Evidence map›Paper›PMID 27170560›Full record

ArticleGenes and immunity2016

Identification of genetic variants associated with susceptibility to West Nile virus neuroinvasive disease.

D Long, X Deng, P Singh, M Loeb, A S Lauring, M Seielstad

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

Article in Genes and immunity, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed, 1 pooled it
1.8field-weighted citation impact, top 13% 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

10 citing papers in PubMed, 1 synthesis or guideline pooled it, 16 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Outcomes of RIP Kinase Signaling During Neuroinvasive Viral Infection.Current topics in microbiology and immunology · 2023
    Review
  5. Article
  6. Article
  7. Repurposing calcium channel blockers as antiviral drugs.Journal of cell communication and signaling · 2020
    Article
  8. Article
  9. Review
  10. Review
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

6 authors at 3 institutions in 2 countries.

D LongSchool of Medicine, University of California, San Francisco, San Francisco, CA, USA.
X DengDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
P SinghDepartment of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
M LoebDepartment of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
A S LauringDivision of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
M SeielstadDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0001-5783-1401
University of California, San Francisco · USMcMaster University · CAUniversity of Michigan · US

Funding

Clinical and Transtional Science InstituteTL1RR024129 · NCRR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JOHNSTON, S. CLAIBORNE · 2006 to 2011
$2.0M
Clinical and Transtional Science InstituteTL1TR000144 · NCATS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GRANDIS, JENNIFER RUBIN · 2012 to 2015
$643k
Population Dynamics an Evolutionary Capacity of Viral QuasispeciesK08AI081754 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI LAURING, ADAM · 2009 to 2012
$500k
Doris Duke Charitable Foundation 2013105NCATS NIH HHS TL1 TR000144NCRR NIH HHS TL1 RR024129NIAID NIH HHS K08 AI081754
6 · The paper itself

Abstract

West Nile virus (WNV) infection results in a diverse spectrum of outcomes, and host genetics are likely to influence susceptibility to neuroinvasive disease (West Nile neuroinvasive disease (WNND)). We performed whole-exome sequencing of 44 individuals with WNND and identified alleles associated with severe disease by variant filtration in cases, kernel association testing in cases and controls and single-nucleotide polymorphism (SNP) imputation into a larger cohort of WNND cases and seropositive controls followed by genome-wide association analysis. Variant filtration prioritized genes based on the enrichment of otherwise rare variants, but did not unambiguously implicate variants shared by a majority of cases. Kernel association demonstrated enrichment for risk and protective alleles in the human leukocyte antigen (HLA)-A and HLA-DQB1 loci that have well understood roles in antiviral immunity. Two loci, HERC5 and an intergenic region between CD83 and JARID2, were implicated by multiple imputed SNPs and exceeded genome-wide significance in a discovery cohort (n=862). SNPs at two additional loci, TFCP2L1 and CACNA1H, achieved genome-wide significance after association testing of directly genotyped and imputed SNPs in a discovery cohort (n=862) and a separate replication cohort (n=1387). The context of these loci suggests that immunoregulatory, ion channel and endothelial barrier functions may be important elements of the host response to WNV.

Indexed as

Genetic LociPolymorphism, Single NucleotideAdultAgedAntigens, CDCalcium Channels, T-TypeCase-Control StudiesCD83 AntigenFemaleHLA-DQ beta-ChainsHumansImmunoglobulinsIntracellular Signaling Peptides and ProteinsMaleMembrane GlycoproteinsMiddle AgedAntigens, CDCACNA1H protein, humanCalcium Channels, T-TypeCD83 AntigenHERC5 protein, humanHLA-DQB1 antigenHLA-DQ beta-ChainsImmunoglobulinsIntracellular Signaling Peptides and ProteinsJARID2 protein, humanMembrane GlycoproteinsPolycomb Repressive Complex 2Repressor ProteinsTFCP2L1 protein, human

Identifiers

PMID27170560
PMCPMC5215919
OpenAlexW2359868867

What OpenQuestion holds

Textmetadata
LicenceTDM
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.