Evidence map›Paper›PMID 23941231›Full record

ArticleAnnals of human genetics2013

Secondary analysis of publicly available data reveals superoxide and oxygen radical pathways are enriched for associations between type 2 diabetes and low-frequency variants.

Mojgan Yazdanpanah, Chuhua Chen, Jinko Graham

Abstract read
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In one paragraph

Article in Annals of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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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

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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

2 citing papers in PubMed.

  1. Article
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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

3 authors.

Mojgan YazdanpanahBritish Columbia Clinical Genomics Network, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Chuhua Chen
Jinko Graham

Funding

Statistical MethodsP01CA087969 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI TWOROGER, SHELLEY S · 2000 to 2019
$77.8M
Validity of Diet and Activity Measures in WomenP01CA055075 · NCI · HARVARD UNIVERSITY (SCH OF PUBLIC HLTH) · PI WILLETT, WALTER C. · 1991 to 2009
$41.8M
A Center for GEI Association StudiesU01HG004424 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY · 2007 to 2010
$21.4M
Statistical Analysis and ProgrammingU19CA055075 · NCI · HARVARD SCHOOL OF PUBLIC HEALTH · PI RIMM, ERIC B · 2010 to 2011
$8.4M
BIOCHEMICAL AND GENETIC MARKERS OF TYPE 2 DIABETES RISKR01DK058845 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI HU, FRANK B · 2001 to 2013
$7.8M
Genome Wide Association Coordinating CenterU01HG004446 · NHGRI · UNIVERSITY OF WASHINGTON · PI WEIR, BRUCE S. · 2007 to 2011
$6.6M
Genes and Environment Initiatives in Type 2 DiabetesU01HG004399 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI HU, FRANK B · 2007 to 2008
$1.2M
NCI NIH HHS CA55075NCI NIH HHS CA87969NCI NIH HHS P01 CA055075NCI NIH HHS P01 CA087969NCI NIH HHS U19 CA055075NHGRI NIH HHS U01 HG004399NHGRI NIH HHS U01HG004399NHGRI NIH HHS U01 HG004424NHGRI NIH HHS U01HG004424NHGRI NIH HHS U01 HG004446NIDDK NIH HHS DK58845NIDDK NIH HHS R01 DK058845
6 · The paper itself

Abstract

Genome-wide association studies explain at most 5%-10% of the heritable components of type 2 diabetes. Some of the "missing type 2 diabetes heritability" could be explained by low-frequency variants. We examined the associations between low-frequency variants and type 2 diabetes, using data from 2538 diabetic and 2977 nondiabetic subjects in the publicly available database of Genotypes and Phenotypes. We applied two approaches. First, we combined information from all low-frequency (1%-5%) variants at a locus in a gene-centric analysis of associations with diabetes. Next, we searched for gene ontology (GO) biological processes that were enriched for gene-centric associations, after correcting for multiple testing to control the false discovery rate (FDR). We found three GO biological processes that were significantly enriched for associations to diabetes: "response to superoxide" (FDR-adjusted p=2.7×10(-3)), "response to oxygen radical" (FDR-adjusted p=2.7×10(-3)), and "heart contraction" (FDR-adjusted p=2.6×10(-2)). There were three genes that contributed to "response to superoxide" and "oxygen radical" pathways, including the SOD1 gene. Gene-centric tests of association with low-frequency variants, followed by analysis to evaluate which biological pathways are enriched for these associations has the potential to recover, at least some proportion of, the "missing heritability" of type 2 diabetes.

Indexed as

Genetic VariationMetabolic Networks and PathwaysDatabases, GeneticDiabetes Mellitus, Type 2FemaleGene FrequencyGenome-Wide Association StudyHumansMalePolymorphism, Single NucleotideReactive Oxygen SpeciesSuperoxidesReactive Oxygen SpeciesSuperoxidescollapsing methodpathway analysisRare variantsSOD1superoxide and oxygen radical pathwaystype 2 diabetes

Identifiers

PMID23941231
PMCPMC4254771

What OpenQuestion holds

Textmetadata
LicenceTDM
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Registered trials

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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.