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	Shi, J., 2008 (c) PMID: 18496208
Citation	Shi, J., J. A. Badner, et al. (2008). "PDLIM5 and susceptibility to bipolar disorder: a family-based association study and meta-analysis." Psychiatr Genet 18(3): 116-121.
Disease Type	Bipolar Disorder
Study Design	family-based
Study Type	Candidate-gene association study
Sample Size	A total of 1103 samples from 290 European American BP families
SNP/Region/Marker Size	5 SNPs
Predominant Ethnicity	Caucasian
Population	CNG, NIMH and the CHIP collections

Detail Info

Sample Diagnosis	DSM-III-R or DSM-IV
Technique	Genotyping was carried out using TaqMan 5_exonuclease assays
Statistical Method	Tests for Hardy-Weinberg equilibrium (HWE) of genotype distribution in founders (unrelated parents in this study) were performed with the software PEDSTATS. Pairwise D' and r², linkage disequilibrium (LD) between any two markers was analyzed using the program Haploview (version 4.0). Haplotype blocks were identified using the solid spine of LD method in Haploview. Allelic association of individual SNPs was tested using the Sibling-Transmission/ Disequilibrium Test (sib_tdt) program in the program package ASPEX 2.5. Haplotypic association tests were carried out using PDTPHASE in the program package UNPHASED. PDTPHASE analyzes whole pedigrees for association, correcting for the effects of linkage. It gives results for the individual haplotypes and a global probability value for a particular combination of SNPs. Given an association with schizophrenia shown in a previous study, we also analyzed our data based on the presence of psychosis in affected offspring.
Result Summary	Our association analysis showed no single SNP associated with BP. A rare haplotype consisted of rs10008257 and rs2433320 had nominal association (p = 0.045), which failed to survive correction for multiple tests.

SNPs reported by this study for BD (count: 5)

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs1543013	PDLIM5	A/C		TDT P-value = 0.26	Our association analysis showed no single SNP associated wit...... Our association analysis showed no single SNP associated with BP. More...	Negative
rs2433320	PDLIM5	G/A		TDT P-value = 0.13	Our association analysis showed no single SNP associated wit...... Our association analysis showed no single SNP associated with BP. More...	Negative
rs10008257	PDLIM5	G/A		TDT P-value = 0.068	Our association analysis showed no single SNP associated wit...... Our association analysis showed no single SNP associated with BP. The SNP rs10008257 reveals a borderline association with BP. More...	Negative
rs774992	PDLIM5	C/T		TDT P-value = 0.39	Our association analysis showed no single SNP associated wit...... Our association analysis showed no single SNP associated with BP. More...	Negative
rs2452594	PDLIM5	A/G		TDT P-value = 0.75	Our association analysis showed no single SNP associated wit...... Our association analysis showed no single SNP associated with BP. More...	Negative

Haplotypes reported by this study for BD (count: 7)

Markers	Haplotype	Related Gene(s)/Region(s)	Statistical Values	Author Comments	Result Category
rs10008257 - rs2433320	AA	PDLIM5	Association analysis showed TDT P-value = 0.77. Meta-analysis showed Z test P-value = 0.168, Z=1.379		Negative
rs10008257 - rs2433320	AG	PDLIM5	Association analysis showed TDT P-value = 0.16. Meta-analysis showed Z test P-value = 0.340, Z=0.955		Negative
rs2452594 - rs1543013	AC	PDLIM5	Association analysis showed TDT P-value = 0.70		Negative
rs2452594 - rs1543013	GA	PDLIM5	Association analysis showed TDT P-value = 0.47		Negative
rs2452594 - rs1543013	GC	PDLIM5	Association analysis showed TDT P-value = 0.70		Negative
rs10008257 - rs2433320	GA	PDLIM5	Association analysis showed TDT P-value = 0.045. Meta-analysis showed Z test P-value = 0.674, Z=0.458	A rare haplotype consisted of rs10008257 and rs2433320 had n...... A rare haplotype consisted of rs10008257 and rs2433320 had nominal association, which failed to survive correction for multiple tests. More...	Positive
rs10008257 - rs2433320	GG	PDLIM5	Association analysis showed TDT P-value = 0.069. Meta-analysis showed Z test P-value = 0.417, Z=0.812	Borderline association signals are also seen at the common h...... Borderline association signals are also seen at the common haplotype GG in individual haplotype association analysis and in a global analysis More...	Negative

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