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	Safari, R., 2014 PMID: 24997227
Citation	Safari, R., et al. (2014). "New alterations at potentially regulated regions of the Glial Derived Neurotrophic Factor gene in bipolar disorder." J Affect Disord 167: 244-250.
Disease Type	Bipolar Disorder
Study Design	case-control and family-based
Study Type	Candidate-gene association study
Sample Size	66 BD patients, 27 first degree relatives and 56 healthy individuals
SNP/Region/Marker Size	10 variants
Predominant Ethnicity	Caucasian
Population	Turkish
Gender	female/male:37/29 in cases;32/24 in healthy volunteers and 19/8 in first degree relatives;
Age Group	adult : mean age=37.0 (SD=10.42) years of BD patients, mean age=26.60 (SD=10.10) years of illness onset, mean age=37.49 (SD=11.52) years of healthy volunteers, mean age=42.19 (SD=13.92) years of first degree relatives

Detail Info

Sample Diagnosis	DSM-IV
Sample Status	Thirty-three of patients were euthymic;15 were in depression and 18 were in manic episode at the time of the study. The majority of patients(s=64) had bipolar disorder type I.
Technique	Purification and sequencing of PCR products were performed by Macrogen sequencing service.
Statistical Method	Hardyâ€“Weinberg equilibrium was evaluated by using SHEsis software online. Odds ratio (OR) and its corresponding 95% confidence interval (CI) were computed to quantify the association of genotype frequency and allele frequency with bipolar disorder risk. Chi-square test was used to test association of SNPs with bipolar disorder. Unpaired t-test was used to compare age of onset of illness between groups with SNPs and without SNPs. Statistical significance was set at p<0.05 for Chi-square test and t-test. The level of significance was corrected for testing of the multiple SNPs (n=10) and the P-value was set at p<0.005.
Result Summary	Seven previously reported polymorphisms and additional three novel allele variants of GDNF were detected. Association test of rs2075680 C>A SNP showed significant difference between patients and healthy subjects with higher allele frequency in healthy subjects performing Chi-square test. However, there was no significant difference after multiple test corrections between groups. There were no significant differences in association test of rs2075680 C>A SNP between first degree relatives and healthy volunteers/patients. rs142426358 T>C SNP was seen only in one patient with an early age of illness onset. New T>A alterations were found in chromosome locations 5:37812784 and 5:37812782 in two male bipolar disorder patients with age of illness onset 12 and 24years.

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

SNP	Related Gene(s)	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
rs147083416	GDNF GDNF-AS1	C/T		P-value=0.12	rs147083416 C>T SNP was observed only in two healthy volunte...... rs147083416 C>T SNP was observed only in two healthy volunteers(casecode:BG331and BG283),but neither in patients nor in their first degree relatives. No significant difference in allele and genotype frequencies was observed among groups. More...	Negative
rs78613670	GDNF GDNF-AS1	C/T		P-value=0.20	No significant association was observed. No significant association was observed.	Negative
rs142426358	GDNF GDNF-AS1	T/C		P-value=0.36	rs142426358 T>C SNP was seen in a female euthymic patient(ca...... rs142426358 T>C SNP was seen in a female euthymic patient(case code:BG056).There was no rs142426358 T>C SNP either in healthy volunteers or in the first degree relatives. There was no significant difference between patients, relatives or healthy volunteers More...	Negative
rs62360370	GDNF GDNF-AS1	G/A		P-value=0.06, OR=2.52, CI=0.9136-6.9504	There were no significant differences between patients group...... There were no significant differences between patients group and healthy participants group in allele (p=0.06; OR=2.52, 95%CI=[0.91â€“6.95]) and genotype frequencies (p=0.05; OR=2.72, 95%CI=[0.64â€“5.18]) for rs62360370 G>A SNP. More...	Negative
rs79669773	GDNF GDNF-AS1	T/C		P-value=0.14, OR=0.38, CI=0.0909-1.4248	rs79669773 T>C SNP had no association with bipolar disorder. rs79669773 T>C SNP had no association with bipolar disorder.	Negative
rs2075680	GDNF GDNF-AS1	C/A		P-value=0.04, OR=2.11,CI=1.0042-4.4434	Performing Chi-square test and considering P-value threshold...... Performing Chi-square test and considering P-value threshold at 0.05 there were significant differences in the allele frequency for rs2075680 C>A SNP between BD patients and healthy volunteers(p=0.04; OR=2.11,95%CI=[1.0042â€“4.4434]) also between male patients and male volunteers(p=0.03; OR=3.55, 95%CI=[1.0367â€“12.17]). However, after multiple test corrections with the P-value of 0.005 the significance disappeared. More...	Positive
rs115322727	GDNF GDNF-AS1	A/C		P-value=0.27	rs115322727 A>C SNP was found in one healthy volunteer(casec...... rs115322727 A>C SNP was found in one healthy volunteer(casecode:BG624), but not in patients or relatives. No significant difference was seen in allele and genotype frequencies among groups. More...	Negative

Other variants reported by this study for BD (count: 3)

Variant Name	Related Gene	Type	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
GDNF Chr5:37814769 G/A	GDNF	point mutation	G/A		P-value=0.27	We also found a new G>A alteration in chromosome location 5:...... We also found a new G>A alteration in chromosome location 5:37814769 in one male healthy participant (case code: BG310). More...	Negative
GDNF Chr5:37812782 T/A	GDNF	point mutation	T/A		P-value=0.19	New T>A alterations were found in chromosome locations 5:378...... New T>A alterations were found in chromosome locations 5:37812784 and 5:37812782 in two male bipolar disorder patients with age of illness onset 12 and 24years. More...	Negative
GDNF Chr5:37812784 T/A	GDNF	point mutation	T/A		P-value=0.19	New T>A alterations were found in chromosome locations 5:378...... New T>A alterations were found in chromosome locations 5:37812784 and 5:37812782 in two male bipolar disorder patients with age of illness onset 12 and 24years. More...	Negative

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