[An analysis method to apply linkage disequilibrium maps to association study].
OBJECTIVE
To apply linkage disequilibrium (LD) maps to associations studies with high throughput single nucleotide polymorphisms (SNPs).


METHODS
Seven hundred and fifty-four SNPs were genotyped in 160 Shanghai Chinese. LD maps were constructed in cases and controls separately. By comparing the decline of LD unit with distance between the two groups, disease susceptible loci were estimated. This method was compared with traditional analyses including LD analysis, single SNP and haplotype analyses.


RESULTS
The analysis of LD maps could detect the chromosome regions with different LD patterns between the cases and controls. The alleles and/or haplotypes frequencies of SNPs within the regions had significantly different distributions or trends of significantly different distributions.


CONCLUSIONS
This method may be applied to analyze the data from association studies with high throughput SNPs genotype information.
Hu
Cheng
C
Shanghai Clinical Medicine Center for Diabetes, Shanghai Diabetes Institute, Department of Endocrinology and Metabolism, Shanghai Jiaotong University Affiliated No.6 People's Hospital, Shanghai, 200233 PR China.
Jia
Wei-ping
WP
Wang
Cong-rong
CR
Zhang
Rong
R
Ma
Xiao-jing
XJ
Fang
Qi-chen
QC
Xiang
Kun-san
KS
D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D004268:DNA-Binding Proteins / Q000235:genetics; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D055106:Genome-Wide Association Study / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011518:Proto-Oncogene Proteins / Q000235:genetics; D047491:Retinoid X Receptor gamma / Q000235:genetics
D004268:DNA-Binding Proteins; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011518:Proto-Oncogene Proteins; D047491:Retinoid X Receptor gamma; C083400:PBX1 protein, human