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	Muhleisen, T. W., 2014 PMID: 24618891
Citation	Muhleisen, T. W., et al. (2014). "Genome-wide association study reveals two new risk loci for bipolar disorder." Nat Commun 5: 3339.
Disease Type	Bipolar Disorder
Study Design	case-control
Study Type	Genome-wide association study
Sample Size	9747 (2266 from MooDS, 7481 from PGC) patients and 14278 (5028 from MooDS, 9250 from PGC) controls
SNP/Region/Marker Size	2,267,487 imputed SNPs
Predominant Ethnicity	Caucasian
Population	German, Polish, Russian, Spanish, Canadian and Australian

Detail Info

Sample Diagnosis	DSM-IV
Sample Status	For MooDS patients, affected subjects received a lifetime diagnosis of BD (type I, type II, schizoaffective disorder bipolar type, BD not otherwise specified) according to DSM-IV criteria using a consensus best-estimate procedure and structured interviews.
Technique	DNA samples were genome-wide genotyped using Infinium assays (Illumina, San Diego, CA, USA) for BeadChips Human660W-Quad (Polish patients) and HumanOmni1-Quad (Canadian, Russian and Spanish patients).
Statistical Method	To produce a fitting marker set for the seven MooDS samples, the SNPs of each MooDS sample were pruned to the least common set (first and second QC) before the imputation and subsequent sample-specific association analyses (followed by a third QC). After the alignment of the MooDS and the PGC sets and another filtering step, the final SNP sets were carried on to the meta-analysis. The first and second QC was performed using several tools from INTERSNP45 (version 1.11) and PLINK46 (version 1.07) as described below. The third QC consisted of manual filtering of data from IMPUTE47 (version 2) and SNPTEST (version 1).
Result Summary	We detect 56 genome-wide significant SNPs in five chromosomal regions including previously reported risk loci ANK3, ODZ4 and TRANK1, as well as the risk locus ADCY2 (5p15.31) and a region between MIR2113 and POU3F2 (6q16.1).

SNPs reported by this study for BD (count: 18)

