PMID- 22201026
OWN - NLM
STAT- MEDLINE
DCOM- 20120712
LR  - 20211021
IS  - 1573-4978 (Electronic)
IS  - 0301-4851 (Linking)
VI  - 39
IP  - 5
DP  - 2012 May
TI  - Genome-wide pathway analysis of a genome-wide association study on psoriasis and 
      Behcet's disease.
PG  - 5953-9
LID - 10.1007/s11033-011-1407-9 [doi]
AB  - The aim of this study was to identify candidate causal single nucleotide 
      polymorphisms (SNPs) and candidate causal mechanisms of psoriasis and Behcets's 
      disease (BD) and to generate an SNP --> gene --> pathway hypothesis. A psoriasis 
      genome-wide association study (GWAS) dataset that included 436,192 SNPs in 1,409 
      psoriasis cases and 1,436 controls of European descent and a BD GWAS dataset that 
      contained 310,324 SNPs in 1,215 BD cases and 1,278 controls were used in this 
      study. Identify candidate causal SNPs and pathways (ICSNPathway) analysis was 
      applied to the GWAS datasets. ICSNPathway analysis identified 15 candidate causal 
      SNPs and 28 candidate causal pathways. The top five candidate causal SNPs were 
      rs1063478 (P = 1.45E-10), rs8084 (P = 2.20E-08), rs7192 (P = 5.18E-08), rs20541 
      (P = 5.30E-06), and rs1130838 (P = 5.65E-06), which with the exception of rs20541 
      [interleukin (IL)-13] are at human leukocyte antigen (HLA) loci. These candidate 
      causal SNPs and pathways provided ten hypothetical biological mechanisms. The 
      most strongly associated pathway concerned HLA. When HLA loci were excluded, 
      ICSNPathway analysis provided one hypothetical biological mechanism. rs20541 
      (non_synonymous_coding) --> IL-13 --> dendritic cell involvement in the regulation of 
      Th1 and Th2 development, and the GATA3 pathway. ICSNPathway analysis identified 
      four candidate causal SNPs, eleven candidate causal pathways, and three 
      hypothetical biological mechanisms. One of them was as follows: rs2072895 
      (non_synonymous_coding & splice-site) and rs2735059 
      (non_synonymous_coding) --> HLA-F --> type I diabetes mellitus, antigen processing 
      and presentation, and autoimmune thyroid disease. The application of ICSNPathway 
      analysis to GWAS dataset of psoriasis and BD resulted in the identification of 
      candidate causal SNPs and candidate pathways that might contribute to psoriasis 
      susceptibility.
FAU - Lee, Young Ho
AU  - Lee YH
AD  - Division of Rheumatology, Department of Internal Medicine, Korea University 
      College of Medicine, Korea University Medical Center, 126-1, Anam-dong 5-ga, 
      Seongbuk-gu, Seoul, 136-705, Korea. lyhcgh@korea.ac.kr
FAU - Choi, Sung Jae
AU  - Choi SJ
FAU - Ji, Jong Dae
AU  - Ji JD
FAU - Song, Gwan Gyu
AU  - Song GG
LA  - eng
PT  - Journal Article
DEP - 20111227
PL  - Netherlands
TA  - Mol Biol Rep
JT  - Molecular biology reports
JID - 0403234
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Behcet Syndrome/*complications/*genetics
MH  - Databases, Genetic
MH  - Genetic Loci/genetics
MH  - Genetic Predisposition to Disease
MH  - Genome, Human/*genetics
MH  - *Genome-Wide Association Study
MH  - HLA Antigens/genetics
MH  - Humans
MH  - Linkage Disequilibrium/genetics
MH  - Meta-Analysis as Topic
MH  - Polymorphism, Single Nucleotide/genetics
MH  - Psoriasis/*complications/*genetics
MH  - Signal Transduction/*genetics
EDAT- 2011/12/28 06:00
MHDA- 2012/07/13 06:00
CRDT- 2011/12/28 06:00
PHST- 2011/10/07 00:00 [received]
PHST- 2011/12/17 00:00 [accepted]
PHST- 2011/12/28 06:00 [entrez]
PHST- 2011/12/28 06:00 [pubmed]
PHST- 2012/07/13 06:00 [medline]
AID - 10.1007/s11033-011-1407-9 [doi]
PST - ppublish
SO  - Mol Biol Rep. 2012 May;39(5):5953-9. doi: 10.1007/s11033-011-1407-9. Epub 2011 
      Dec 27.