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Study Report
| Comment on Study | View All Comments on Study |
Basic Info
| Reference | Noor A., 2014 PMID: 24700553 |
|---|---|
| Citation | Noor, A., et al. (2014). "Copy number variant study of bipolar disorder in Canadian and UK populations implicates synaptic genes." Am J Med Genet B Neuropsychiatr Genet 165(4): 303-313. |
| Disease Type | Bipolar Disorder |
| Study Design | case-control |
| Study Type | Genome-wide CNV study |
| Sample Size | 936 BD individuals and 940 healthy controls |
| SNP/Region/Marker Size | 39 CNVs |
| Predominant Ethnicity | Caucasian |
| Population | Canadian and English |
| Age Group | adults |
Detail Info
| Sample Diagnosis | DSMIV/ICD 10 BD I or II |
|---|---|
| Sample Status | The Canadian case/control set comprised of 431 BD subjects and 440 controls of North European ancestry recruited at The Centre for Addiction and Mental Health (CAMH) in Toronto. The UK set included 1,005 samples (505 BD subjects and 500 controls) recruited at the Institute of Psychiatry (IOP), London, UK. |
| Technique | Genome-wide genotyping was performed for the Toronto and London case/control sets by microarray using the Illumina Sentrix HumanHap 550 Bead Chip (Illumina, Inc., San Diego, CA). 280 samples (97 cases and 183 controls) from the Toronto set were genotyped at the Genome Quebec facility. For the de novo CNV discovery set, Affymetrix 5.0 arrays (Affymetrix, Santa Clara, CA) were used, and genotyped by the London Regional Genomics Centre (London, ON, Canada). |
| Statistical Method | Intra-chip normalization was performed using Illumina1 Bead Studio software. Only arrays meeting QC thresholds of Log R ratio (LRR) standard deviation<0.35 and B-allele frequency (BAF) standard deviation<0.17 were used for further analysis. An unpaired two-tailed Student's t-test was used to assess the difference in CNV burden between BD cases and controls. |
| Result Summary | Using multiple CNV calling algorithms, and validating using in vitro molecular analyses, we identified CNVs implicating several candidate genes that encode synaptic proteins, such as DLG1, DLG2, DPP6, NRXN1, NRXN2, NRXN3, SHANK2, and EPHA5, as well as the neuronal splicing regulator RBFOX1 (A2BP1), and neuronal cell adhesion molecule CHL1. We have also identified recurrent CNVs on 15q13.3 and 16p11.2-regions previously reported as risk loci for neuropsychiatric disorders. In addition, we performed CNV analysis of individuals from 215 BD trios and identified de novo CNVs involving the NRXN1 and DRD5 genes. Our study provides further evidence of the occasional involvement of genomic mutations in the etiology of BD,however, there is no evidence of an increased burden of CNV sin BD.Further, the identification of CNVs at multiple members of the neurexin gene family in BD individuals, supports the role of synaptic disruption in the etiology of BD. |
| Name | Position | Type | Author Comments |
|---|---|---|---|
| CNV_Abdul Noor[2014]_8 | chr5:122197444-122353529 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_9 | chr6:162504743-162738093 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_6 | chr4:65754311-66056508 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_7 | chr5:409381-706343 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_12 | chr10:56465084-58506956 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_13 | chr10:68825642-68977724 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_10 | chr7:110617273-111138748 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_11 | chr7:152925592-153338318 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_1 | chr1:144943150-146293282 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_4 | chr3:192548094-192552686 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_5 | chr3:198394479-198832486 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_2 | chr3:1294698-1449128 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_3 | chr3:152495187-152534813 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_38 | chrX:122153999-122195582 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_39 | chrX:122153999-122195582 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_30 | chr7:110866148-111029397 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_31 | chr7:110866148-110987007 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_32 | chr11:64234575-64639365 | duplication | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_33 | chr11:69878242-70154458 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_34 | chr16:87762449-87791352 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_35 | chrX:122153999-122195582 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_36 | chrX:122153999-122195582 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_37 | chrX:122153999-122195582 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_23 | chr16:76767852-76781687 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_22 | chr16:7042998-7066733 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_25 | chr3:38411-3305438 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_24 | chr2:50735657-50800548 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_27 | chr7:102938672-102941273 | deletion | Selected stringent CNVs not validated by qPCR from BD case data Selected stringent CNVs not validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_26 | chr3:198394479-198828573 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_29 | chr7:110810558-111103676 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_28 | chr7:110765939-110953401 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_15 | chr11:83821345-83990370 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_14 | chr10:126644888-126692039 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_17 | chr14:78385349-78459898 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_16 | chr11:83789032-84032216 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_19 | chr14:80620641-80648455 | duplication | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_18 | chr15:49418771-49482945 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_21 | chr22:38799826-38892173 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| CNV_Abdul Noor[2014]_20 | chr22:32420689-32524745 | deletion | Selected stringent CNVs validated by qPCR from BD case data Selected stringent CNVs validated by qPCR from BD case data |
