Evidence map›Paper›PMID 38297326›Full record

ArticleGenome biology2024

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci.

Sarah Fazal, Matt C Danzi, Isaac Xu, Shilpa Nadimpalli Kobren, Shamil Sunyaev, Chloe Reuter, Shruti Marwaha, Matthew Wheeler, Egor Dolzhenko, Francesca Lucas and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
5.1field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed, 20 citations in OpenAlex.

  1. Article
  2. Population-scale detection of methylation outliers from long-read genome sequencing.medRxiv : the preprint server for health sciences · 2026
    Article
  3. Review
  4. Article
  5. Review
  6. A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.Genetics in medicine : official journal of the American College of Medical Genetics · 2025
    Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Review
  13. Article
  14. Article
  15. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 5 institutions in 2 countries.

Sarah FazalDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
Matt C DanziDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
Isaac XuDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
Shilpa Nadimpalli KobrenDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, 02155, USA.
Shamil SunyaevDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, 02155, USA.
Chloe ReuterStanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA.
Shruti MarwahaStanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA.
Matthew WheelerStanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA.
Egor DolzhenkoIllumina Inc., San Diego, CA, 92112, USA.
Francesca LucasDepartment of Computer Science, Delft University of Technology, Delft, The Netherlands.
Stefan WuchtyDepartment of Computer Science, University of Miami, Miami, FL, USA.
Mustafa TekinDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
Stephan ZüchnerDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA. szuchner@med.miami.edu.ORCID 0000-0002-8498-5235
Vanessa Aguiar-PulidoDepartment of Computer Science, University of Miami, Miami, FL, USA.
University of Miami · USStanford University · USHarvard University · USDelft University of Technology · NLIllumina (United States) · US

Funding

GENOME STUDIES IN HEREDITARY SPASTIC PARAPLEGIA - beyond the exomeR01NS072248 · NINDS · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI Stephan Zuchner · 2011 to 2026
$9.2M
NINDS NIH HHS R01 NS072248
6 · The paper itself

Abstract

Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.

Indexed as

Machine LearningTandem Repeat SequencesVirulenceMachine learningRare diseasesRepeat expansions

Identifiers

PMID38297326
PMCPMC10832122
OpenAlexW4391380715

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.