Evidence map›Paper›PMID 31467281›Full record

ArticleNature communications2019

A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.

Cristina M Lanata, Ishan Paranjpe, Joanne Nititham, Kimberly E Taylor, Milena Gianfrancesco, Manish Paranjpe, Shan Andrews, Sharon A Chung, Brooke Rhead, Lisa F Barcellos and 6 more

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

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed, 2 pooled it
6.4field-weighted citation impact, top 3% 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

30 citing papers in PubMed, 2 syntheses or guidelines pooled it, 64 citations in OpenAlex.

  1. Pooled it
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  3. Targeting FcRn for immunomodulation: a promising therapy in autoimmune inflammatory rheumatic diseases.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors at 2 institutions in 1 country.

Cristina M LanataRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-6017-4921
Ishan ParanjpeBakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
Joanne NitithamRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Kimberly E TaylorRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Milena GianfrancescoRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Manish ParanjpeBakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
Shan AndrewsBakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
Sharon A ChungRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Brooke RheadUniversity of California, Berkeley, CA, USA.
Lisa F BarcellosUniversity of California, Berkeley, CA, USA.
Laura TrupinRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Patricia KatzRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Maria Dall'EraRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Jinoos YazdanyRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Marina SirotaBakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
Lindsey A CriswellRussell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. Lindsey.Criswell@ucsf.edu.
University of California, San Francisco · USUniversity of California, Berkeley · US

Funding

Virology CoreP30AI027763 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Monica Gandhi · 1988 to 2026
$93.6M
The Interplay of Sociodemographic and Genetic Factors in SLE Health DisparitiesP60AR053308 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KATZ, PATRICIA P · 2006 to 2016
$11.8M
RESOURCE-BASED CENTER FOR THE ADVANCEMENT OF PRECISION MEDICINE IN RHEUMATOLOGYP30AR070155 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Mary C Nakamura · 2016 to 2026
$8.2M
Advancing Quality and Outcomes Measurement in RheumatologyK24AR074534 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Jinoos Yazdany · 2019 to 2026
$1.5M
Elucidating the Role of the Genetic and Environmental Determinants of Preterm Birth Using Integrative Computational ApproachesK01LM012381 · NLM · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SIROTA, MARINA · 2016 to 2018
$531k
Examining the causal effect of sociodemographic and genetic factors on patient safety outcomes in individuals prescribed high-risk immunosuppressive medicationsF32AR070585 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GIANFRANCESCO, MILENA ANNE · 2017 to 2018
$125k
NCCDPHP CDC HHS U01 DP005120NCCDPHP CDC HHS U01 DP006486NIAID NIH HHS P30 AI027763NIAMS NIH HHS F32 AR070585NIAMS NIH HHS K24 AR074534NIAMS NIH HHS P30 AR070155NIAMS NIH HHS P60 AR053308NLM NIH HHS K01 LM012381
6 · The paper itself

Abstract

Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters that vary according to disease severity. Methylation association analysis identifies a set of 256 differentially methylated CpGs across clusters, including 101 CpGs in genes in the Type I Interferon pathway, and we validate these associations in an external cohort. A cis-methylation quantitative trait loci analysis identifies 744 significant CpG-SNP pairs. The methylation signature is enriched for ethnic-associated CpGs suggesting that genetic and non-genetic factors may drive outcomes and ethnic-associated methylation differences. Our computational approach highlights molecular differences associated with clusters rather than single outcome measures. This work demonstrates the utility of applying integrative methods to address clinical heterogeneity in multifactorial multi-ethnic disease settings.

Indexed as

Computational BiologyGenomicsMultigene FamilyCohort StudiesDNA MethylationEpigenomicsEthnicityFemaleGenetic Association StudiesGenotypeHumansLupus Erythematosus, SystemicMaleQuantitative Trait LociSeverity of Illness IndexUnited States

Identifiers

PMID31467281
PMCPMC6715644
OpenAlexW2970170315

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.