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs10509129	ANK3	T/G	T	MooDS: P-value=0.34, OR=1.09; PGC: P-value=5.57E-9, OR=1.36; MooDS-PGC: P-value=3.64E-8, adjusted P-value=4.77E-8, OR=1.29	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs9834970	TRANK1 LRBA	C/T	C	MooDS: P-value=0.0014, OR=1.15; PGC: P-value=6.19E-6, OR=1.11; MooDS-PGC: P-value=3.67E-8, adjusted P-value=4.81E-8, OR=1.12	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10994308	ANK3	A/G	A	MooDS: P-value=0.24, OR=1.10; PGC: P-value=3.83E-9, OR=1.36; MooDS-PGC: P-value=2.73E-8, adjusted P-value=3.59E-8, OR=1.27	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10994415	ANK3	C/T	C	MooDS: P-value=0.0096, OR=1.15; PGC: P-value=6.97E-10, OR=1.31; MooDS-PGC: P-value=4.69E-11, adjusted P-value=6.88E-11, OR=1.27	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10994397	ANK3	T/C	T	MooDS: P-value=0.0315, OR= 1.14; PGC: P-value=5.54E-10, OR=1.35; MooDS-PGC: P-value=2.00E-10, adjusted P-value=2.86E-10, OR=1.29	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs1938540	ANK3	T/C	T	MooDS: P-value=0.0317, OR= 1.15; PGC: P-value=1.90E-9, OR=1.32; MooDS-PGC: P-value=5.85E-10, adjusted P-value=8.22E-10, OR=1.27	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs12290811	TENM4	A/T	A	MooDS: P-value=0.0023, OR=1.19; PGC: P-value=9.25E-8, OR=1.19; MooDS-PGC: P-value=7.81E-11, adjusted P-value=1.09E-9, OR=1.19	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs12576775	TENM4	G/A	G	MooDS: P-value=0.0294, OR=1.13; PGC: P-value=2.66E-8, OR=1.18; MooDS-PGC: P-value=3.27E-9, adjusted P-value=4.46E-9, OR=1.17	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs7932890	TENM4	G/A	G	MooDS: P-value=0.0263, OR=1.14; PGC: P-value=7.26E-8, OR=1.18; MooDS-PGC: P-value=6.94E-9, adjusted P-value=9.35E-9, OR=1.17	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs17826816	ADCY2	G/A	G	MooDS: P-value=1.04E-5, OR=1.19; PGC: P-value=3.99E-5, OR=1.12; MooDS-PGC: P-value=7.35E-9, adjusted P-value=9.89E-9, OR=1.14	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs12202969	MIR2113 POU3F2	A/G	A	MooDS: P-value=2.16E-8, OR=1.22; PGC: P-value=6.57E-4, OR=1.08; MooDS-PGC: P-value=8.06E-9, adjusted P-value=1.08E-8, OR=1.12	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10821745	ANK3	G/T	G	MooDS: P-value=0.1691, OR=1.08; PGC: P-value=2.33E-9, OR=1.35; MooDS-PGC: P-value=9.41E-9, adjusted P-value=1.26E-8, OR=1.27	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs17138171	TENM4	C/T	C	MooDS: P-value=0.0261, OR=1.14; PGC: P-value=1.06E-7, OR=1.18; MooDS-PGC: P-value=1.02E-8, adjusted P-value=1.37E-8, OR=1.16	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10821736	ANK3	T/C	T	MooDS: P-value=0.2407, OR=1.06; PGC: P-value=1.31E-9, OR=1.36; MooDS-PGC: P-value=1.16E-8, adjusted P-value=1.55E-8, OR=1.28	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs6550435	TRANK1	G/T	G	MooDS: P-value=7.16E-4, OR=1.15; PGC: P-value=4.80E-6, OR=1.12; MooDS-PGC: P-value=1.54E-8, adjusted P-value=2.05E-8, OR=1.13	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10994430	ANK3	T/G	T	MooDS: P-value=4.96E-4, OR=1.22; PGC: P-value=6.43E-6, OR=1.17; MooDS-PGC: P-value=1.61E-8, adjusted P-value=2.14E-8, OR=1.18	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs10994336	ANK3	T/C	T	MooDS: P-value=0.171, OR=1.11; PGC: P-value=4.01E-9, OR=1.35; MooDS-PGC: P-value=1.76E-8, adjusted P-value=2.34E-8, OR=1.27	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
rs11237799	TENM4	C/A	C	MooDS: P-value=0.8125, OR=1.14; PGC: P-value=2.20E-7, OR=1.17; MooDS-PGC: P-value=1.91E-8, adjusted P-value=2.53E-8, OR=1.16	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive

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

Gene	Statistical Values/Author Comments	Result Category
MIR2113	The genome-wide significant top SNP (rs12202969) is located 104 kb downstream of MIR2113. The genome-wide significant top SNP (rs12202969) is located 104 kb downstream of MIR2113.	Positive
TRANK1	The fifth best-supported locus in 6 our study (top: rs6550435-G, PGC=2.0510-8,OR=1.13). The fifth best-supported locus in 6 our study (top: rs6550435-G, PGC=2.0510-8,OR=1.13).	Positive
TENM4	Our second most significant locus was marked by 10 genome-wide significant SNPs in ODZ4. Our second most significant locus was marked by 10 genome-wide significant SNPs in ODZ4.	Positive
ANK3	The most significant association signal and the largest number of genome-wide significant SNPs (n=26...... The most significant association signal and the largest number of genome-wide significant SNPs (n=26) were identified in ANK3 (ankyrin 3) on chromosome 10q21.2 rs10994415-C, PGC=6.88E-11,OR=1.27). More...	Positive
POU3F2	As the fourth most significant finding in our study As the fourth most significant finding in our study	Positive
ADCY2	As the third most significant finding in our study As the third most significant finding in our study	Positive