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	Major Depressive Disorder Working Group of the Psychiatric, G. C., 2013 PMID: 22472876
Citation	Major Depressive Disorder Working Group of the Psychiatric, G. C., et al. (2013). "A mega-analysis of genome-wide association studies for major depressive disorder." Mol Psychiatry 18(4): 497-511.
Disease Type	Bipolar Disorder & Major Depressive Disorder
Study Design	case-control
Study Type	mega-analysis of Genome-wide association study
Sample Size	9,238 MDD cases plus 8,039 controls and 6,998 BIP cases plus 7,775 controls
SNP/Region/Marker Size	819 SNPs
Predominant Ethnicity	Caucasian
Population	Psychiatric GWAS Consortium collection

Detail Info

Sample Diagnosis	DSM-IV
Sample Status	The PGC BIP mega-analysis included 7,481 cases with BIP and 9,250 controls in its discovery phase. The BIP samples went through the same QC pipeline used for the MDD data.
Technique	genotyping
Statistical Method	For the MDD replication samples, the top SNP in each region was tested for association, and fixed-effect meta-analysis was used for the replication samples, and for the combination of PGC discovery and replication data.
Result Summary	In the MDD-bipolar cross-disorder analysis, 15 SNPs exceeded genome-wide significance (P<5 x 10(-8)), and all were in a 248 kb interval of high LD on 3p21.1 (chr3:52 425 083-53 822 102, minimum P=5.9 x 10(-9) at rs2535629). Although this is the largest genome-wide analysis of MDD yet conducted, its high prevalence means that the sample is still underpowered to detect genetic effects typical for complex traits. Therefore, we were unable to identify robust and replicable findings. We discuss what this means for genetic research for MDD. The 3p21.1 MDD-BIP finding should be interpreted with caution as the most significant SNP did not replicate in MDD samples, and genotyping in independent samples will be needed to resolve its status.

Genetic factors reported by this study for BD

SNPs reported by this study for BD (count: 15)

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs13068293	PBRM1			P-value=0.0000001127, OR=0.8738 for BIP, P-value=0.00000002904, OR=0.9104 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.6. More...	Positive
rs11130315	PBRM1			P-value=0.0000001217, OR=1.144 for BIP, P-value=0.00000003019, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.7. More...	Positive
rs1561337	PBRM1			P-value=0.0000001146, OR=0.874 for BIP, P-value=0.0000000283, OR=0.9103 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.4. More...	Positive
rs2289250	PBRM1			P-value=0.0000001109, OR=0.8738 for BIP, P-value=0.00000002893, OR=0.9106 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.5. More...	Positive
rs2251219	PBRM1 SMIM4 RNU6-856P			P-value=0.0000000438, OR=1.149 for BIP, P-value=0.00000001913, OR=1.1 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.2. More...	Positive
rs33967311	PBRM1			P-value=0.00000009152, OR=0.873 for BIP, P-value=0.00000002789, OR=0.9105 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.3. More...	Positive
rs2535629	ITIH3			P-value=0.000000362, OR=0.8687 for BIP, P-value=0.000000005883, OR=0.8998 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.1. More...	Positive
rs2336149	PBRM1			P-value=0.0000001009, OR=0.8747 for BIP, P-value=0.00000004847, OR=0.9127 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.14. More...	Positive
rs7611731	PBRM1			P-value=0.00000009983, OR=1.143 for BIP, P-value=0.00000004995, OR=1.096 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.15. More...	Positive
rs12496634	PBRM1			P-value=0.0000001509, OR=1.143 for BIP, P-value=0.00000003439, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.12. More...	Positive
rs11130317	GLT8D1 GNL3 SNORD69			P-value=0.0000001963, OR=0.876 for BIP, P-value=0.00000004832, OR=0.912 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.13. More...	Positive
rs13064064	PBRM1			P-value=0.0000001221, OR=1.144 for BIP, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.10. More...	Positive
rs2268026	NEK4			P-value=0.0000001104, OR=1.145 for BIP, P-value=0.00000003412, OR=1.099 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.11. More...	Positive
rs3755806	PBRM1			P-value=0.0000001175, OR=1.144 for BIP, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.8. More...	Positive
rs12487591	PBRM1			P-value=0.0000001186, OR=1.144 for BIP, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.9. More...	Positive

Genetic factors reported by this study for SZ and/or MDD

SNPs reported by this study for SZ/MDD

Disease	SNP	Related Gene(s)	Statistical Values	Description	Result Category
MDD	rs2251219	PBRM1 SMIM4 RNU6-856P	P-value=0.008059, OR=1.062 for MDD, P-value=0.00000001913, OR=1.1 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.2.	Positive
MDD	rs33967311	PBRM1	P-value=0.007529, OR=0.9413 for MDD, P-value=0.00000002789, OR=0.9105 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.3.	Positive
MDD	rs1561337	PBRM1	P-value=0.006834, OR=0.9404 for MDD, P-value=0.0000000283, OR=0.9103 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.4.	Positive
MDD	rs2289250	PBRM1	P-value=0.007089, OR=0.9408 for MDD, P-value=0.00000002893, OR=0.9106 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.5.	Positive
MDD	rs2535629	ITIH3	P-value=0.0009575, OR=0.9239 for MDD, P-value=0.000000005883, OR=0.8998 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.1.	Positive
MDD	rs7611731	PBRM1	P-value=0.01077, OR=1.059 for MDD, P-value=0.00000004995, OR=1.096 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.15.	Positive
MDD	rs2336149	PBRM1	P-value=0.01088, OR=0.9443 for MDD, P-value=0.00000004847, OR=0.9127 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.14.	Positive
MDD	rs12487591	PBRM1	P-value=0.006943, OR=1.063 for MDD, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.9.	Positive
MDD	rs3755806	PBRM1	P-value=0.006818, OR=1.063 for MDD, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.8.	Positive
MDD	rs11130315	PBRM1	P-value=0.007335, OR=1.063 for MDD, P-value=0.00000003019, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.7.	Positive
MDD	rs13068293	PBRM1	P-value=0.007035, OR=0.9407 for MDD, P-value=0.00000002904, OR=0.9104 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.6.	Positive
MDD	rs11130317	GLT8D1 GNL3 SNORD69	P-value=0.007697, OR=0.9415 for MDD, P-value=0.00000004832, OR=0.912 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.13.	Positive
MDD	rs12496634	PBRM1	P-value=0.007207, OR=1.063 for MDD, P-value=0.00000003439, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.12.	Positive
MDD	rs2268026	NEK4	P-value=0.007732, OR=1.063 for MDD, P-value=0.00000003412, OR=1.099 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.11.	Positive
MDD	rs13064064	PBRM1	P-value=0.006704, OR=1.063 for MDD, P-value=0.00000003091, OR=1.098 for combined sample	In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.10.	Positive