, Heng Li, David Reich, Richard Durbin, Matthew E. Hurles, Senduran Balasubramaniam, John H. Burton, Petr Danecek, Thomas Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael A. Quail, Qasim Ayub, Yuan Chen, Alison J. Coffey, Vincenza Colonna, Ni Huang, Luke Jostins, Aylwyn Scally, Klaudia Walter, Yali Xue, Ben Blackburne, Sarah Lindsay, Zemin Ning, Adam Frankish, Jennifer Harrow, Chris Tyler‐Smith, Gonalo R. Abecasis, Hyun Min Kang, Paul Anderson, Tom Blackwell, Fabio Busonero, Christian Fuchsberger, Goo Jun, Andrea Maschio, Eleonora Porcu, Carlo Sidore, Adrian Tan, Mary Kate Trost, David Bentley, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael A. Eberle, Lisa Murray, Richard J. Shaw, Aravinda Chakravarti, Andrew G. Clark, Alon Keinan, Juan L. Rodríguez-Flores, Francisco M. De La Vega, Jeremiah D. Degenhardt, Evan E. Eichler, Paul Flicek, Laura Clarke, Rasko Leinonen, Richard E. Smith, Xiangqun Zheng-Bradley, Kathryn Beal, Fiona Cunningham, Javier Herrero, William McLaren, Graham R. S. Ritchie, Gavin Kelman, Eugene Kulesha, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Ian Streeter, Iliana Toneva, Richard A. Gibbs, Huyen Dinh, Christie Kovar, Lora Lewis, Donna M. Muzny, Jeff Reid, Min Wang, Fuli Yu, Matthew N. Bainbridge, Danny Challis, Uday S. Evani, James T. Lu, Uma Nagaswamy, Aniko Sabo, Yibin Wang, Jin Yu, Gerald Fowler, Walker Hale, Divya Kalra, Eric D. Green, Bartha Maria Knoppers, Jan O. Korbel, Tobias Rausch, Adrian M. Sttz, Charles Lee, Lauren Griffin, Chih-Heng Hsieh, Ryan E. Mills, Marcin von Grotthuss, Chengsheng Zhang, Xinghua Shi, Hans Lehrach, Ralf Sudbrak, Vyacheslav Amstislavskiy, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie‐Laure Yaspo, Sudbrak, Ralf Herwig, Elaine R. Mardis, Richard K. Wilson, Lucinda Fulton, Robert E. Fulton, George M. Weinstock, Asif Chinwalla, Jun Li, David J. Dooling, Daniel C. Koboldt, Michael D. McLellan, John W. Wallis, Michael C. Wendl, Qunyuan Zhang, Gábor Marth, Erik Garrison, Deniz Kural, Wan-Ping Lee, Wen Fung Leong, Alistair Ward, Jiantao Wu, Mengyao Zhang, Deborah A. Nickerson, Can Alkan, Fereydoun Hormozdiari, Arthur Ko, Peter H. Sudmant, Jeanette P. Schmidt, Christopher J. Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Stephen T. Sherry, Chunlin Xiao, Deanna M. Church, Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valérie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas J. Slotta, Hua Zhang, Jun Wang, Xiaodong Fang, Xiaosen Guo, Min Jian, Hui Jiang, Xin Jin, Guoqing Li, Jingxiang Li, Yingrui Li, Xiao Liu, Yao Lu, Xuedi Ma, Shuaishuai Tai, Tang Meifang, Bo Wang, Guangbiao Wang, Honglong Wu, Renhua Wu, Ye Yin, Wenwei Zhang, Jiao Zhao, Meiru Zhao, Xiaole Zheng, Lachlan Coin, Lin Fang, Qibin Li, Zhenyu Li, Haoxiang Lin, Binghang Liu, Ruibang Luo, Haojing Shao, Bingqiang Wang, Yinlong Xie, Chen Ye, Chang Yu, Hancheng Zheng, Hongmei Zhu, Hongyu Cai, Hongzhi Cao, Yeyang Su, Zhongming Tian, Huanming Yang, Ling Yang, Jiayong Zhu, Zhiming Cai, Jian Wang, Marcus W. Albrecht, Tatiana Borodina, Adam Auton, Seungtai Yoon, Jayon Lihm, Vladimir Makarov, Han‐Jun Jin, Wook Kim, Ki Cheol Kim, Srikanth Gottipati, D. A. Jones, D.N. Cooper, Edward V. Ball, Peter D. Stenson, Bret Barnes, Scott D. Kahn, Kai Ye, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Daniel