Copy Number Variants / 13q31.2-q31.3

13q31.2-q31.3

Case population data
Control population data
Type
Duplication
Average Length
1942570
Range
89941209-90012488
Associated Human Genes
-
Associated Animal Models
-
Autism Reports
6
Populations
12 (6 case / 6 control)
Individuals
8 (7 case / 1 control)
Summary

Summary statement in development

Reports related to 13q31.2-q31.3 (6 Reports)
# Type Title Author, Year
1 Major Functional impact of global rare copy number variation in autism spectrum disorders. Pinto D , et al. (2010)
2 Major An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili... Kaminsky EB , et al. (2011)
3 Minor A discovery resource of rare copy number variations in individuals with autism spectrum disorder. Prasad A , et al. (2013)
4 Major Reciprocal duplication of the Williams-Beuren syndrome deletion on chromosome 7q11.23 is associated with schizophrenia. Mulle JG , et al. (2013)
5 Minor Performance of case-control rare copy number variation annotation in classification of autism. Engchuan W , et al. (2015)
6 Minor Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. C Yuen RK , et al. (2017)
Show all Case Details Show all Cohort Details

13q31.2-q31.3

Description:

ASD genomes (1745 ASD probands, 879 ASD-affected siblings, 1 ASD-affected father, and 1 ASD-affected grandfather) from AGRE (n=730), the AGRE; Autism Treatment Network cohort (n=192) ,the ASD: Genomes to Outcomes Study cohort (n=1421), the Baby Siblings Research Consortium (n=43), the Baby Siblings Research Consortium; The Autism Simplex Collection cohort (n=6), the Infant Sibling Study (n=62), th

Diagnosis:

ASD diagnosis of research quality when meeting criteria on one (n=437) or both (n=1361) of the diagnostic measures ADI-R and ADOS; clinical diagnosis of ASD (n=819) when given by expert clinician according to DSM-IV or DSM-5

C Yuen RK , et al. (2017)
Cohort Size: 2626

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 5469999

Deletion: 0
Duplication: 2

Total CNV: 2
Discovery Method:

WGS

Validation Method:

None (CNV validation not available, CNV not detected by validation method, or CNV not detected by WGS but was detected by validation methodology)

Platform: Complete Genomics (n=1233), Illumina HiSeq 2000 (n=561), HiSeq X (n=3411)
Software: -
Algorithm: -
Geographical Ancestry: N/A

13q31.2-q31.3

Description:

Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals

Diagnosis:

ASD (ADI-R and ADOS): strict, broad, or spectrum ASD

Pinto D , et al. (2010)
Cohort Size: 996

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 71280

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), and/or array SNP (Affy 500K)

Platform: Illumina Infinium 1M SNP microarray
Software: -
Algorithm: QuantiSNP & iPattern
Geographical Ancestry: European

13q31.2-q31.3

Description:

Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children in Toronto, Ontario; McMaster University, Hamilton, Ontario; Memorial University of Newfoundland, St. John's, Newfoundland); the majority of these cases had been previously genotyped by SNP arrays with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were exclu

Diagnosis:

Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS

Prasad A , et al. (2013)
Cohort Size: 676

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 74857

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: Agilent 1M
Software: DNA Analytics v4.0.85 (Agilent), DNAcopy
Algorithm: ADM-2, DNAcopy (R Bioconductor)
Geographical Ancestry: Canada

13q31.2-q31.3

Description:

SCZ probands of Ashkenazi Jewish descent recruited nationally over a 6-year period

Diagnosis:

Diagnosis of schizophrenia based on meeting DSM-IV citeria

Mulle JG , et al. (2013)
Cohort Size: 554

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 1312056

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

Array SNP

Validation Method:

Solid phase hybridization

Platform: Affymetrix Human Genome-Wide SNP array 6.0
Software: Affymetrix power tools software v1.12.0
Algorithm: GLAD, GADA, & BEAST
Geographical Ancestry: Ashkenazi Jewish

13q31.2-q31.3

Description:

Samples from the Autism Genome Project (AGP)

Diagnosis:

Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)

