Evidence map›Paper›PMID 39375560›Full record

ReviewNature reviews. Genetics2025

Genome-wide association testing beyond SNPs.

Laura Harris, Ellen M McDonagh, Xiaolei Zhang, Katherine Fawcett, Amy Foreman, Petr Daneck, Panagiotis I Sergouniotis, Helen Parkinson, Francesco Mazzarotto, Michael Inouye and 3 more

Abstract readReview
In one paragraph

Review in Nature reviews. Genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

25 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Review
  12. Article
  13. Article
  14. Article
  15. Review
  16. Article
  17. Article
  18. Article
  19. Review
  20. Article
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

13 authors.

Laura Harris *European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Ellen M McDonagh *European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Xiaolei Zhang *European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Katherine FawcettEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Amy ForemanEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Petr DaneckWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Panagiotis I SergouniotisEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0003-0986-4123
Helen ParkinsonEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Francesco MazzarottoDepartment of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
Michael InouyeBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0001-9413-6520
Edward J HolloxDepartment of Genetics and Genome Biology, University of Leicester, Leicester, UK.ORCID http://orcid.org/0000-0002-0115-2298
Ewan BirneyEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK.
Tomas FitzgeraldEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UK. tomas@ebi.ac.uk.ORCID http://orcid.org/0000-0002-2370-8496

Funding

GWAS CatalogU41HG007823 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI PARKINSON, HELEN ELIZABETH · 2014 to 2021
$6.7M
Strengthening community knowledge bases for genetic association studies and polygenic scores, the GWAS and PGS CatalogsU24HG012542 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Michael Inouye, Helen Elizabeth Parkinson · 2022 to 2026
$5.2M
NHGRI NIH HHS U24 HG012542NHGRI NIH HHS U41 HG007823
6 · The paper itself

Abstract

Decades of genetic association testing in human cohorts have provided important insights into the genetic architecture and biological underpinnings of complex traits and diseases. However, for certain traits, genome-wide association studies (GWAS) for common SNPs are approaching signal saturation, which underscores the need to explore other types of genetic variation to understand the genetic basis of traits and diseases. Copy number variation (CNV) is an important source of heritability that is well known to functionally affect human traits. Recent technological and computational advances enable the large-scale, genome-wide evaluation of CNVs, with implications for downstream applications such as polygenic risk scoring and drug target identification. Here, we review the current state of CNV-GWAS, discuss current limitations in resource infrastructure that need to be overcome to enable the wider uptake of CNV-GWAS results, highlight emerging opportunities and suggest guidelines and standards for future GWAS for genetic variation beyond SNPs at scale.

Indexed as

DNA Copy Number VariationsGenome-Wide Association StudyPolymorphism, Single NucleotideGenetic Predisposition to DiseaseGenome, HumanHumansMultifactorial Inheritance

Identifiers

PMID39375560
PMCPMC12329314

What Socratic holds

Textmetadata
LicenceTDM
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 Socratic graph.