G. MacArthur, Monkol Lek, Mark D. Shriver, Carlos D. Bustamante, Simon Gravel, Eimear E. Kenny, Jeffrey M. Kidd, Phil Lacroute, Brian K. Maples, Andrés Moreno‐Estrada, Fouad Zakharia, Brenna M. Henn, Karla Sandoval, Jake Byrnes, Eran Halperin, Yael Baran, David W. Craig, Alexis Christoforides, Tyler Izatt, Ahmet Kurdoglu, Shripad Sinari, Nils Homer, Kevin Squire, Jonathan Sebat, Vineet Bafna, Kenny Ye, Esteban G. Burchard, Ryan D. Hernandez, Christopher R. Gignoux, David Haussler, Sol Katzman, Wm. Kent, Bryan Howie, Andrés Ruiz‐Linares, Emmanouil T. Dermitzakis, Tuuli Lappalainen, Scott E. Devine, Xinyue Liu, Ankit Maroo, Luke J. Tallon, Jeffrey Rosenfeld, Leslie P. Michelson, Andrea Angius, Francesco Cucca, Serena Sanna, Abigail W. Bigham, Chris Jones, Fred Reinier, Yun Li, Robert Lyons, David Schlessinger, Philip Awadalla, Alan Hodgkinson, Tarás K. Oleksyk, Juan Carlos Martínez‐Cruzado, Yun‐Xin Fu, Xiaoming Liu, Momiao Xiong, Lynn B. Jorde, David J. Witherspoon, Jinchuan Xing, Brian L. Browning, Iman Hajirasouliha, Ken Chen, Cornelis A. Albers, Mark Gerstein, Alexej Abyzov, Jieming Chen, Yao Fu, Lukas Habegger, Arif Harmanci, Xinmeng Jasmine Mu, Cristina Sisu, Suganthi Balasubramanian, Ekta Khurana, Declan Clarke, Jacob J. Michaelson, Chris O’Sullivan, Kathleen C. Barnes, Neda Gharani, Lorraine H. Toji, Norman P. Gerry, Jane Kaye, Alastair Kent, Rasika A. Mathias, Pilar N. Ossorio, Michael Parker, Charles N. Rotimi, Charmaine Royal, Sarah A. Tishkoff, Marc Vía, Walter F. Bodmer, Gabriel Bedoya, Gao Yang, Chu Jia You, Andrés C. García‐Montero, Alberto Órfão, Julie Dutil, Lisa Brooks, Adam L. Felsenfeld, Jean E. McEwen, Nicholas C. Clemm, Mark S. Guyer, Jane L. Peterson, Audrey Duncanson, Michael J. Dunn, Leena Peltonenz
Bibliographic record
VenueNature Communications · 2014
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenetic Associations and Epidemiology
Canadian institutionsSimon Fraser UniversityUniversité de MontréalCentre Hospitalier Universitaire Sainte-JustineMcGill UniversityMcGill University and Génome Québec Innovation Centre
FundersNational Institute on Minority Health and Health DisparitiesNational Institute of Environmental Health SciencesNational Human Genome Research InstituteBiotechnology and Biological Sciences Research CouncilNational Cancer InstituteMedical Research CouncilWellcome Trust
KeywordsHaplotypeImputation (statistics)1000 Genomes ProjectSingle-nucleotide polymorphismIndelGeneticsGenome-wide association studyHaplotype estimationSNPBiologyGenomeReference genomeGenotypeWhole genome sequencingComputational biologyTag SNPGenomicsComputer scienceGeneMissing data
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.
How this classification was reachedexpand
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)0.001
metaresearch head score (Gemma)0.001
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: Empirical · Consensus signal: Empirical
Teacher disagreement score0.917
Threshold uncertainty score0.434
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| 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 head0.120
GPT teacher head0.377
Teacher spread0.257 · 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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations457
Published2014
Admission routes1
Has abstractno