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Whole-genome sequencing of patients with rare diseases in a national health system
Ernest Turro, Karyn Mégy, Olga Shamardina, Hana Lango Allen, Alba Sanchis‐Juan, Mattia Frontini, Chantal Thys, Jonathan Stephens, Rutendo Mapeta, Oliver S. Burren, Kate Downes, Matthias Haimel, Salih Tuna, Sri V. V. Deevi, Timothy J. Aitman, David Bennett, Keren Carss, Patrick F. Chinnery, Peter Dixon, Daniel P. Gale, Ania Koziell, Eamonn R. Maher, Hugh S. Markus, Nicholas W. Morrell, Andrew Mumford, Augusto Rendon, Sylvia Richardson, Irene Roberts, Noémi Roy, Hannah Stark, Rhea Tan, Hugh Watkins, Andrew R. Webster, Catherine Williamson, Stephen Abbs, Lara Abulhoul, Julian Adlard, Munaza Ahmed, Hana Alachkar, David Allsup, J. P. Almeida, Philip Ancliff, Richard Antrobus, Ruth Armstrong, Gavin Arno, Anthony Attwood, Paul Aurora, Christian Babbs, Chiara Bacchelli, Tamam Bakchoul, Siddharth Banka, Tadbir K. Bariana, Julian Barwell, Joana Batista, Helen Baxendale, Phil Beales, Agnieszka Bierżyńska, Tina Biss, Maria Bitner‐Glindzicz, Graeme C. Black, Marta Bleda, Iulia Blesneac, Detlef Böckenhauer, Harm Jan Bogaard, Christian Bourne, Sara Boyce, John R. Bradley, Eugene Bragin, Gerome Breen, Paul Brennan, Carole Brewer, Matthew A. Brown, Andrew C. Browning, Michael J. Browning, Rachel Buchan, Matthew Buckland, Teofila Bueser, Carmen Bugarin Diz, John Burn, Siobhan O. Burns, Nigel Burrows, Carolyn Campbell, Gerald Carr‐White, Ruth Casey, Jenny Chambers, John C. Chambers, Melanie Chan, Floria Cheng, Manali Chitre, Martin Christian, Colin Church, Jill Clayton‐Smith, Maureen Cleary, Naomi Clements Brod, Gerry Coghlan, Elizabeth Colby, Trevor Cole, Janine Collins, Peter W. Collins, Camilla Colombo, Cecilia Compton, Robin Condliffe, Stuart A. Cook, H. Terence Cook, Nichola Cooper, Paul A. Corris, Abigail Furnell, Fiona Cunningham, Nicola Curry, Antony J. Cutler, Matthew J. Daniels, Mehul Dattani, Louise C. Daugherty, John Davis, Anthony De Soyza, Timothy Dent, Charu Deshpande, Eleanor Dewhurst, Sofia Douzgou, Anna M. Drazyk, Elizabeth Drewe, Daniel Duarte, Tina Dutt, David Edgar, Karen L. Edwards, William Egner, Melanie N. Ekani, Perry Elliott, Wendy N. Erber, Marie Erwood, Maria C. Estiú, D. Gareth Evans, Gillian Evans, Tamara Everington, Mélanie Eyries, Hiva Fassihi, Rémi Favier, Jack Findhammer, Debra Fletcher, Frances Flinter, R. Andrés Floto, Tom Fowler, James Fox, Amy Frary, Courtney E. French, Kathleen Freson, Henning Gall, Vijeya Ganesan, Michael Gattens, Claire Geoghegan, Terence S. A. Gerighty, Ali G. Gharavi, Stefano Ghio, J. Simon R. Gibbs, Kate Gibson, Kimberly Gilmour, Barbara Girerd, Nicholas Gleadall, Sarah Goddard, David B. Goldstein, Keith Gomez, Pavels Gordins, David Gosal, Jodie Graham, Luigi Grassi, Lynn Greenhalgh, Andreas Greinacher, Paolo Gresele, Philip G. Griffiths, Sofia Grigoriadou, Russell Grocock, Detelina Grozeva, Mark Gurnell, Scott Hackett, Charaka Hadinnapola, William M. Hague, Rosie Hague, Matthew Hall, Helen Hanson, Eshika Haque, Kirsty Harkness, Andrew R. Harper, Claire L. Harris, Daniel P. Hart, Ahamad Hassan, Grant Hayman, Alex Henderson, Archana Herwadkar, Jonathan Hoffman, Simon Holden, Rita Horváth, Henry Houlden, Arjan C. Houweling, Luke Howard, Fengyuan Hu, Gavin Hudson, Joseph Hughes, Aarnoud Huissoon, Marc Humbert, Sarah Hunter, Matthew E. Hurles, Melita Irving, Louise Izatt, Sally Johnson, Stephen Jolles, Jennifer Jolley, Dragana Josifova, Neringa Jurkutė, Tim Karten, Johannes Karten, Mary Kasanicki, Hanadi Kazkaz, Rashid Kazmi, Peter Kelleher, Anne M. Kelly, Wilf Kelsall, Carly Kempster, David G. Kiely, Nathalie Kingston, Robert Klima, Nils Koelling, Myrto Kostadima, Gábor Kovács, Roman Kreuzhuber, Taco W. Kuijpers, Ajith Kumar, Dinakantha Kumararatne, Manju A. Kurian, Fiona Lalloo, Michele P. Lambert, Allan Lawrie, D. Mark Layton, Nicholas Lench, Claire Lentaigne, Tracy Lester, Rachel Linger, Hilary Longhurst, Lorena Lorenzo, Eleni Louka, Paul Lyons, Rajiv D. Machado, Robert V. MacKenzie Ross, Bella Madan, Jesmeen Maimaris, Samantha Malka, Sarah Mangles, Kevin J. Marchbank, Stephen D. Marks, Hanns–Ulrich Marschall, Andrew Marshall, Jennifer M. Martin, Mary Mathias, Emma Matthews, Heather