Study Report
Basic Info
| Reference |
Emily, M.,2009 PMID: 19277065
|
| Citation |
Emily, M., T. Mailund, et al. (2009). "Using biological networks to search for interacting loci in genome-wide association studies." Eur J Hum Genet 17(10): 1231-1240.
|
| Disease Type |
Bipolar Disorder |
| Study Design |
case-control |
| Study Type |
Genetic interaction study |
| Sample Size |
2000 BPD cases versus 3000 control subjects |
| SNP/Region/Marker Size |
3,107,904-3,850,339 SNPs |
| Predominant Ethnicity |
|
| Population |
WTCCC collection |
Detail Info
| Statistical Method |
In this study, we propose to test the interaction between a pair of SNPs by performing a likelihood ratio test. This test aims at comparing a logistic regression that takes into account only marginal effects of both SNPs with a full logistic regression model that includes pairwise interaction between the two SNPs. |
| Result Summary |
A statistical interaction was found between rs2237091 (chromosome 5q32) and rs1798011 (chromosome 12q22 located in the PDGFR-B gene and the KITLG gene,respectively). These SNPs have a MAF of 0.10 and 0.43,respectively. The genotype pairs (GG, CT), (GA,TT) and (GG, TT) are overrepresented in affected individuals,resembling the interaction pattern M11 reported by Evans et al. also shows the risks relative to genotype (AA, CC) and shows that the relative risk for (GA, TT) was 1.88 (95% CI: 1.31-2.71) and for (GG, CT) it was 1.34 (95% CI:0.58-3.05). The joint OR, which combined the three at-risk genotypes, has a value of 1.92(95% CI: 1.4-2.64), significantly larger than 1 (Fisher's exact test P=5.68E-05), confirming that carrying at least three minor alleles combining rs2237091 and rs1798011 is a risk predictor for bipolar disorder in the WTCCC data set. |
Haplotypes reported by this study for BD (count: 1)
| Markers |
Haplotype |
Related Gene(s)/Region(s) |
Statistical Values |
Author Comments |
Result Category |
| rs2237091 - rs1798011 |
|
PDGFRB
KITLG
|
SNP-SNP interaction analysis:allelic X<sup>2</sup> test:Marginal effect 1, Pval=0.86, RR=1.01; Marginal effect 2, Pval=0.69, RR=1.02; Interaction test, P-value = 1.13E-09
|
Significant association was found.
Significant association was found.
|
Positive
|
Gene-gene interactions reported by this study for BD (count: 1)
| Gene Group |
Markers |
Statistical Values |
Author Comments |
Result Category |
|
PDGFRB
KITLG
|
rs2237091 - rs1798011 |
SNP-SNP interaction analysis:allelic X2 test:Marginal effect 1, Pval=0.86, RR=1.01;Marginal effect 2, Pval=0.69, RR=1.02;Interaction test, P-value = 1.13E-09
|
Significant association was found.
Significant association was found.
|
Positive
|