Engchuan W , et al. (2015)
Cohort Size: 1892

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 71279

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

Platform: Illumina 1M
Software: -
Algorithm: -
Geographical Ancestry: Caucasian

13q31.2-q31.3

Description:

Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium

Diagnosis:

Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome

Kaminsky EB , et al. (2011)
Cohort Size: 15749

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 1751440

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis

Platform: Agilent 44K or 105K
Software: Feature Extraction & DNA Analytics
Algorithm: -
Geographical Ancestry: NA
Show all Case Details Show all Cohort Details

pinto_10_ASD_discovery_cases-case5370_3

Clinical Profile:

No epilepsy, no dysmorphic features, brain CT normal

Cognitive Profile:

NA

Pinto D , et al. (2010)
Primary Diagnosis: Autism

Age: NA

Gender: M
Primary Disorder Inheritence: -

Family Profile: NA
CNV Start: 89288955
CNV End: 89360234
CNV Size: 71280
Validation Description: Agilent1M
Primary Disorder Inheritence: -
CNV Inheritance: paternal
Family Profile: NA
Genome Build: GRCh38
Gene Content: -

prasad_12_ASD_discovery_cases-case52026

Clinical Profile:

Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study

Cognitive Profile:

-

Prasad A , et al. (2013)
Primary Diagnosis: ASD

Age: NA

Gender: M
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: -
CNV End: -
CNV Size: 74857
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: -
Gene Content: -

yuen_17_ASD_discovery_cases-caseAU1964303

Clinical Profile:

Case cohort: AGRE. Clinical description: N/A

Cognitive Profile:

-

C Yuen RK , et al. (2017)
Primary Diagnosis: ASD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: Multiplex
CNV Start: 88128746
CNV End: 93598747
CNV Size: 5469999
Validation Description: Not available
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Multiplex
Genome Build: GRCh38
Gene Content: RPL29P29, LINC00433, LINC00560, GRPEL2P1, TRIM60P13, SP3P, LINC00353, LINC02336, PEX12P1, RNA5SP34, FAR1P1, KRT18P27, MIR622, RNU6-75P, BRK1P2, LINC00380, PPIAP23, MIR17HG, MIR17, MIR18A, MIR19A, MIR20A, MIR19B1, MIR92A1, RNU4ATAC3P, FABP5P4, MIR548AS, LINC00363, HNRNPA1P29, LINC01047, LINC00440, LINC01040, RPL7L1P1, LINC00559, LINC01049, LINC00410, LINC00379, GPC5-AS2, GPC5-IT1, GPC5-AS1, GPC6, GPC5

yuen_17_ASD_discovery_cases-caseAU1964304

Clinical Profile:

Case cohort: AGRE. Clinical description: N/A

Cognitive Profile:

-

C Yuen RK , et al. (2017)
Primary Diagnosis: ASD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: Multiplex
CNV Start: 88128746
CNV End: 93598747
CNV Size: 5469999
Validation Description: Not available
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Multiplex
Genome Build: GRCh38
Gene Content: RPL29P29, LINC00433, LINC00560, GRPEL2P1, TRIM60P13, SP3P, LINC00353, LINC02336, PEX12P1, RNA5SP34, FAR1P1, KRT18P27, MIR622, RNU6-75P, BRK1P2, LINC00380, PPIAP23, MIR17HG, MIR17, MIR18A, MIR19A, MIR20A, MIR19B1, MIR92A1, RNU4ATAC3P, FABP5P4, MIR548AS, LINC00363, HNRNPA1P29, LINC01047, LINC00440, LINC01040, RPL7L1P1, LINC00559, LINC01049, LINC00410, LINC00379, GPC5-AS2, GPC5-IT1, GPC5-AS1, GPC6, GPC5

engchuan_15_ASD_discovery_cases-case5370_3

Clinical Profile:

Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)

Cognitive Profile:

-

Engchuan W , et al. (2015)
Primary Diagnosis: ASD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: 89288955
CNV End: 89360234
CNV Size: 71279
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: -

mulle_13_SCZ_discovery_cases_1-caseAJ_8996_1

Clinical Profile:

N/A

Cognitive Profile:

