Autoimmune disease classification by inverse association with SNP alleles.

With multiple genome-wide association studies (GWAS) performed across autoimmune diseases, there is a great opportunity to study the homogeneity of genetic architectures across autoimmune disease. Previous approaches have been limited in the scope of their analysis and have failed to properly incorp...

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Main Authors: Marina Sirota, Marc A Schaub, Serafim Batzoglou, William H Robinson, Atul J Butte
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2009-12-01
Series:PLoS Genetics
Online Access:http://europepmc.org/articles/PMC2791168?pdf=render
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spelling doaj-514fbfaa02dd45b29cca4704f13460702020-11-24T21:44:32ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042009-12-01512e100079210.1371/journal.pgen.1000792Autoimmune disease classification by inverse association with SNP alleles.Marina SirotaMarc A SchaubSerafim BatzoglouWilliam H RobinsonAtul J ButteWith multiple genome-wide association studies (GWAS) performed across autoimmune diseases, there is a great opportunity to study the homogeneity of genetic architectures across autoimmune disease. Previous approaches have been limited in the scope of their analysis and have failed to properly incorporate the direction of allele-specific disease associations for SNPs. In this work, we refine the notion of a genetic variation profile for a given disease to capture strength of association with multiple SNPs in an allele-specific fashion. We apply this method to compare genetic variation profiles of six autoimmune diseases: multiple sclerosis (MS), ankylosing spondylitis (AS), autoimmune thyroid disease (ATD), rheumatoid arthritis (RA), Crohn's disease (CD), and type 1 diabetes (T1D), as well as five non-autoimmune diseases. We quantify pair-wise relationships between these diseases and find two broad clusters of autoimmune disease where SNPs that make an individual susceptible to one class of autoimmune disease also protect from diseases in the other autoimmune class. We find that RA and AS form one such class, and MS and ATD another. We identify specific SNPs and genes with opposite risk profiles for these two classes. We furthermore explore individual SNPs that play an important role in defining similarities and differences between disease pairs. We present a novel, systematic, cross-platform approach to identify allele-specific relationships between disease pairs based on genetic variation as well as the individual SNPs which drive the relationships. While recognizing similarities between diseases might lead to identifying novel treatment options, detecting differences between diseases previously thought to be similar may point to key novel disease-specific genes and pathways.http://europepmc.org/articles/PMC2791168?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Marina Sirota
Marc A Schaub
Serafim Batzoglou
William H Robinson
Atul J Butte
spellingShingle Marina Sirota
Marc A Schaub
Serafim Batzoglou
William H Robinson
Atul J Butte
Autoimmune disease classification by inverse association with SNP alleles.
PLoS Genetics
author_facet Marina Sirota
Marc A Schaub
Serafim Batzoglou
William H Robinson
Atul J Butte
author_sort Marina Sirota
title Autoimmune disease classification by inverse association with SNP alleles.
title_short Autoimmune disease classification by inverse association with SNP alleles.
title_full Autoimmune disease classification by inverse association with SNP alleles.
title_fullStr Autoimmune disease classification by inverse association with SNP alleles.
title_full_unstemmed Autoimmune disease classification by inverse association with SNP alleles.
title_sort autoimmune disease classification by inverse association with snp alleles.
publisher Public Library of Science (PLoS)
series PLoS Genetics
issn 1553-7390
1553-7404
publishDate 2009-12-01
description With multiple genome-wide association studies (GWAS) performed across autoimmune diseases, there is a great opportunity to study the homogeneity of genetic architectures across autoimmune disease. Previous approaches have been limited in the scope of their analysis and have failed to properly incorporate the direction of allele-specific disease associations for SNPs. In this work, we refine the notion of a genetic variation profile for a given disease to capture strength of association with multiple SNPs in an allele-specific fashion. We apply this method to compare genetic variation profiles of six autoimmune diseases: multiple sclerosis (MS), ankylosing spondylitis (AS), autoimmune thyroid disease (ATD), rheumatoid arthritis (RA), Crohn's disease (CD), and type 1 diabetes (T1D), as well as five non-autoimmune diseases. We quantify pair-wise relationships between these diseases and find two broad clusters of autoimmune disease where SNPs that make an individual susceptible to one class of autoimmune disease also protect from diseases in the other autoimmune class. We find that RA and AS form one such class, and MS and ATD another. We identify specific SNPs and genes with opposite risk profiles for these two classes. We furthermore explore individual SNPs that play an important role in defining similarities and differences between disease pairs. We present a novel, systematic, cross-platform approach to identify allele-specific relationships between disease pairs based on genetic variation as well as the individual SNPs which drive the relationships. While recognizing similarities between diseases might lead to identifying novel treatment options, detecting differences between diseases previously thought to be similar may point to key novel disease-specific genes and pathways.
url http://europepmc.org/articles/PMC2791168?pdf=render
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AT serafimbatzoglou autoimmunediseaseclassificationbyinverseassociationwithsnpalleles
AT williamhrobinson autoimmunediseaseclassificationbyinverseassociationwithsnpalleles
AT atuljbutte autoimmunediseaseclassificationbyinverseassociationwithsnpalleles
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