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	The Wellcome Trust Case Control Consortium, 2007 PMID: 17554300
Citation	WTCCC (2007). "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls." Nature 447(7145): 661-678.
Disease Type	Bipolar Disorder
Study Design	case-control
Study Type	Genome-wide association study
Sample Size	1,868 cases, 2,938 controls
SNP/Region/Marker Size	500,568 SNPs
Predominant Ethnicity	Caucasian
Population	WTCCC collection
Gender	37% male and 63% female for cases
Age Group	adolescents and adults : >16 years (30% <40 years, 29% 40-49 years, 24% 50-59 years, 14% 60-69 years, 3% >70 years)

Detail Info

Sample Diagnosis	Research Diagnostic Criteria (RDC)
Sample Status	Individuals who had been in contact with mental health services were recruited if they suffered with a major mood disorder in which clinically significant episodes of elevated mood had occurred. Bipolar subtypes include: bipolar I disorder (71% cases), schizoaffective disorder bipolar type (15% cases), bipolar II disorder (9% cases) and manic disorder (5% cases)
Technique	SNP genotyping was performed with the commercial release of the GeneChip 500K arrays at Affymetrix Services Lab. A modified version of the genotyping assay developed for the 100K Mapping Array was used.
Statistical Method	CHIAMO to simultaneously call the genotypes from all individuals; snpMatrix and SNPTEST for genome-wide association analysis; C11 program IMPUTE for imputation
Result Summary	Case-control comparisons identified 24 independent association signals at P<5E-07: 1 in bipolar disorder, 1 in coronary artery disease, 9 in Crohn's disease, 3 in rheumatoid arthritis, 7 in type 1 diabetes and 3 in type 2 diabetes. Across all diseases, they identified a large number of further signals (including 58 loci with single-point P values between 1E-05 and 5E-07) likely to yield additional susceptibility loci.

SNPs reported by this study for BD (count: 14)

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs2953145	RNPEPL1	C/G	C	Genotypic P-value = 6.57E-06; Heterozygote OR (95%CI)=1.84 (1.31-2.58); Homozygote OR (95%CI)=2.14 (1.53-2.98)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs3761218	CDC25B	T/C	T	Genotypic P-value = 6.71E-06; Heterozygote OR (95%CI)=0.97 (0.81-1.15); Homozygote OR (95%CI)=1.31 (1.09-1.57)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs1375144	DPP10	A/G	A	Genotypic P-value = 1.31E-05; Heterozygote OR (95%CI)=1.32 (1.07-1.63); Homozygote OR (95%CI)=1.59 (1.29-1.96)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs2609653			C	Trend P-value = 6.86E-06; no genotypic P-value; Heterozygote OR (95%CI)=1.43 (1.19-1.71); Homozygote OR (95%CI)=3.62 (1.26-10.44)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs11622475	TDRD9	C/T	C	Genotypic P-value = 8.14E-06; Heterozygote OR (95%CI)=1.13 (0.89-1.44); Homozygote OR (95%CI)=1.47 (1.17-1.86)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs1344484		T/C	T	Genotypic P-value = 1.03E-05; Heterozygote OR (95%CI)=1.24 (1.03-1.48); Homozygote OR (95%CI)=1.52 (1.27-1.82)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs10134944	SLC35F4		T	Genotypic P-value = 6.89E-06; Heterozygote OR (95%CI)=1.45 (1.24-1.68); Homozygote OR (95%CI)=1.32 (0.74-2.33)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs10982256	DFNB31	T/C	T	Genotypic P-value = 4.41E-05; Heterozygote OR (95%CI)=1.26 (1.08-1.47); Homozygote OR (95%CI)=1.47 (1.24-1.74)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs683395	LAMP3		G	Genotypic P-value = 5.11E-06; Heterozygote OR (95%CI)=1.47 (1.26-1.71); Homozygote OR (95%CI)=1.30 (0.69-2.46)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs7570682			A	Genotypic P-value = 1.64E-05; Heterozygote OR (95%CI)=1.23 (1.09-1.40); Homozygote OR (95%CI)=1.64 (1.28-2.12)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs4276227	CMTM8	C/T	C	Genotypic P-value = 2.62E-05; Heterozygote OR (95%CI)=1.20 (0.99-1.46); Homozygote OR (95%CI)=1.49 (1.23-1.81)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs6458307	GLTSCR1L		T	Genotypic P-value = 4.35E-06; Heterozygote OR (95%CI)=0.84 (0.75-0.96); Homozygote OR (95%CI)=1.39 (1.13-1.69)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs4027132	LPIN1	A/G	A	Genotypic P-value = 9.68E-06; Heterozygote OR (95%CI)=1.39 (1.19-1.64); Homozygote OR (95%CI)=1.51 (1.27-1.79)	showing moderate evidence of association with BD showing moderate evidence of association with BD	Trend
rs420259	PALB2	A/G	A	Genotypic P-value = 6.29E-08; Heterozygote OR (95%CI)=2.08(1.60-2.71); Homozygote OR (95%CI)=2.07 (1.6-2.69)	The strongest signal in BD was with rs420259 at chromosome 1...... The strongest signal in BD was with rs420259 at chromosome 16p12 and the best-fitting genetic model was recessive, but was not additionally supported by the expanded reference group analysis. More...	Positive