Maxwell, Paul McAlinden, Mark I. McCarthy, Harriet McKinney, Aoife McMahon, Stuart Meacham, Adam J. Mead, Ignacio Medina Castello, Sarju Mehta, Michel Michaelides, Carolyn M. Millar, Shehla Mohammed, Shahin Moledina, David Montani, Anthony T. Moore, Monika Mozere, Keith W. Muir, Andrea H. Németh, William G. Newman, Michael Newnham, Sadia Noorani, Paquita Nurden, Jennifer O’Sullivan, Samya Obaji, Chris A. Odhams, Steven Okoli, Andrea Olschewski, Horst Olschewski, Kai Ren Ong, S. Oram, Willem H. Ouwehand, Claire Palles, Sofia Papadia, Soo‐Mi Park, David Parry, Smita Y. Patel, Joan Paterson, Andrew J. Peacock, Simon H. S. Pearce, John F. Peden, Kathelijne Peerlinck, Christopher J. Penkett, Joanna Pepke‐Żaba, R. Petersen, Clarissa Pilkington, Kenneth Poole, Radhika Prathalingam, Bethan Psaila, Angela Pyle, Richard Quinton, Shamima Rahman, Anupama Rao, F. Lucy Raymond, Paula Rayner-Matthews, Christine A. Rees, Tara Renton, Christopher J. Rhodes, Andrew S.C. Rice, Alex Richter, Leema Robert, Anthony S. Rogers, Sarah J. Rose, Robert Ross‐Russell, Catherine Roughley, Deborah Ruddy, Omid Sadeghi‐Alavijeh, Nilesh J. Samani, Crina Samarghitean, Ravishankar Sargur, Robert N. Sarkany, Simon C. Satchell, Sinisa Savic, John A. Sayer, Genevieve Sayer, Laura Scelsi, Andrew M. Schaefer, Sol Schulman, Richard H. Scott, Marie Scully, Claire Searle, Werner Seeger, Arjune Sen, William A. Sewell, Denis Seyres, Neil V. Shah, Susan Shapiro, Adam Shaw, Patrick Short, Keith Sibson, Lucy Side, Ilenia Simeoni, Michael A. Simpson, Matthew C. Sims, Suthesh Sivapalaratnam, Damian Smedley, Katherine R. Smith, Katie Snape, Nicole Soranzo, Florent Soubrier, Laura Southgate, Olivera Spasić-Bošković, Simon Staines, Emily Staples, Charles A. Steward, Kathleen Stirrups, Alexander Stuckey, Jay Suntharalingam, Emilia M. Swietlik, Petros Syrris, Robert C. Tait, Kate Talks, Katie Tate, John Taylor, Jenny C. Taylor, James E. Thaventhiran, Ellen Thomas, David Thomas, Moira Thomas, Patrick Thomas, Kate Thomson, Glen Threadgold, Tobias Tilly, Marc Tischkowitz, Catherine Titterton, John A. Todd, Cheng‐Hock Toh, Bas Tolhuis, Ian Tomlinson, Mark Toshner, Matthew Traylor, Carmen Treacy, Paul Treadaway, Richard C. Trembath, Wojciech Turek, Philip Twiss, Tom Vale, Chris Van Geet, Natalie R. van Zuydam, Maarten Vandekuilen, Anthony M. Vandersteen, Marta Vazquez‐Lopez, Julie von Ziegenweidt, Anton Vonk Noordegraaf, Annette Wagner, Quinten Waisfisz, Suellen M. Walker, Neil Walker, Klaudia Walter, James S. Ware, C. Ian F. Watt, Lucy R. Wedderburn, Wei Wei, Steven Welch, Julie Wessels, Sarah K. Westbury, John‐Paul Westwood, John Wharton, Deborah Whitehorn, Andrew O.M. Wilkie, Brian T. Wilson, Edwin Wong, Nicholas Wood, Yvette Wood, C. Geoffrey Woods, Emma R. Woodward, Stephen J. Wort, Austen Worth, Michael Wright, Katherine Yates, Patrick Yong, Timothy M. Young, Ping Yu, Patrick Yu‐Wai‐Man, Eliska Zlamalova
Bibliographic record
VenueNature · 2020
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Rare Diseases
Canadian institutionsIzaak Walton Killam Health CentreDalhousie University
FundersMedical Research CouncilNorthwest Regional Development AgencyRosetrees TrustDiabetes UKNational Institute for Health and Care ResearchKidney Research UKNIHR BioResourceCancer Research UKBowel Cancer UKBarts CharityNHS Blood and TransplantSight Research UKScottish GovernmentBritish Heart FoundationWellcome Trust
KeywordsGenomeWhole genome sequencingComputational biologyBiologyGeneticsMedicineGene
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 machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.002
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Observational · Consensus signal: Observational
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.045
Threshold uncertainty score0.089
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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 head0.006
GPT teacher head0.221
Teacher spread0.215 · 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 source (direct Gemma or distilled Codex), not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designObservational
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
Citations582
Published2020
Admission routes1
Has abstractno