| Gene | Statistical Values/Author Comments | Result Category |
|---|---|---|
| GJA8 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| GJA5 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| GPR87 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| GLDN | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| EPHA5 | A 300 kb loss CNV at EPHA5 was identified in a single BD case. A 300 kb loss CNV at EPHA5 was identified in a single BD case. | Positive |
| DPP6 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| FMO5 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| EXOC3 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CTTN | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CTNNA3 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| DLG2 | Two deletions and one duplication involving the post-synaptic density gene DLG2 were detected and va...... Two deletions and one duplication involving the post-synaptic density gene DLG2 were detected and validated in three unrelated cases. More... | Positive |
| DLG1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CNTN6 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CNTN4 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CTBP2 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CRBN | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CDH15 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CEP72 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CHD1L | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CHL1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| AHRR | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| BDH1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| EXOC3-AS1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| CCDC50 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| RBFOX1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| ACP6 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| ZRANB1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| WWOX | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| TSHR | A duplication of 5 (or 6, depending on isoform) out of 10 coding exons of the thyroid stimulating ho...... A duplication of 5 (or 6, depending on isoform) out of 10 coding exons of the thyroid stimulating hormone receptor gene, TSHR, was identified in another BD case. More... | Positive |
| TNRC6B | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| ZWINT | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| PCDH15 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| PPFIA1 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| P2RY13 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| PARK2 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| SLC9A3 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| SNX24 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| RELN | Selected stringent CNV related to this gene is not validated by qPCR from BD case data. Selected stringent CNV related to this gene is not validated by qPCR from BD case data. | Negative |
| SHANK2 | In another case, we identified a 276 kb duplication encompassing several genes, including the seven ...... In another case, we identified a 276 kb duplication encompassing several genes, including the seven 30-most exons of the SHANK2 gene(NM_012309). More... | Positive |
| LARGE | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| LOC220729 | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| GRIA3 | Selected stringent CNV related to this gene is not validated by qPCR from BD case data. Selected stringent CNV related to this gene is not validated by qPCR from BD case data. | Negative |
| IMMP2L | Deletions involving the IMMP2L gene were identified in five unrelated cases. Deletions involving the IMMP2L gene were identified in five unrelated cases. | Positive |
| NRXN2 | Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin fami...... Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin family of genes, including a loss and a gain - both exonic - at NRXN1 (also see de novo loss at NRXN1 in another BD subject, below), an intronic deletion in NRXN3 and a partial duplication (exonic) of NRXN2. More... | Positive |
| NRXN3 | Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin fami...... Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin family of genes, including a loss and a gain - both exonic - at NRXN1 (also see de novo loss at NRXN1 in another BD subject, below), an intronic deletion in NRXN3 and a partial duplication (exonic) of NRXN2. More... | Positive |
| MED12L | Selected stringent CNV related to this gene is validated by qPCR from BD case data. Selected stringent CNV related to this gene is validated by qPCR from BD case data. | Positive |
| NRXN1 | Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin fami...... Interestingly, in four unrelated BD cases, we identified CNVs involving members of the neurexin family of genes, including a loss and a gain - both exonic - at NRXN1 (also see de novo loss at NRXN1 in another BD subject, below), an intronic deletion in NRXN3 and a partial duplication (exonic) of NRXN2. More... | Positive |
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Last update: March 31, 2016