Evidence map›Paper›PMID 35393596›Full record

ArticleNature genetics2022

Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores.

Omer Weissbrod, Masahiro Kanai, Huwenbo Shi, Steven Gazal, Wouter J Peyrot, Amit V Khera, Yukinori Okada, Biobank Japan Project, Alicia R Martin, Hilary K Finucane and 1 more

Open access · greenAbstract read
In one paragraph

Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
185citing papers in PubMed, 4 pooled it
47.3field-weighted citation impact, top 1% 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

185 citing papers in PubMed, 4 syntheses or guidelines pooled it, 272 citations in OpenAlex.

  1. Pooled it
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  4. Predicted Proteome Association Studies of Breast, Prostate, Ovarian, and Endometrial Cancers Implicate Plasma Protein Regulation in Cancer Susceptibility.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2023
    Pooled it
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125 more citing papers are in PubMed but not listed here.

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

11 authors at 16 institutions in 4 countries.

Omer Weissbrod *Epidemiology Department, Harvard School of Public Health, Boston, MA, USA. oweissbrod@hsph.harvard.edu.ORCID http://orcid.org/0000-0001-9860-0626
Masahiro Kanai *Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-5165-4408
Huwenbo Shi *Epidemiology Department, Harvard School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0001-9886-877X
Steven GazalEpidemiology Department, Harvard School of Public Health, Boston, MA, USA.
Wouter J PeyrotEpidemiology Department, Harvard School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0001-7954-8383
Amit V KheraBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yukinori OkadaDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.ORCID http://orcid.org/0000-0002-0311-8472
Biobank Japan Project
Alicia R MartinBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-0241-3522
Hilary K FinucaneBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-3864-9828
Alkes L PriceEpidemiology Department, Harvard School of Public Health, Boston, MA, USA. aprice@hsph.harvard.edu.ORCID http://orcid.org/0000-0002-2971-7975
Tokyo University of Science · JPBroad Institute · USNihon University · JPFukuoka Tokushukai Hospital · JPHarvard University · USJapan Anti Tuberculosis Association · JPShiga University of Medical Science · JPAso Iizuka Hospital · JPIwate Medical University · JPJuntendo University · JPNippon Medical School · JPOsaka National Hospital · JPRIKEN Center for Integrative Medical Sciences · JPSIB Swiss Institute of Bioinformatics · CHTokyo Metropolitan Geriatric Hospital · JPUniversity of Southern California · US

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Ramnik J Xavier · 1991 to 2026
$35.3M
Statistical methods for studies of rare variantsR01MH101244 · NIMH · HARVARD MEDICAL SCHOOL · PI Benjamin Michael Neale, ALKES L PRICE · 2013 to 2026
$9.4M
Statistical methods to localize disease heritability and identify biological mechanismsR37MH107649 · NIMH · BROAD INSTITUTE, INC. · PI Benjamin Michael Neale · 2019 to 2026
$7.0M
Methods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3M
Enabling improved applicability and transferability of polygenic scores across populationsU01HG011719 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI Alicia Martin · 2021 to 2026
$5.5M
Predicting the impact of genetic variants, genes and pathways on human DiseaseU01HG012009 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ALKES L PRICE, Soumya Raychaudhuri · 2021 to 2026
$4.2M
Functionally specialized components of disease heritability in ENCODE dataU01HG009379 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L, RAYCHAUDHURI, SOUMYA · 2017 to 2021
$2.5M
Polygenic prediction of common, complex diseasesK08HG010155 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI KHERA, AMIT VIKRAM · 2018 to 2021
$1.1M
Generalizing polygenic risk prediction methods across populations for insights into psychiatric diseaseR00MH117229 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI MARTIN, ALICIA · 2020 to 2022
$724k
Generalizing polygenic risk prediction methods across populations for insights into psychiatric diseaseK99MH117229 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI MARTIN, ALICIA · 2018 to 2019
$262k
Medical Research Council MC_PC_17228Medical Research Council MC_QA137853NHGRI NIH HHS K08 HG010155NHGRI NIH HHS R01 HG006399NHGRI NIH HHS U01 HG009379NHGRI NIH HHS U01 HG011719NHGRI NIH HHS U01 HG012009NIDDK NIH HHS P30 DK043351NIMH NIH HHS K99 MH117229NIMH NIH HHS R00 MH117229NIMH NIH HHS R01 MH101244NIMH NIH HHS R37 MH107649
6 · The paper itself

Abstract

Polygenic risk scores suffer reduced accuracy in non-European populations, exacerbating health disparities. We propose PolyPred, a method that improves cross-population polygenic risk scores by combining two predictors: a new predictor that leverages functionally informed fine-mapping to estimate causal effects (instead of tagging effects), addressing linkage disequilibrium differences, and BOLT-LMM, a published predictor. When a large training sample is available in the non-European target population, we propose PolyPred

Indexed as

Genome-Wide Association StudyMultifactorial InheritanceHumansLinkage DisequilibriumPolymorphism, Single NucleotideRisk Factors

Identifiers

PMID35393596
PMCPMC9009299
OpenAlexW4223474278

What OpenQuestion holds

Textmetadata
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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.