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	Cruceanu, C., 2013 PMID: 24237345
Citation	Cruceanu, C., A. Ambalavanan, et al. (2013). "Family-based exome-sequencing approach identifies rare susceptibility variants for lithium-responsive bipolar disorder." Genome 56(10): 634-640.
Disease Type	Bipolar Disorder
Study Design	family-based
Study Type	Rare variant association study
Sample Size	DNA samples collected from multigenerational family units consist of 3-7 affected individuals across 1-3 generations, with as many as 36 total individuals sampled per family. 25 multigenerational families and over 1000 controls.
SNP/Region/Marker Size	250 exomes
Predominant Ethnicity	Caucasian
Population	Canadian

Detail Info

Sample Diagnosis	Research Diagnostic Criteria
Sample Status	Inclusion and exclusion criteria include the following: (1) current diagnosis of BD (either type I or type II); (2) clear-cut response to Li monotherapy defined by previously published criteria. The probands were recruited from affective disorders clinics in Canada
Technique	Exome capture, sequencing, and variant calling
Statistical Method	Single nucleotide variants were called for each exome using primarily the Genome Analysis Toolkit (GATK), and small insertions and deletions were called using the Dindel pipeline; the toolkit VarScanwas also used for variant calling. Finally, variants were annotated with the Annovar software. To prioritize variants with potentially important roles in the genetic susceptibility of BD, according to our hypothesis we first focused on rarity (Â²1% frequency in the population based). Sequence information from three publicly-available repositories of genomic datasets (exomes and whole genomes) were used to assess the frequency of each variant in the general population: 1000 Genomes, Exome Variant Server (EVS), and Complete Genomics.
Result Summary	To identify such rare variants, we are using a targeted exome capture and high-throughput DNA sequencing approach, and analyzing the entire coding sequences of BD affected individuals from multigenerational families. We are prioritizing rare variants with a frequency of less than 1% in the population that segregate with affected status within each family, as well as being potentially highly penetrant (e.g., protein truncating, missense, or frameshift) or functionally relevant (e.g., 3'UTR, 5'UTR, or splicing). By focusing on rare variants in a familial cohort, we hope to explain a significant portion of the missing heritability in BD, as well as to narrow our current insight on the key biochemical pathways implicated in this complex disorder.

Other variants reported by this study for BD (count: 15)

Variant Name	Related Gene	Type	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
ID1 Chr20:30193296 T/G	ID1	Missense	T/G		no P-value	rare variant found in this study. rare variant found in this study.	Trend
CDV3 Chr3:133305557 A/T	CDV3	Missense	A/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
ODZ2 Chr5:167627125 C/T	TENM2	Missense	C/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
MTOR Chr1:11194520 C/T	MTOR	Splicing	C/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
TAB2 Chr6:149699617 G/A	TAB2	Missense	G/A		no P-value	rare variant found in this study. rare variant found in this study.	Trend
SLC25A21 Chr14:37147560 C/T	SLC25A21	others	C/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
CASP1 Chr11:104901923	CASP1	Nonframeshift del			no P-value	rare variant found in this study. rare variant found in this study.	Trend
ZPR1 Chr11:116652892 A/T	ZNF259	Missense	A/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
CARD16 Chr11:104916205 A/G	CARD16	Upstream	A/G		no P-value	rare variant found in this study. rare variant found in this study.	Trend
WWC1 Chr5:167896045 G/A	WWC1	others	G/A		no P-value	rare variant found in this study. rare variant found in this study.	Trend
SLU7 Chr5:159840980 T/C	SLU7	Missense	T/C		no P-value	rare variant found in this study. rare variant found in this study.	Trend
ARV1 Chr1:231114915 A/T	ARV1	Missense	A/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
DNAH14 Chr1:225586971 A/T	DNAH14	Stoploss	A/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend
CFAP46 Chr10:134730168 G/A	CFAP46	Missense	G/A		no P-value	rare variant found in this study. rare variant found in this study.	Trend
SLK Chr10:105779646 C/T	SLK	Missense	C/T		no P-value	rare variant found in this study. rare variant found in this study.	Trend

Genes reported by this study for BD (count: 15)

Gene	Statistical Values/Author Comments	Result Category
SLK	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
MTOR	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
ID1	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
SLU7	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
CDV3	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
DNAH14	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
TAB2	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
ZNF259	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
CFAP46	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
ARV1	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
WWC1	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
CARD16	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
TENM2	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
CASP1	Rare variant was found within this gene. Rare variant was found within this gene.	Trend
SLC25A21	Rare variant was found within this gene. Rare variant was found within this gene.	Trend