Study Report

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Basic Info

Reference	Lee, H. J., 2013 PMID: 22925353
Citation	Lee, H. J., et al. (2013). "A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder." J Affect Disord 145(2): 200-207.
Disease Type	Bipolar Disorder
Study Design	case-control
Study Type	Genome-wide association study
Sample Size	1001 BD cases and 1033 controls for the initial sample, 1190 BDcases, 401 controls for the second sample
SNP/Region/Marker Size	724,067 SNPs
Predominant Ethnicity
Population	NIMH Genetics Initiative collections

Detail Info

Sample Diagnosis	Diagnostic Interview for Genetic Studies (DIGS)
Sample Status	For genotyping as part of the Bipolar Genome Study (BiGS), BDI subjects were selected from those collected by the NIMH Genetics Initiative for bipolar disorder in five waves at 11 sites across the United States as described elsewhere in detail (Smith etal.,2009).
Technique	The initial sample was genotyped at the Broad Institute as part of the Genetic Association Information Network (GAIN) using the Affymetrix 6.0 (1MSNP) array. The second sample was similarly genotyped at the Translational Genomics Institute (TGEN). An additional round of QC performed on the merged GAIN and TGEN samples resulted in 703,012 passing SNPs.
Statistical Method	All association analyses were performed using logistic regression in PLINK with covariate adjustment for sex. Missing SNP swere imputed using the expectation-maximization (E-M) algorithmin PLINK and the HapMap CEU r23a reference panel.
Result Summary	A bipolar case-only analysis identified three genomic regions that differed between seasonal and non-seasonal patterned manic episodes of bipolar subjects. The most significant association was for rs41350144, which lies within an intron of NF1A gene on 1p31 (P=3.08x10(-7), OR=2.27). Haplotype construction using flanking three SNPs (rs41453448, rs1125777, and rs12568010) spanning 7549bp showed a more significant association (P=2.12x10(-7), OR=0.4). These data suggest that genetic variants in the NF1A gene region may predispose to seasonal patterned of mania in bipolar disorder.

SNPs reported by this study for BD (count: 23)

SNP	Related Gene(s)	Statistical Values	Author Comments	Result Category
rs550448	JAZF1-AS1 JAZF1	P-value=1.20E-04, Permutated P-value=7.20E-05, OR=0.3987, Confidence Interval (CI)=0.25-0.64	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs498475	JAZF1-AS1	P-value=6.68E-04, Permutated P-value=6.35E-04, OR=0.5876, Confidence Interval (CI)=0.43-0.8	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs552707	JAZF1	P-value=3.75E-05, Permutated P-value=2.70E-05, OR=0.4815, Confidence Interval (CI)=0.34-0.68	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs849320	JAZF1	P-value=2.70E-04, Permutated P-value=2.34E-04, OR=0.4276, Confidence Interval (CI)=0.27-0.68	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs41350144	NFIA NFIX	P-value=3.08E-07, Permutated P-value=1.00E-06, OR=2.269, Confidence Interval (CI)=1.66-3.11	The most significant association was for rs41350144, which l...... The most significant association was for rs41350144, which lies within an intron of NF1A gene on 1p31. More...	Trend
rs2024789	NFIA NFIX	P-value=7.24E-07, Permutated P-value=2.00E-06, OR=2.202, Confidence Interval (CI)=0.27-0.72	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Trend
rs7556462	NFIA NFIX	P-value=4.06E-07, Permutated P-value=1.00E-06, OR=2.264, Confidence Interval (CI)=1.61-3.01	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Trend
rs9403314		P-value=2.27E-04, Permutated P-value=2.55E-04, OR=0.5243, Confidence Interval (CI)=0.37-0.73	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs1125777	NFIA NFIX	P-value=1.77E-06, Permutated P-value=3.00E-06, OR=2.142, Confidence Interval (CI)=0.24-0.56	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Trend
rs7553582	NFIA NFIX	P-value=4.93E-06, Permutated P-value=4.00E-06, OR=0.3662, Confidence Interval (CI)=0.22-0.63	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Trend
rs4915737	NFIA NFIX	P-value=1.80E-04, Permutated P-value=1.04E-04, OR=0.374, Confidence Interval (CI)=1.65-3.11	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs9403346		P-value=2.92E-05, Permutated P-value=2.00E-05, OR=1.9, Confidence Interval (CI)=1.46-2.68	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs9376643		P-value=4.23E-05, Permutated P-value=2.80E-05, OR=1.868, Confidence Interval (CI)=1.43-2.62	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs1415913		P-value=2.04E-05, Permutated P-value=1.40E-05, OR=1.934, Confidence Interval (CI)=1.48-2.73	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs9376641		P-value=7.34E-05, Permutated P-value=6.33E-05, OR=1.839, Confidence Interval (CI)=1.41-2.59	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs864745	JAZF1	P-value=2.44E-05, Permutated P-value=2.10E-05, OR=0.5114, Confidence Interval (CI)=0.37-0.7	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs849139	JAZF1	P-value=2.04E-04, Permutated P-value=1.30E-04, OR=0.537, Confidence Interval (CI)=0.39-0.75	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs10274928	JAZF1	P-value=7.25E-05, Permutated P-value=4.53E-05, OR=0.5328, Confidence Interval (CI)=0.39-0.73	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs6971086	JAZF1	P-value=4.51E-04, Permutated P-value=3.77E-04, OR=0.5477, Confidence Interval (CI)=0.39-0.77	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs537124	JAZF1	P-value=3.75E-05, Permutated P-value=2.70E-05, OR=0.4815, Confidence Interval (CI)=0.34-0.68	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs530649	JAZF1	P-value=2.55E-04, Permutated P-value=1.71E-04, OR=0.4221, Confidence Interval (CI)=0.27-0.67	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs1635853	JAZF1	P-value=1.53E-04, Permutated P-value=1.06E-04, OR=0.5421, Confidence Interval (CI)=0.39-0.74	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative
rs849141	JAZF1	P-value=7.06E-05, Permutated P-value=3.30E-05, OR=0.4931, Confidence Interval (CI)=0.35-0.7	No genome-wide significant association was found in this stu...... No genome-wide significant association was found in this study. More...	Negative

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

Markers	Haplotype	Related Gene(s)/Region(s)	Statistical Values	Author Comments	Result Category
rs41453448 - rs1125777 - rs12568010	G-C-A	NFIA	P-value=2.12E-07, OR=0.427	Haplotype construction using flanking three SNPs (rs41453448...... Haplotype construction using flanking three SNPs (rs41453448, rs1125777, and rs12568010) spanning 7549bp showed a more significant association. More...	Trend

Genes reported by this study for BD (count: 3)

Gene	Statistical Values/Author Comments	Result Category
JAZF1-AS1	No significant association was found. No significant association was found.	Negative
JAZF1	No significant association was found. No significant association was found.	Negative
NFIX	These data suggest that genetic variants in the NF1A gene region may predispose to seasonal patterne...... These data suggest that genetic variants in the NF1A gene region may predispose to seasonal patterned of mania in bipolar disorder. More...	Trend