Study Report

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Basic Info

Reference	Ross, K. A.,2011 PMID: 21291537
Citation	Ross, K. A. (2011). "Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes." BMC Med 9: 12.
Disease Type	Bipolar Disorder
Study Design	case-control
Study Type	Genome-wide association study
Sample Size	2000 cases and 1500 controls
SNP/Region/Marker Size	459,653 SNPs
Predominant Ethnicity
Population	WTCCC collection

Detail Info

Statistical Method	chi-squared test and Fisher's exact test(For the stringent filter,only SNPs with an increase in the no-call rate in the disease population and a chi-squared statistic corresponding to P < 5 E-05 in a one-sided test are retained by this initial selection.For further selection,only SNPs with a chi-squared statistic corresponding to P < 5E-04 in a two-sided test in the disease population and a chi-squared statistic corresponding to P > 0.01 in the control population are retained.)
Result Summary	RESULTS: Of 28 disease/locus pairs meeting stringent conditions, 22 show various degrees of disease association, compared with only 8 of 70 in a mock study designed to measure the background association rate (P < 10-9). Additional candidate genes are identified using less stringent filtering conditions. In some cases, somatic deletions appear likely. RA has a distinctive pattern of events relative to other diseases. Similarities in patterns are apparent between BD and HT. CONCLUSIONS: The associations derived represent the first evidence that somatic gene conversion could be a significant causative factor in each of the seven diseases. The specific genes provide potential insights about disease mechanisms, and are strong candidates for further study.

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

SNP	Related Gene(s)	Allele Change	Statistical Values	Author Comments	Result Category
rs12070036	ZNF678	C/T	Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.00028	No significant association was observed in BD. No significant association was observed in BD.	Negative
rs9378249	HLA-B	T/G	Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.00000005	Suggestive association was found. Suggestive association was found.	Trend
rs9551988	PSPC1	C/T	Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.0063	No significant association was observed in BD. No significant association was observed in BD.	Negative
rs2122231		T/A	Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.0002	No significant association was observed in BD. No significant association was observed in BD.	Negative
rs4850057		T/C	Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.000025	No significant association was observed in BD. No significant association was observed in BD.	Negative

Haplotypes reported by this study for BD (count: 21)

Markers	Related Gene(s)/Region(s)	Statistical Values	Author Comments	Result Category
rs12227938 - rs9551988	PSPC1	SNP interactions:P-value = 0.38	No significant association was found . No significant association was found .	Negative
rs10502407 - rs9551988	PSPC1	SNP interactions:P-value = 0.000055	No significant association was found . No significant association was found .	Negative
rs10502407 - rs12070036	ZNF678	SNP interactions:P-value = 0.0000084	There is a trend for significant association. There is a trend for significant association.	Trend
rs9551988 - (SNP A-1797773)	PSPC1	SNP interactions:P-value = 0.74	No significant association was found . No significant association was found .	Negative
rs4850057 - rs9551988	PSPC1	SNP interactions:P-value = 0.62	No significant association was found . No significant association was found .	Negative
rs2122231 - rs9551988	PSPC1	SNP interactions:P-value = 0.35	No significant association was found . No significant association was found .	Negative
rs10502407 - rs4850057		SNP interactions:P-value = 0.93	No significant association was found . No significant association was found .	Negative
rs12227938 - (SNP A-1797773)		SNP interactions:P-value = 0.38	No significant association was found . No significant association was found .	Negative
rs12227938 - rs2122231		SNP interactions:P-value = 0.9	No significant association was found . No significant association was found .	Negative
rs12227938 - rs4850057		SNP interactions:P-value = 0.39	No significant association was found . No significant association was found .	Negative
rs2122231 - (SNP A-1797773)		SNP interactions:P-value = 0.82	No significant association was found . No significant association was found .	Negative
rs2122231 - rs4850057		SNP interactions:P-value = 0.42	No significant association was found . No significant association was found .	Negative
rs4850057 - (SNP A-1797773)		SNP interactions:P-value = 0.38	No significant association was found . No significant association was found .	Negative
rs12070036 - (SNP A-1797773)	ZNF678	SNP interactions:P-value = 0.00000000026	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs12070036 - rs12227938	ZNF678	SNP interactions:P-value = 0.87	No significant association was found . No significant association was found .	Negative
rs12070036 - rs2122231	ZNF678	SNP interactions:P-value = 0.72	No significant association was found . No significant association was found .	Negative
rs12070036 - rs4850057	ZNF678	SNP interactions:P-value = 0.45	No significant association was found . No significant association was found .	Negative
rs12070036 - rs9551988	ZNF678 PSPC1	SNP interactions:P-value = 0.09	No significant association was found . No significant association was found .	Negative
rs10502407 - (SNP A-1797773)		SNP interactions:P-value = 0.0000000000039	Significant association was found in BPD. Significant association was found in BPD.	Positive
rs10502407 - rs12227938		SNP interactions:P-value = 0.44	No significant association was found . No significant association was found .	Negative
rs10502407 - rs2122231		SNP interactions:P-value = 0.98	No significant association was found . No significant association was found .	Negative

Other variants reported by this study for BD (count: 1)

Variant Name	Related Gene	Type	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
LNX1 SNP A-1948953	LNX1	point mutation	C/T		Using the stringent filter, two-sided chi-squared test, genotype P-value = 0.00000000000015	Significant association was found in BPD. Significant association was found in BPD.	Positive

Genes reported by this study for BD (count: 4)

Gene	Statistical Values/Author Comments	Result Category
ZNF678	No significant association of this gene was observed in BD. No significant association of this gene was observed in BD.	Negative
HLA-B	Suggestive association was found at rs9378249. Suggestive association was found at rs9378249.	Trend
PSPC1	No significant association of this gene was observed in BD. No significant association of this gene was observed in BD.	Negative
LNX1	Significant associations of LNX1 SNP A-1948953 were found in BPD patients.LNX1 SNP A-1948953 Significant associations of LNX1 SNP A-1948953 were found in BPD patients.LNX1 SNP A-1948953	Positive