BDgene

Core Gene from Gene Prioritization Pathways from PBA (Pathway-based Analysis) Enriched Pathways for Core Genes Enriched Pathways for Cross-disorder Genes

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Study Report

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Basic Info

Reference	Sun, H. S., 2004 PMID: 15167705
Citation	Sun, H. S., H. C. Wang, et al. (2004). "Sequence variants and haplotype analysis of serotonin transporter gene and association with bipolar affective disorder in Taiwan." Pharmacogenetics 14(3): 173-179.
Disease Type	Bipolar I Disorder
Study Design	case-control
Study Type	Candidate-gene association study
Sample Size	90 bipolar disorder, type I patients and 103 controls
SNP/Region/Marker Size	10 polymorphisms
Predominant Ethnicity	Mongloid
Population	Chinese
Gender	47 male and 43 female patients, 55 male and 48 female controls

Detail Info

Sample Diagnosis	DSM-IV
Sample Status	Probands were recruited since 1998 from bipolar outpatients in several participating cohorts including the Chung-Shan Medical University Hospital and the Taichung Rehabilitation Hospital (Dr Lai), the Ching-Ho Hospital in Taichung City (Dr Li), and the Tao-Yuan Veterans Hospital in Tao-Yuan (Dr Wang). Patients' assessment was purely by direct clinical interview by the treating clinician according to the procedure described in the DSM-VI diagnoses of lifetime major depressive disorder and bipolar I.
Technique	genotyping using fluorescent-based genotyping systems
Statistical Method	Because sample sizes in some of the cells from the contingency table were small, we have applied Fisher's exact test (two-tailed) implemented by SAS program to detect the differences in allele or genotype frequencies between cases and controls for each marker. In addition, haplotypes were constructed by the expectation-maximization (EM) method by use of the SNP Alyze program, and then Fisher's exact test was applied to test the differences in haplotype frequencies between cases and controls. Estimation of the relative risk of BPD associated with a particular haplotype was performed using the RelRisk.
Result Summary	Two SNPs were not informative in a Taiwanese population and the other eight polymorphic markers were analyzed by Fisher's exact test and haplotype analysis. No association was detected for any single SLC6A4 marker and BPD. Additional statistic analyses including other factors also showed lack of association between the SLC6A4 gene polymorphisms and BPD. Significant linkage disequilibrium was obtained among eight SLC6A4 markers and eight common haplotypes were constructed that can be found in 95% of the total subjects. The four commonest haplotypes in both patients and controls were identical. However, the fifth commonest haplotype differed in patients and controls and was significantly associated with a protection from BPD. This study suggested that a particular SLC6A4 haplotype harboring functional sequence variant could play a significant role in BPD etiology in Taiwan. However, due to its modest sample size, the conclusion is not final and should be confirmed in the future studies.

SNPs reported by this study for BD (count: 6)

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs1532042	NSRP1 SLC6A4	A/C		Fisher's exact test, allelic P-value = 0.7, genotypic P-value = 0.91	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
rs1042173	SLC6A4	G/T		Fisher's exact test, allelic P-value = 0.8, genotypic P-value = 0.97	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
rs6354	SLC6A4	A/C		Fisher's exact test, allelic P-value = 1, genotypic P-value = 0.96	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
rs956304	SLC6A4	A/G		Fisher's exact test, allelic P-value = 0.18, genotypic P-value = 0.18	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
rs25528	SLC6A4	A/C		Fisher's exact test, allelic P-value = 1, genotypic P-value = 0.95	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
rs6352	SLC6A4	A/C		Fisher's exact test, allelic P-value = 0.11, genotypic P-value = 0.1	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative

Haplotypes reported by this study for BD (count: 8)

Markers	Haplotype	Related Gene(s)/Region(s)	Statistical Values	Author Comments	Result Category
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	2-1-2-2-1-1-1-1	SLC6A4	Fisher's exact test, P-value = 0.756, OR (95% CI)=0.76 (0.21-2.73)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	2-2-1-1-1-2-1-1	SLC6A4	Fisher's exact test, P-value = 0.293, OR (95% CI)=0.37 (0.07-1.88)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	1-1-1-1-2-1-2-2	SLC6A4	Fisher's exact test, P-value = 0.793, OR (95% CI)=1.15 (0.40-3.34)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	2-1-1-1-2-1-2-2	SLC6A4	Fisher's exact test, P-value = 0.037, OR (95% CI)=0.27 (0.08-0.99)	Further analysis using the RelRisk program indicated that th...... Further analysis using the RelRisk program indicated that the haplotype (i.e. 21112122) was associated with a significant protective effect. More...	Positive
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	1-1-2-2-1-1-2-2	SLC6A4	Fisher's exact test, P-value = 1, OR (95% CI)=1.06 (0.47-2.39)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	2-1-2-2-1-1-2-2	SLC6A4	Fisher's exact test, P-value = 0.359, OR (95% CI)=0.60 (0.23-1.54)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	1-1-1-1-1-1-1-1	SLC6A4	Fisher's exact test, P-value = 0.181, OR (95% CI)=1.34 (0.89-2.01)		Negative
SLC6A4_5HTTLPR - rs956304 - rs25528 - rs6354 - SLC6A4_5HTTVNTR - rs6352 - rs1042173 - rs1532042	2-1-1-1-1-1-1-1	SLC6A4	Fisher's exact test, P-value = 0.475, OR (95% CI)=1.27 (0.73-2.22)		Negative

Other variants reported by this study for BD (count: 2)

Variant Name	Related Gene	Type	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
SLC6A4 intron2 VNTR	SLC6A4	VNTR	10/12 repeated units		Fisher's exact test, allelic P-value = 1, genotypic P-value = 1	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative
5HTTLPR	SLC6A4	microsatellite	s/l		Fisher's exact test, allelic P-value = 0.41, genotypic P-value = 0.71	No association can be obtained between any of the SLC6A4 gen...... No association can be obtained between any of the SLC6A4 gene polymorphisms and BPD. More...	Negative

Genes reported by this study for BD (count: 1)