title: Gene-based single nucleotide polymorphisms and linkage disequilibrium patterns of 29 asthma candidate genes in the chromosome 5q31-33 region in Koreans.
abstract: METHODS
  Numerous genetic studies have mapped asthma susceptibility genes to a region on chromosome 5q31-33 in several populations. This region contains a cluster of cytokines and other immune-related genes important in immune response. In the present study, to determine the genetic variations and patterns of linkage disequilibrium (LD), we resequenced all the exons and promoter regions of the 29 asthma candidate genes in the chromosome 5q31-33 region.
  
  
  RESULTS
  We identified a total of 314 genetic variants, including 289 single nucleotide polymorphisms (SNPs), 22 insertion/deletion polymorphisms and 3 microsatellites. Standardized variance data for allele frequency revealed substantial differences in SNP allele frequencies among different ethnic groups. Interestingly, significant ethnic differences were observed mainly in intron SNPs. LD block analysis using 174 common SNPs with a frequency of >10% disclosed strong LD within most candidate genes. No significant LD was observed across genes, except for one LD block (CD14-IK block). Gene-based haplotype analyses showed that 1-5 haplotype-tagging SNPs may be used to define the six or fewer common haplotypes with a frequency of >5%, regardless of the number of SNPs.
  
  
  CONCLUSIONS
  Overall, our results provide useful information for the identification of immune-mediated disease genes in the chromosome 5q31-33 region, as well as valuable evidence for gene-based haplotype analysis in disease association studies.
authors.affiliation: National Genome Research Institute, National Institute of Health, Seoul, and Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Hospital, Gyeonggi-Do, Korea.
authors.forename: Ha-Jung
authors.initials: HJ
authors.lastname: Ryu
authors.forename: Ho-Youl
authors.initials: HY
authors.lastname: Jung
authors.forename: Jung-Sun
authors.initials: JS
authors.lastname: Park
authors.forename: Gil-Mi
authors.initials: GM
authors.lastname: Ryu
authors.forename: Jee Yeon
authors.initials: JY
authors.lastname: Heo
authors.forename: Jae-Jung
authors.initials: JJ
authors.lastname: Kim
authors.forename: Song-Mean
authors.initials: SM
authors.lastname: Moon
authors.forename: Hung-Tae
authors.initials: HT
authors.lastname: Kim
authors.forename: Jong-Young
authors.initials: JY
authors.lastname: Lee
authors.forename: Insong
authors.initials: I
authors.lastname: Koh
authors.forename: Jun-Woo
authors.initials: JW
authors.lastname: Kim
authors.forename: Jae Kyun
authors.initials: JK
authors.lastname: Rho
authors.forename: Bok-Ghee
authors.initials: BG
authors.lastname: Han
authors.forename: Hyungtae
authors.initials: H
authors.lastname: Kim
authors.forename: Choon-Sik
authors.initials: CS
authors.lastname: Park
authors.forename: Bermseok
authors.initials: B
authors.lastname: Oh
authors.forename: Chan
authors.initials: C
authors.lastname: Park
authors.forename: Jong-Keuk
authors.initials: JK
authors.lastname: Lee
authors.forename: Kuchan
authors.initials: K
authors.lastname: Kimm
mesh_terms: D000483:Alleles; D001249:Asthma / Q000235:genetics* / Q000276:immunology; D002895:Chromosomes, Human, Pair 5 / Q000235:genetics* / Q000276:immunology; D004247:DNA / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics / Q000276:immunology; D006801:Humans; D007723:Korea; D015810:Linkage Disequilibrium; D011110:Polymorphism, Genetic; D012044:Regression Analysis; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA