9p13.1CNV Type: Deletion
Largest CNV size: 27956 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
Nongenic deletion within this region identified in an ASD case (Prasad et al., 2012).
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_cases
Samples from the Autism Genome Project (AGP)
1892
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
N/A
85.78% Male
175123
1
0
1
poultney_13_ASD_discovery_cases
ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
299
Cases diagnosed with ASD
N/A
79.86% Male (before filtering)
808689
0
2
2
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
27956
1
0
1
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
911513
0
3
3
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_controls
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)
2342
Controls; subjects had no previous psychiatric history
N/A
46.67% Male
1173343
0
1
1
poultney_13_ASD_discovery_controls
Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
260
Control
N/A
47.49% Male (before filtering)
800358
0
1
1
prasad_12_ASD_discovery_controls
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.
5139
Control
NA
NA (PDx controls 50.2% male)
27956
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
qPCR
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
engchuan_15_ASD_discovery_cases-case8552_203
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
39908046
40083169
175123
NCBI36
Deletion
No
poultney_13_ASD_discovery_cases-case04HI3101A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0976302; NDAR ID NDAR_INVGE211ABY)
39078380
39887068
808689
GRCh37
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0944
N/A
M
ASD
ASD case from AGRE (AGRE ID AU058003; NDAR ID NDAR_INVGK583YBV)
39078380
39887068
808689
GRCh37
Duplication
No
prasad_12_ASD_discovery_cases-case58936L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
38674180
38702135
27956
Unknown
Deletion
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1058-0
N/A
N/A
ACC
Diagnosis of agenesis of the corpus callosum (ACC). ASD: yes. Seizures: unknown.
Developmental delay: yes. Intellectual disability: yes.
39088698
39960742
872045
NCBI36
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1318-0
N/A
N/A
ACC-CBLH
Diagnosis of agenesis of the corpus callosum (ACC) and cerebellar hypoplasia (CBLH). ASD: no. Seizures: no.
Developmental delay: yes. Intellectual disability: unknown.
39098701
39189036
90336
GRCh38
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-caseDP99-022a1
N/A
N/A
ACC-CBLH
Diagnosis of agenesis of the corpus callosum (ACC) and cerebellar hypoplasia (CBLH). ASD: N/A. Seizures: N/A.
Developmental delay: N/A. Intellectual disability: N/A.
39049230
39960742
911513
NCBI36
Duplication
Yes
Controls
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
engchuan_15_ASD_discovery_controls-controlB776710_1007853997
N/A
N/A
Control
No previous psychiatric history
38791697
39445729
654033
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C29011A
N/A
F
Control
NIMH Control (NIMH ID 12943)
39086711
39887068
800358
GRCh37
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case8552_203
Unknown
0 genes
poultney_13_ASD_discovery_cases-case04HI3101A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
CNTNAP3,SPATA31A2,SPATA31A1
poultney_13_ASD_discovery_cases-case99HI0944
Unknown
Unknown (likely multiplex/AGRE)
Unknown
CNTNAP3,SPATA31A2,SPATA31A1
prasad_12_ASD_discovery_cases-case58936L
Unknown
Unknown
Unknown
0 genes
sajan_13_ACC/CBLH/PMG_discovery_cases-case1058-0
Not tested by qPCR
Unknown
Unknown
Unknown
CNTNAP3,DKFZp572C163,FAM75A2,KIAA1714,ZNF658B
sajan_13_ACC/CBLH/PMG_discovery_cases-case1318-0
Not tested by qPCR
Unknown
Unknown
Unknown
RBM17P1,CNTNAP3
sajan_13_ACC/CBLH/PMG_discovery_cases-caseDP99-022a1
qPCR
Unknown
Unknown
Unknown
CNTNAP3,DKFZp572C163,FAM75A2,KIAA1714,ZNF658B
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB776710_1007853997
Unknown
RBM17P1,RN7SL640P,SPATA31A1,FAM74A1,VN2R3P,CNTNAP3,ZNF658B
poultney_13_ASD_discovery_controls-control04C29011A
Unknown
CNTNAP3,SPATA31A2,SPATA31A1
No Animal Model Data Available