Evidence map›Paper›PMID 30057032›Full record

ArticleAmerican journal of human genetics2018

An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.

Christopher E Gillies, Rosemary Putler, Rajasree Menon, Edgar Otto, Kalyn Yasutake, Viji Nair, Paul Hoover, David Lieb, Shuqiang Li, Sean Eddy and 8 more

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

Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers, 15 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
121citing papers in PubMed, 15 pooled it
16.8field-weighted citation impact, top 1% 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

121 citing papers in PubMed, 15 syntheses or guidelines pooled it, 182 citations in OpenAlex.

  1. Pooled it
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  4. Genome-Wide Association Study for eGFR in a Taiwanese Population.Clinical journal of the American Society of Nephrology : CJASN · 2022
    Pooled it
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  8. Guideline
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  16. Trial
  17. Inherited Susceptibility to Urinary Tract Infections from Kidney Papilla to Bladder.medRxiv : the preprint server for health sciences · 2026
    Article
  18. Article
  19. Review
  20. Article

61 more citing papers are in PubMed but not listed here.

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

18 authors at 4 institutions in 1 country.

Christopher E GilliesDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Rosemary PutlerDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Rajasree MenonDepartment of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Edgar OttoDepartment of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Kalyn YasutakeDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Viji NairDepartment of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Paul HooverDepartment of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.
David LiebBroad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.
Shuqiang LiBroad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.
Sean EddyDepartment of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Damian FerminDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Michelle T McNultyDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Nephrotic Syndrome Study Network (NEPTUNE)
Nir HacohenDepartment of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.
Krzysztof KirylukDepartment of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA.
Matthias KretzlerDepartment of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA; Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
Xiaoquan WenDepartment of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
Matthew G SampsonDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA. Electronic address: mgsamps@med.umich.edu.
Michigan Medicine · USUniversity of Michigan · USBroad Institute · USColumbia University · US

Funding

Training Program in Clinical & Translationa Research in Human Glomerular DiseaseU54DK083912 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GIPSON, DEBBIE S · 2009 to 2023
$20.3M
University of Michigan Training Program in Genomic ScienceT32HG000040 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Sebastian Zoellner · 1995 to 2026
$16.4M
Genetics of IgA nephropathy by integrative network-based association studiesR01DK105124 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Krzysztof Kiryluk · 2015 to 2026
$4.8M
APOL1 - associated nephropathy from human-derived, intrarenal perspectiveR01DK108805 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MATTHEW Gordon SAMPSON, Simone Sanna-Cherchi · 2016 to 2026
$3.4M
NHGRI NIH HHS T32 HG000040NIDDK NIH HHS R01 DK105124NIDDK NIH HHS R01 DK108805NIDDK NIH HHS U54 DK083912
6 · The paper itself

Abstract

Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and, in disease research, can be particularly illuminating when using the tissues directly impacted by the condition. In nephrology, there is a paucity of eQTL studies of human kidney. Here, we used whole-genome sequencing (WGS) and microdissected glomerular (GLOM) and tubulointerstitial (TI) transcriptomes from 187 individuals with nephrotic syndrome (NS) to describe the eQTL landscape in these functionally distinct kidney structures. Using MatrixEQTL, we performed cis-eQTL analysis on GLOM (n = 136) and TI (n = 166). We used the Bayesian "Deterministic Approximation of Posteriors" (DAP) to fine-map these signals, eQTLBMA to discover GLOM- or TI-specific eQTLs, and single-cell RNA-seq data of control kidney tissue to identify the cell type specificity of significant eQTLs. We integrated eQTL data with an IgA Nephropathy (IgAN) GWAS to perform a transcriptome-wide association study (TWAS). We discovered 894 GLOM eQTLs and 1,767 TI eQTLs at FDR < 0.05. 14% and 19% of GLOM and TI eQTLs, respectively, had >1 independent signal associated with its expression. 12% and 26% of eQTLs were GLOM specific and TI specific, respectively. GLOM eQTLs were most significantly enriched in podocyte transcripts and TI eQTLs in proximal tubules. The IgAN TWAS identified significant GLOM and TI genes, primarily at the HLA region. In this study, we discovered GLOM and TI eQTLs, identified those that were tissue specific, deconvoluted them into cell-specific signals, and used them to characterize known GWAS alleles. These data are available for browsing and download via our eQTL browser, "nephQTL."

Indexed as

AdolescentAdultAllelesBayes TheoremFemaleGene Expression ProfilingGenome-Wide Association StudyHumansKidneyMaleMiddle AgedNephrotic SyndromePolymorphism, Single NucleotideQuantitative Trait LociTranscriptomeYoung AdulteQTLexpression quantitative trait locifocal segmental glomerulosclerosisgenomicsglomeruluskidneyminimal change diseasenephrotic syndromepodocyteproteinuriasingle-cell RNA sequencing

Identifiers

PMID30057032
PMCPMC6081280
OpenAlexW2952295900

What OpenQuestion holds

Textmetadata
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.