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Record W2611574484 · doi:10.1016/j.ajhg.2017.04.003

International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases

2017· article· en· W2611574484 on OpenAlexafffund
Kym M. Boycott, Ana Rath, Jessica X. Chong, Taila Hartley, Fowzan S. Alkuraya, Gareth Baynam, Anthony J. Brookes, Michael Brudno, Ángel Carracedo, Johan T. den Dunnen, Stephanie O. M. Dyke, Xavier Estivill, Jack Goldblatt, Catherine Gonthier, Stephen C. Groft, Marta Gut, Ada Hamosh, Philip Hieter, Sophie Höhn, Matthew E. Hurles, Petra Kaufmann, Bartha Maria Knoppers, Jeffrey P. Krischer, Milan Maçek, Gert Matthijs, Annie Olry, Samantha Parker, Justin Paschall, Anthony Philippakis, Heidi L. Rehm, Peter N. Robinson, Pak C. Sham, Румен Стефанов, Domenica Taruscio, Divya Unni, Megan R. Vanstone, Feng Zhang, Han G. Brunner, Michael J. Bamshad, Hanns Lochmüller

Bibliographic record

VenueThe American Journal of Human Genetics · 2017
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Rare Diseases
Canadian institutionsCanada's Michael Smith Genome Sciences CentreUniversity of TorontoUniversity of British ColumbiaMcGill UniversityChildren's Hospital of Eastern OntarioUniversity of Ottawa
FundersNational Human Genome Research InstituteNational Heart, Lung, and Blood InstituteMedical Research CouncilOntario Genomics InstituteCanadian Institutes of Health ResearchGenome CanadaOntario GenomicsWellcome TrustEuropean CommissionJohns Hopkins UniversityUniversity of Washington
KeywordsComputer scienceComputational biologyBiology

Abstract

fetched live from OpenAlex

Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not 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)0.025
metaresearch head score (Gemma)0.022
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.030
Threshold uncertainty score0.135

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0250.022
Meta-epidemiology (narrow)0.0010.000
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0030.002
Science and technology studies0.0020.002
Scholarly communication0.0030.002
Open science0.0020.008
Research integrity0.0040.006
Insufficient payload (model declined to judge)0.0300.011

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 head0.015
GPT teacher head0.292
Teacher spread0.277 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine 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 designNot applicable
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

Citations453
Published2017
Admission routes2
Has abstractyes

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