Evidence map›Paper›PMID 39187616›Full record

ArticleNature genetics2024

Fine-mapping across diverse ancestries drives the discovery of putative causal variants underlying human complex traits and diseases.

Kai Yuan, Ryan J Longchamps, Antonio F Pardiñas, Mingrui Yu, Tzu-Ting Chen, Shu-Chin Lin, Yu Chen, Max Lam, Ruize Liu, Yan Xia and 12 more

Abstract read
In one paragraph

Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 12 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
82citing papers in PubMed, 12 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

82 citing papers in PubMed, 12 syntheses or guidelines pooled it.

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22 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Kai YuanAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-8460-6581
Ryan J LongchampsAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Antonio F PardiñasCentre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.ORCID http://orcid.org/0000-0001-6845-7590
Mingrui YuAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-2749-0690
Tzu-Ting ChenCenter for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan.ORCID http://orcid.org/0000-0001-5669-9066
Shu-Chin LinCenter for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan.
Yu ChenAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Max LamAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-4256-7844
Ruize LiuAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Yan XiaAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Zhenglin GuoStanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Wenzhao ShiDigital Health China Technologies Corp. Ltd, Beijing, China.
Chengguo ShenDigital Health China Technologies Corp. Ltd, Beijing, China.
Schizophrenia Workgroup of Psychiatric Genomics Consortium
Mark J DalyAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-0949-8752
Benjamin M NealeAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-1513-6077
Yen-Chen A FengInstitute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan.
Yen-Feng LinCenter for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan.ORCID http://orcid.org/0000-0003-3017-6026
Chia-Yen ChenBiogen, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9548-5597
Michael C O'DonovanCentre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.ORCID http://orcid.org/0000-0001-7073-2379
Tian GeStanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA. tge1@mgh.harvard.edu.ORCID http://orcid.org/0000-0003-4785-4444
Hailiang HuangAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. hhuang@broadinstitute.org.ORCID http://orcid.org/0000-0003-1461-5762

Funding

Statistical methods for studies of rare variantsR01MH101244 · NIMH · HARVARD MEDICAL SCHOOL · PI Benjamin Michael Neale, ALKES L PRICE · 2013 to 2026
$9.4M
1/4 Asian Bipolar Genetics Network (A-BIG-NET)R01MH130675 · NIMH · BROAD INSTITUTE, INC. · PI Hailiang Huang · 2022 to 2026
$9.0M
Statistical methods to localize disease heritability and identify biological mechanismsR37MH107649 · NIMH · BROAD INSTITUTE, INC. · PI Benjamin Michael Neale · 2019 to 2026
$7.0M
2/7 Psychiatric Genomics Consortium: Finding Actionable VariationU01MH109539 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI DALY, MARK JOSEPH · 2016 to 2020
$4.7M
Identification and characterization of inflammatory bowel disease causal variantsR01DK129364 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Hailiang Huang · 2022 to 2026
$3.4M
Improving Methods and Practices for Trans-Ethnic Genetic StudiesR01HG012354 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI Tian Ge · 2023 to 2026
$2.2M
Genetics and gene regulation in the inflammatory bowel diseasesK01DK114379 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI HUANG, HAILIANG · 2017 to 2021
$632k
Medical Research Council MR/L011794/1NHGRI NIH HHS R01 HG012354NIDDK NIH HHS K01 DK114379NIDDK NIH HHS R01 DK129364NIMH NIH HHS R01 MH101244NIMH NIH HHS R01 MH130675NIMH NIH HHS R37 MH107649NIMH NIH HHS U01 MH109539U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) R01MH130675
6 · The paper itself

Abstract

Genome-wide association studies (GWAS) of human complex traits or diseases often implicate genetic loci that span hundreds or thousands of genetic variants, many of which have similar statistical significance. While statistical fine-mapping in individuals of European ancestry has made important discoveries, cross-population fine-mapping has the potential to improve power and resolution by capitalizing on the genomic diversity across ancestries. Here we present SuSiEx, an accurate and computationally efficient method for cross-population fine-mapping. SuSiEx integrates data from an arbitrary number of ancestries, explicitly models population-specific allele frequencies and linkage disequilibrium patterns, accounts for multiple causal variants in a genomic region and can be applied to GWAS summary statistics. We comprehensively assessed the performance of SuSiEx using simulations. We further showed that SuSiEx improves the fine-mapping of a range of quantitative traits available in both the UK Biobank and Taiwan Biobank, and improves the fine-mapping of schizophrenia-associated loci by integrating GWAS across East Asian and European ancestries.

Indexed as

Chromosome MappingGenome-Wide Association StudyLinkage DisequilibriumPolymorphism, Single NucleotideQuantitative Trait LociComputer SimulationEast Asian PeopleGene FrequencyGenetic Predisposition to DiseaseGenetic VariationGenome, HumanHumansModels, GeneticMultifactorial InheritanceSchizophreniaWhite People

Identifiers

PMID39187616
PMCPMC11888783

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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.