Evidence map›Paper›PMID 30349113›Full record

ArticleScientific reports2018

Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy.

Khun Zaw Latt, Kenjiro Honda, Myo Thiri, Yuki Hitomi, Yosuke Omae, Hiromi Sawai, Yosuke Kawai, Shunsuke Teraguchi, Kazuko Ueno, Masao Nagasaki and 5 more

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

Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
1.7field-weighted citation impact, top 17% 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

6 citing papers in PubMed, 12 citations in OpenAlex.

  1. Article
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  3. Review
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  5. Review
  6. 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

15 authors at 4 institutions in 1 country.

Khun Zaw LattDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Kenjiro HondaDepartment of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan.
Myo ThiriDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Yuki HitomiDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0002-6713-7875
Yosuke OmaeDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0001-9978-4869
Hiromi SawaiDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Yosuke KawaiDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Shunsuke TeraguchiDepartment of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.ORCID http://orcid.org/0000-0002-5104-0227
Kazuko UenoDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Masao NagasakiDepartment of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
Akihiko MabuchiDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Hajime KagaDepartment of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan.
Atsushi KomatsudaDepartment of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan.
Katsushi TokunagaDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. tokunaga@m.u-tokyo.ac.jp.
Eisei NoiriDepartment of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan. noiri-tky@umin.ac.jp.ORCID http://orcid.org/0000-0002-9515-7582
The University of Tokyo · JPAkita University · JPTohoku University · JPUniversity of Tokyo Hospital · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still need to be determined. We used Japanese-specific SNP genotyping array and imputation using 2,048 sequenced Japanese samples to fine-map PLA2R1 region in 98 patients and 413 controls. The most significant SNPs were replicated in a separate sample set of 130 patients and 288 controls. A two-SNP haplotype of intronic and missense SNPs showed the strongest association. The intronic SNP is strongly associated with PLA2R1 expression in the Genotype-Tissue Expression (GTEx) database, and the missense SNP is predicted to alter peptide binding with HLA-DRB1*15:01 by the Immune Epitope Database (IEDB). In HLA region, we performed relative predispositional effect (RPE) tests and identified additional risk alleles in both HLA-DRB1 and HLA-DQB1. We collapsed the risk alleles in each of HLA-DRB1 and HLA-DQB1 into single risk alleles. Reciprocal conditioning of these collapsed risk alleles showed more residual significance for HLA-DRB1 collapsed risk than HLA-DQB1 collapsed risk. These results indicate that changes in the expression levels of structurally different PLA2R protein confer risk for IMN in the presence of risk HLA-DRB1 alleles.

Indexed as

Polymorphism, Single NucleotideGlomerulonephritis, MembranousHaplotypesHLA-DRB1 ChainsHumansReceptors, Phospholipase A2HLA-DRB1 ChainsPLA2R1 protein, humanReceptors, Phospholipase A2

Identifiers

PMID30349113
PMCPMC6197221
OpenAlexW2897581908

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.