Evidence map›Paper›PMID 33669563›Full record

ArticleJournal of personalized medicine2021

The Role of SNP Interactions when Determining Independence of Novel Signals in Genetic Association Studies-An Application to

Ryan Walsh, Kirsten Voorhies, Merry-Lynn McDonald, Michael McGeachie, Joanne E Sordillo, Christoph Lange, Ann Chen Wu, Sharon M Lutz

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

Article in Journal of personalized medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 98% 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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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

8 authors at 3 institutions in 1 country.

Ryan WalshDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA.
Kirsten VoorhiesDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA.
Merry-Lynn McDonaldDivision of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Michael McGeachieChanning Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Joanne E SordilloDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA.
Christoph LangeDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
Ann Chen WuDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA.ORCID 0000-0003-0599-9063
Sharon M LutzDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA.
Harvard University · USBrigham and Women's Hospital · USUniversity of Alabama at Birmingham · US

Funding

Genetic Epidemiology of COPDU01HL089897 · NHLBI · NATIONAL JEWISH HEALTH · PI CRAPO, JAMES D · 2007 to 2021
$56.9M
Genetic Epidemiology of COPDU01HL089856 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI SILVERMAN, EDWIN K · 2007 to 2021
$20.7M
Asthma Exacerbations and MicroRNA prediction: Treatment Response in an Underserved Ethnicity (AEM-TRUE)R01HL139634 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI MCGEACHIE, MICHAEL JOHN · 2018 to 2022
$4.3M
Age-Dependent Pharmacogenomics of Asthma Treatment (ADAPT)R01HD085993 · NICHD · HARVARD PILGRIM HEALTH CARE, INC. · PI WU, ANN CHEN · 2016 to 2020
$3.1M
Common Genetic Pathways Underlying CVD and COPDK01HL125858 · NHLBI · UNIVERSITY OF COLORADO DENVER · PI LUTZ, SHARON MARIE · 2015 to 2019
$721k
Eunice Kennedy Shriver National Institute of Child Health and Human Development R01HD085993NHLBI NIH HHS K01 HL125858NHLBI NIH HHS K01HL125858NHLBI NIH HHS R01 HL139634NHLBI NIH HHS U01HL089856NHLBI NIH HHS U01HL089897
6 · The paper itself

Abstract

Genome-wide association studies (GWAS) play a critical role in identifying many loci for common diseases and traits. There has been a rapid increase in the number of GWAS over the past decade. As additional GWAS are being conducted, it is unclear whether a novel signal associated with the trait of interest is independent of single nucleotide polymorphisms (SNPs) in the same region that has been previously associated with the trait of interest. The general approach to determining whether the novel association is independent of previous signals is to examine the association of the novel SNP with the trait of interest conditional on the previously identified SNP and/or calculate linkage disequilibrium (LD) between the two SNPs. However, the role of epistasis and SNP by SNP interactions are rarely considered. Through simulation studies, we examined the role of SNP by SNP interactions when determining the independence of two genetic association signals. We have created an R package on Github called gxgRC to generate these simulation studies based on user input. In genetic association studies of asthma, we considered the role of SNP by SNP interactions when determining independence of signals for SNPs in the

Indexed as

ARG1bronchodilator responseepistasisGWASindependenceSNP by SNP interactions

Identifiers

PMID33669563
PMCPMC7922125
OpenAlexW3132297604

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.