liu.seSearch for publications in DiVA
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Novel risk genes for systemic lupus erythematosus predicted by random forest classification
Uppsala University, Sweden.
Uppsala University, Sweden.
Uppsala University, Sweden.
Uppsala University, Sweden; Karolinska Institute, Sweden.
Show others and affiliations
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 6236Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies have identified risk loci for SLE, but a large proportion of the genetic contribution to SLE still remains unexplained. To detect novel risk genes, and to predict an individuals SLE risk we designed a random forest classifier using SNP genotype data generated on the "Immunochip" from 1,160 patients with SLE and 2,711 controls. Using gene importance scores defined by the random forest classifier, we identified 15 potential novel risk genes for SLE. Of them 12 are associated with other autoimmune diseases than SLE, whereas three genes (ZNF804A, CDK1, and MANF) have not previously been associated with autoimmunity. Random forest classification also allowed prediction of patients at risk for lupus nephritis with an area under the curve of 0.94. By allele-specific gene expression analysis we detected cis-regulatory SNPs that affect the expression levels of six of the top 40 genes designed by the random forest analysis, indicating a regulatory role for the identified risk variants. The 40 top genes from the prediction were overrepresented for differential expression in B and T cells according to RNA-sequencing of samples from five healthy donors, with more frequent over-expression in B cells compared to T cells.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP , 2017. Vol. 7, article id 6236
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:liu:diva-140068DOI: 10.1038/s41598-017-06516-1ISI: 000406260100040OAI: oai:DiVA.org:liu-140068DiVA, id: diva2:1136593
Note

Funding Agencies|Knut and Alice Wallenberg Foundation; Swedish Research Council for Medicine and Health [521-2014-2263, 521-2013-2830]; Swedish Rheumatism Association; King Gustaf V 80-year Foundation; COMBINE

Available from: 2017-08-28 Created: 2017-08-28 Last updated: 2018-01-13

Open Access in DiVA

fulltext(1356 kB)11 downloads
File information
File name FULLTEXT01.pdfFile size 1356 kBChecksum SHA-512
8fc820d13f658ffde0724a97c765b735da019fa1104126f9ca90a685e327626556516696a9358821be8c022ca671580f3bc5fed31a3e1a0604498a7489ece05d
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Sjöwall, Christopher
By organisation
Division of Neuro and Inflammation ScienceFaculty of Medicine and Health SciencesDepartment of Rheumatology
In the same journal
Scientific Reports
Medical Genetics

Search outside of DiVA

GoogleGoogle Scholar
Total: 11 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 63 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf