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Pathway-based analy...
Pathway-based analysis of genetic susceptibility to cervical cancer in situ : HLA-DPB1 affects risk in Swedish women
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- Ivansson, Emma L. (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Juko-Pecirep, Ivana (author)
- Uppsala universitet,Genomik,Science for Life Laboratory, SciLifeLab
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Erlich, H. A. (author)
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- Gyllensten, Ulf B. (author)
- Uppsala universitet,Genomik,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2011-06-30
- 2011
- English.
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In: Genes and Immunity. - : Springer Science and Business Media LLC. - 1466-4879 .- 1476-5470. ; 12:8, s. 605-614
- Related links:
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https://www.nature.c...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- We have conducted a pathway-based analysis of genome-wide single-nucleotide polymorphism (SNP) data in order to identify genetic susceptibility factors for cervical cancer in situ. Genotypes derived from Affymetrix 500k or 5.0 arrays for 1076 cases and 1426 controls were analyzed for association, and pathways with enriched signals were identified using the SNP ratio test. The most strongly associated KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were Asthma (empirical P=0.03), Folate biosynthesis (empirical P=0.04) and Graft-versus-host disease (empirical P=0.05). Among the 11 top-ranking pathways were 6 related to the immune response with the common denominator being genes in the major histocompatibility complex (MHC) region on chromosome 6. Further investigation of the MHC revealed a clear effect of HLA-DPB1 polymorphism on disease susceptibility. At a functional level, DPB1 alleles associated with risk and protection differ in key amino-acid residues affecting peptide-binding motifs in the extracellular domains. The results illustrate the value of pathway-based analysis to mine genome-wide data, and point to the importance of the MHC region and specifically the HLA-DPB1 locus for susceptibility to cervical cancer.
Keyword
- cervical cancer
- CIN III
- genetic risk factors
- HLA-DPB1
- pathway analysis
- GWA
Publication and Content Type
- ref (subject category)
- art (subject category)
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