Evidence map›Paper›PMID 38168385›Full record

ArticleResearch square2023

Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.

Martin Jinye Zhang, Arun Durvasula, Colby Chiang, Evan M Koch, Benjamin J Strober, Huwenbo Shi, Alison R Barton, Samuel S Kim, Omer Weissbrod, Po-Ru Loh and 3 more

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In one paragraph

Article in Research square, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in
0citing papers in PubMed
–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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Martin Jinye ZhangRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.ORCID 0000-0003-0006-2466
Arun DurvasulaDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0003-0631-3238
Colby ChiangDepartment of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
Evan M KochDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Benjamin J StroberDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Huwenbo ShiDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Alison R BartonDepartment of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.ORCID 0000-0003-0882-0196
Samuel S KimDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0003-0491-0784
Omer WeissbrodDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Po-Ru LohProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-5542-9064
Steven GazalCenter for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California.ORCID 0000-0003-4510-5730
Shamil SunyaevDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-5715-5677
Alkes L PriceDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0002-2971-7975

Funding

TRAINING GRANT IN GENETICST32GM007748 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Anne O'Donnell-Luria, Louise Wilkins-Haug · 1985 to 2026
$12.0M
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
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
NHGRI NIH HHS R01 HG006399NHGRI NIH HHS U01 HG009379NHGRI NIH HHS U01 HG012009NIGMS NIH HHS T32 GM007748NIMH NIH HHS R01 MH101244NIMH NIH HHS R37 MH107649
6 · The paper itself

Abstract

The genetic architecture of human diseases and complex traits has been extensively studied, but little is known about the relationship of causal disease effect sizes between proximal SNPs, which have largely been assumed to be independent. We introduce a new method, LD SNP-pair effect correlation regression (LDSPEC), to estimate the correlation of causal disease effect sizes of derived alleles between proximal SNPs, depending on their allele frequencies, LD, and functional annotations; LDSPEC produced robust estimates in simulations across various genetic architectures. We applied LDSPEC to 70 diseases and complex traits from the UK Biobank (average

Identifiers

PMID38168385
PMCPMC10760228

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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.