N/A

Mulle JG , et al. (2013)
Primary Diagnosis: Schizophrenia

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 88399235
CNV End: 89677627
CNV Size: 1312056
Validation Description: Solid phase hybridization
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: LINC00433, LINC00560, GRPEL2P1, TRIM60P13, SP3P, LINC00353, LINC02336, LINC01047, LINC00440, LINC01040

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003887

Clinical Profile:

Clinical profile NA

Cognitive Profile:

Cognitive profile NA

Kaminsky EB , et al. (2011)
Primary Diagnosis: Developmental delay/intellectual disability/ASD

Age: NA

Gender: NA
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 88823852
CNV End: 90575292
CNV Size: 1751440
Validation Description: FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: GRPEL2P1, TRIM60P13, SP3P, LINC00353, LINC02336, PEX12P1, RNA5SP34, FAR1P1, KRT18P27, MIR622, LINC01047, LINC00440, LINC01040, RPL7L1P1, LINC00559, LINC01049
Show all Control Details Show all Cohort Details

13q31.2-q31.3

Description:

PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.

Diagnosis:

Control

Prasad A , et al. (2013)
Cohort Size: 5139

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 74857

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

aCGH (PDx controls)

Validation Method:

-

Platform: Agilent 1M (PDx controls)
Software: PDx controls: DNA Analytics v4.0.85 (Agilent), DNAcopy
Algorithm: PDx controls: ADM-2, DNAcopy (R Bioconductor)
Geographical Ancestry: NA

13q31.2-q31.3

Description:

Control subjects selected from three cohorts: a study of Crohn's disease in the Ashkenazim, a study of neuromuscular disease in the Ashkenazim, and the Ashkenazi Jewish Control Registry hosted at Johns Hopkins University.

Diagnosis:

Control. Control subjects from Crohn's and neuromuscular cohorts were not screened for psychiatric disease; Ashkenazi Jewish Control Registry subjects administered a questionnaire about psychiatric conditions.

Mulle JG , et al. (2013)
Cohort Size: 1014

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: N/A

Deletion: N/A
Duplication: N/A

Total CNV: N/A
Discovery Method:

Array SNP

Validation Method:

None

Platform: Affymetrix Human Genome-Wide SNP array 6.0
Software: Affymetrix power tools software v1.12.0
Algorithm: GLAD, GADA, & BEAST
Geographical Ancestry: Ashkenazi Jewish

13q31.2-q31.3

Description:

Matched siblings of autistic probands from the Simons Simplex Collection (SSC).

Diagnosis:

Controls

Sanders SJ , et al. (2011)
Cohort Size: 872

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 1319648

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

-

Platform: Illumina 1M v1 or Illumina 1M v3
Software: -
Algorithm: PennCNV, QuantiSNP, & GNOSIS
Geographical Ancestry: -

13q31.2-q31.3

Description:

Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)

Diagnosis:

Controls; subjects had no previous psychiatric history

Engchuan W , et al. (2015)
Cohort Size: 2342

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 0

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

Solid phase hybridization

Validation Method:

None

Platform: Illumina 1M
Software: -
Algorithm: -
Geographical Ancestry: Caucasian

13q31.2-q31.3

Description:

Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium

Diagnosis:

Controls

Kaminsky EB , et al. (2011)
Cohort Size: 10118

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: NA

Deletion: NA
Duplication: NA

Total CNV: NA
Discovery Method:

aCGH

Validation Method:

-

Platform: Agilent 44K or 105K
Software: Feature Extraction & DNA Analytics
Algorithm: -
Geographical Ancestry: NA
Show all Control Details Show all Cohort Details

sanders_11_ASD_discovery_controls-12623.s1

Clinical Profile:

NA

Cognitive Profile:

NA

Sanders SJ , et al. (2011)
Primary Diagnosis: Control (matched sibling)

Age: 8.8

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 88391071
CNV End: 89677627
CNV Size: 1319648
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: LINC00433, LINC00560, GRPEL2P1, TRIM60P13, SP3P, LINC00353, LINC02336, LINC01047, LINC00440, LINC01040
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