Evidence map›Paper›PMID 27482468›Full record

ArticleNPJ genomic medicine

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions.

Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardeux, Jianrong Li, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S Ramos and 4 more

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

Article in NPJ genomic medicine. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed, 1 pooled it
2.7field-weighted citation impact, top 10% 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

14 citing papers in PubMed, 1 synthesis or guideline pooled it, 23 citations in OpenAlex.

  1. Pooled it
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  3. Review
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  7. On fusion methods for knowledge discovery from multi-omics datasets.Computational and structural biotechnology journal · 2020
    Review
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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

14 authors at 6 institutions in 1 country.

Haiquan LiBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA.
Ikbel AchourBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA.
Lisa BastaracheDepartments of Biomedical Informatics and Medicine, Vanderbilt University, TN, USA.
Joanne BerghoutBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA.
Vincent GardeuxBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA.
Jianrong LiBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA.
Younghee LeeSection of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA.
Lorenzo PesceComputation Institute, Argonne National Laboratory and University of Chicago, IL, USA.
Xinan YangSection of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA; Department of Pediatrics, University of Chicago, USA.
Kenneth S RamosDepartment of Medicine, University of Arizona, Tucson, AZ, USA.
Ian FosterComputation Institute, Argonne National Laboratory and University of Chicago, IL, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Chicago, IL, USA; Department of Computer Science, University of Chicago, Chicago, IL, USA.
Joshua C DennyDepartments of Biomedical Informatics and Medicine, Vanderbilt University, TN, USA.
Jason H MooreDepartment of Genetics, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA; Penn Institute for Biomedical Informatics, Perelman School of Medicine, the University of Pennsylvania, PA, USA.
Yves A LussierBIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA; Computation Institute, Argonne National Laboratory and University of Chicago, IL, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory & University of Chicago, IL, USA; University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA; Section for Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, USA; Department of Biopharmaceutical Sciences, University of Illinois at Chicago, IL, USA.
University of Arizona · USArgonne National Laboratory · USVanderbilt University · USDartmouth College · USUniversity of Chicago · USUniversity of Illinois Chicago · US

Funding

VITAMIN AP30CA023074 · NCI · UNIVERSITY OF ARIZONA · PI Dan Theodorescu · 1985 to 2026
$110.2M
VANDERBILT UNIVERSITY CTSA FOR PEDIATRIC RESEARCHUL1RR024975 · NCRR · VANDERBILT UNIVERSITY · PI BERNARD, GORDON RAPHAEL · 2007 to 2011
$45.7M
The Vanderbilt Institute for Clinical and Translational Research (VICTR)UL1TR000445 · NCATS · VANDERBILT UNIVERSITY MEDICAL CENTER · PI BERNARD, GORDON RAPHAEL · 2012 to 2016
$41.4M
Translational Research Support CoreP30ES013508 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI Rebecca A Simmons · 2006 to 2026
$35.3M
Center for Clinical and Translational ScienceUL1TR000050 · NCATS · UNIVERSITY OF ILLINOIS AT CHICAGO · PI AZAR, DIMITRI T, MERMELSTEIN, ROBIN J. · 2012 to 2014
$9.8M
Beagle: A Supercomputer for Computational Biology, Simulation, and Data AnalysisS10RR029030 · NCRR · UNIVERSITY OF CHICAGO · PI FOSTER, IAN · 2010 to 2010
$7.0M
From GWAS to PheWAS: Scanning the EMR Phenome for Gene-disease AssociationsR01LM010685 · NLM · VANDERBILT UNIVERSITY MEDICAL CENTER · PI BASTARACHE, LISA · 2011 to 2022
$6.3M
Bioinformatics Strategies for Genome-Wide Association StudiesR01LM010098 · NLM · UNIVERSITY OF PENNSYLVANIA · PI MOORE, JASON H., WILLIAMS, SCOTT MATTHEW · 2009 to 2023
$5.1M
Machine Learning Prediction of Cancer SusceptibilityR01LM009012 · NLM · UNIVERSITY OF PENNSYLVANIA · PI MOORE, JASON H. · 2006 to 2014
$3.3M
Semantic Approaches to Phenotypic Databases AnalysesK22LM008308 · NLM · UNIVERSITY OF CHICAGO · PI LUSSIER, YVES A · 2004 to 2006
$468k
NCATS NIH HHS UL1 TR000050NCATS NIH HHS UL1 TR000445NCI NIH HHS P30 CA023074NCRR NIH HHS S10 RR029030NCRR NIH HHS UL1 RR024975NIEHS NIH HHS P30 ES013508NLM NIH HHS K22 LM008308NLM NIH HHS R01 LM009012NLM NIH HHS R01 LM010098NLM NIH HHS R01 LM010685
6 · The paper itself

Abstract

Functionally altered biological mechanisms arising from disease-associated polymorphisms, remain difficult to characterize when those variants are intergenic, or, fall between genes. We sought to identify shared downstream mechanisms by which inter- and intragenic single nucleotide polymorphisms (SNPs) contribute to a specific physiopathology. Using computational modeling of 2 million pairs of disease-associated SNPs drawn from genome wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology functional annotations, we predicted 3,870 inter-intra and inter-intra SNP pairs with convergent biological mechanisms (FDR<0.05). These prioritized SNP pairs with overlapping mRNA targets or similar functional annotations were more likely to be associated with the same disease than unrelated pathologies (OR>12). We additionally confirmed synergistic and antagonistic genetic interactions for a subset of prioritized SNP pairs in independent studies of Alzheimer's disease (entropy p=0.046), bladder cancer (entropy p=0.039), and rheumatoid arthritis (PheWAS case-control p<10

Identifiers

PMID27482468
PMCPMC4966659
OpenAlexW2343211263

What OpenQuestion holds

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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.