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	Hu, X.,2010 PMID: 20502444
Citation	Hu, X., Q. Liu, et al. (2010). "SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder." Cell Res 20(7): 854-857.
Disease Type	Bipolar Disorder
Study Design	case-control
Study Type	Genetic interaction study
Sample Size	1869 cases and 2940 controls in WTCCC's BPD GWAS data
Predominant Ethnicity	Caucasian and Mongloid
Population	WTCCC collection and Chinese
Gender	255 males and 220 females for BPD patients and 280 males and 200 females for controls in Chinese samples
Age Group	Adults : Mean age(SD)(year):37.4(9.9) in BPD patients,36.4(7.2) in controls for Chinese samples

Detail Info

Sample Diagnosis	DSM
Replication Size	475 unrelated BPD patients and 480 normal controls for Chinese sample,
Technique	genotyping
Statistical Method	In this study, we used CUDA (Compute Unified Device Architecture) to develop a GPU-based algorithm,named as SHEsisEpi,which can efficiently scan all pairwise SNP-SNP interactions in GWAS, and report purely risk epistasis without single-locus association contamination.
Result Summary	The first pair that fit all criteria was rs10124883-rs178069 (P = 5.37 E?12), and their related genes were ASTN2 and SNAP29, respectively. rs6004133,which is located in PIK4CA, was close to rs178069 in position, and SNP pair rs10124883-rs6004133 (P = 6.49E?12) also fit all the criteria.Both of the significant findings from genome-wide scan, rs10124883-rs178069 (P = 0.026) and rs10124883-rs6004133 (P = 0.021),were replicated in our independent sample set. We also found rs10124883-rs6004133 (P = 0.027), rs10124883-rs165730 (P = 0.038), rs10124883-rs165596 (P = 0.035),and rs10124883-rs178069 (P = 0.031) to be risk epistasis pairs in our independent sample set. Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 or ASTN2 and PIK4CA, or other genes in linkage disequilibrium with any genes in these pairs, were risk factors of BPD, in both Caucasian and Chinese Han populations.

Haplotypes reported by this study for BD (count: 8)

Markers	Haplotype	Related Gene(s)/Region(s)	Statistical Values	Author Comments	Result Category
rs10123629 - rs178069		ASTN2 SNAP29	SNP-SNP interaction:P-value = 0.021 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10124883 - rs165596		ASTN2 SNAP29	SNP-SNP interaction:P-value = 0.035 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10124883 - rs178069		ASTN2 SNAP29	SNP-SNP interaction:P-value = 5.37E-12 for WTCCC data, P-value = 0.031 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10124883 - rs165730		ASTN2 PI4KA	SNP-SNP interaction:P-value = 0.038 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10123629 - rs6004133		ASTN2 PI4KA	SNP-SNP interaction:P-value = 0.026 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10123629 - rs165596		ASTN2 SNAP29	SNP-SNP interaction:P-value = 0.132 for replication study(Chinese sample).	No significant association was found . No significant association was found .	Negative
rs10124883 - rs6004133		ASTN2 PI4KA	SNP-SNP interaction:P-value = 6.49E-12 for WTCCC data, P-value = 0.027 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10123629 - rs165730		ASTN2 PI4KA	SNP-SNP interaction:P-value = 0.085 for replication study(Chinese sample).	No significant association was found . No significant association was found .	Negative

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

Gene	Statistical Values/Author Comments	Result Category
PI4KA	Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 o...... Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 or ASTN2 and PIK4CA, or other genes in linkage disequilibrium with any genes in these pairs, were risk factors of BPD, in both Caucasian and Chinese Han populations. More...	Positive
SNAP29	Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 o...... Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 or ASTN2 and PIK4CA, or other genes in linkage disequilibrium with any genes in these pairs, were risk factors of BPD, in both Caucasian and Chinese Han populations. More...	Positive
ASTN2	Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 o...... Our results indicate that interactions between neurological pathway-related genes ASTN2 and SNAP29 or ASTN2 and PIK4CA, or other genes in linkage disequilibrium with any genes in these pairs, were risk factors of BPD, in both Caucasian and Chinese Han populations. More...	Positive

Gene-gene interactions reported by this study for BD (count: 2)

Gene Group	Markers	Statistical Values	Author Comments	Result Category
ASTN2 SNAP29	rs10124883 - rs178069; rs10123629 - rs165596; rs10123629 - rs178069; rs10124883 - rs165596; rs10124883 - rs178069	SNP-SNP interaction: for markers "rs10124883 - rs178069", P-value = 5.37E-12 for WTCCC data. For markers "rs10123629 - rs165596", P-value = 0.132 for replication study(Chinese sample). For markers "rs10123629 - rs178069", P-value = 0.021 for replication study(Chinese sample). For markers "rs10124883 - rs165596", P-value = 0.035 for replication study(Chinese sample). For markers "rs10124883 - rs178069", P-value = 0.031 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive
ASTN2 PI4KA	rs10124883 - rs6004133; rs10123629 - rs6004133; rs10123629 - rs165730; rs10124883 - rs6004133; rs10124883 - rs165730	SNP-SNP interaction: for markers "rs10124883 - rs6004133", P-value = 6.49E-12 for WTCCC data. For markers "rs10123629 - rs6004133", P-value = 0.026 for replication study(Chinese sample). For markers "rs10123629 - rs165730", P-value = 0.085 for replication study(Chinese sample). For markers "rs10124883 - rs6004133", P-value = 0.027 for replication study(Chinese sample). For markers "rs10124883 - rs165730", P-value = 0.038 for replication study(Chinese sample).	Significant association was found in BPD. Significant association was found in BPD.	Positive