Evidence map›Paper›PMID 25014791›Full record

ArticleMolecular medicine (Cambridge, Mass.)2014

Immunochip identifies novel, and replicates known, genetic risk loci for rheumatoid arthritis in black South Africans.

Nimmisha Govind, Ananyo Choudhury, Bridget Hodkinson, Claudia Ickinger, Jacqueline Frost, Annette Lee, Peter K Gregersen, Richard J Reynolds, S Louis Bridges, Scott Hazelhurst and 2 more

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

Article in Molecular medicine (Cambridge, Mass.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed, 1 pooled it
1.2field-weighted citation impact, top 21% 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

17 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.

  1. Pooled it
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  8. DNA methylation patterns in CD4Frontiers in immunology · 2023
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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

12 authors at 4 institutions in 2 countries.

Nimmisha GovindDivision of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Ananyo ChoudhurySydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Bridget HodkinsonDivision of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Claudia IckingerDivision of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Jacqueline FrostDivision of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Annette LeeFeinstein Institute for Medical Research, Manhasset, New York, United States of America.
Peter K GregersenFeinstein Institute for Medical Research, Manhasset, New York, United States of America.
Richard J ReynoldsDivision of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
S Louis BridgesDivision of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
Scott HazelhurstSydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
Michèle RamsaySydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Mohammed TiklyDivision of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
University of the Witwatersrand · ZAFeinstein Institute for Medical Research · USUniversity of Alabama at Birmingham · USChris Hani Baragwanath Hospital · ZA

Funding

Genome-Wide Association Study in African-Americans with Rheumatoid ArthritisR01AR057202 · NIAMS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI BRIDGES, S LOUIS · 2009 to 2013
$4.2M
Discovering Novel Genetic and Environmental Risk Factors for RA in African AmericK01AR060848 · NIAMS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI REYNOLDS, RICHARD JAMES · 2011 to 2015
$641k
NIAMS NIH HHS K01 AR060848NIAMS NIH HHS K01AR060848NIAMS NIH HHS R01 AR057202
6 · The paper itself

Abstract

The aim of this study was to identify genetic variants associated with rheumatoid arthritis (RA) risk in black South Africans. Black South African RA patients (n = 263) were compared with healthy controls (n = 374). Genotyping was performed using the Immunochip, and four-digit high-resolution human leukocyte antigen (HLA) typing was performed by DNA sequencing of exon 2. Standard quality control measures were implemented on the data. The strongest associations were in the intergenic region between the HLA-DRB1 and HLA-DQA1 loci. After conditioning on HLA-DRB1 alleles, the effect in the rest of the extended major histocompatibility (MHC) diminished. Non-HLA single nucleotide polymorphisms (SNPs) in the intergenic regions LOC389203|RBPJ, LOC100131131|IL1R1, KIAA1919|REV3L, LOC643749|TRAF3IP2, and SNPs in the intron and untranslated regions (UTR) of IRF1 and the intronic region of ICOS and KIAA1542 showed association with RA (p < 5 × 10(-5)). Of the SNPs previously associated with RA in Caucasians, one SNP, rs874040, locating to the intergenic region LOC389203|RBPJ was replicated in this study. None of the variants in the PTPN22 gene was significantly associated. The seropositive subgroups showed similar results to the overall cohort. The effects observed across the HLA region are most likely due to HLA-DRB1, and secondary effects in the extended MHC cannot be detected. Seven non-HLA loci are associated with RA in black South Africans. Similar to Caucasians, the intergenic region between LOC38920 and RBPJ is associated with RA in this population. The strong association of the R620W variant of the PTPN22 gene with RA in Caucasians was not replicated since this variant was monomorphic in our study, but other SNP variants of the PTPN22 gene were also not associated with RA in black South Africans, suggesting that this locus does not play a major role in RA in this population.

Indexed as

Genetic Predisposition to DiseaseAdaptor Proteins, Signal TransducingArthritis, RheumatoidBlack PeopleDNA-Binding ProteinsDNA-Directed DNA PolymeraseFemaleGenotypeHumansImmunoglobulin J Recombination Signal Sequence-Binding ProteinInducible T-Cell Co-Stimulator ProteinInterferon Regulatory Factor-1MalePolymorphism, Single NucleotideProtein Tyrosine Phosphatase, Non-Receptor Type 22Receptors, Interleukin-1 Type IAdaptor Proteins, Signal TransducingDNA-Binding ProteinsDNA-Directed DNA PolymeraseICOS protein, humanIL1R1 protein, humanImmunoglobulin J Recombination Signal Sequence-Binding ProteinInducible T-Cell Co-Stimulator ProteinInterferon Regulatory Factor-1IRF1 protein, humanProtein Tyrosine Phosphatase, Non-Receptor Type 22PTPN22 protein, humanRBPJ protein, humanReceptors, Interleukin-1 Type IREV3L protein, humanTRAF3IP2 protein, humanTumor Necrosis Factor Receptor-Associated Peptides and Proteins

Identifiers

PMID25014791
PMCPMC4153842
OpenAlexW2409697203

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.