7p13CNV Type: Deletion
Largest CNV size: 3222 bp
Statistics Box:
Number of Reports: 9
Number of Reports: 9
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
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
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Deletion
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
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
bitar_19_ASD_discovery_cases
ASD cases selected through specialized institutions and NGOs specializing in mental disorders throughout Lebanon
19
Cases diagnosed with ASD using DSM-IV criteria and CARS
N/A
84.21% Male
75000
1
0
1
brandler_18_ASD_replication_cases
Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
1979
Cases diagnosed with ASD
N/A
N/A
314
1
0
1
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
69595
1
0
1
girirajan_11_ASD_discovery_cases
ASD cases with sporadic autism from the Simons Simplex Collection (SSC)
336
Diagnosis of ASD based on meeting criteria on ADOS, ADI-R, and expert clinical judgment. 246 cases with no intellectual disability, 90 cases with intellectual disability. Exclusion criteria: significant hearing, vision, or motor problems; significant birth complications; a diagnosis of ASD-related disorders, such as Fragile X; or having a relative (up to 3rd degree) with ASD or sibling showing ASD-related symptoms.
59769
1
0
1
kaminsky_11_DD/ID/ASD_discovery_cases
Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium
15749
Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome
NA
NA
2365011
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)
51996
0
1
1
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
16434
2
0
2
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
116205
0
1
1
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
3222
2
0
2
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
128287
0
1
1
girirajan_11_ASD_discovery_controls
Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
337
Control. Individuals screened specifically for eight mental health disorders.
59769
0
0
0
kaminsky_11_DD/ID/ASD_discovery_controls
Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium
10118
Controls
NA
NA
NA
NA
NA
NA
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)
0
0
0
0
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)
16434
0
0
0
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
bitar_19_ASD_discovery_cases
Lebanon
aCGH
Agilent SurePrint G3 2x400K
ADM-2
Agilent Cytogenomics v.3.0.6.6, Agilent Feature Extraction
qPCR
brandler_18_ASD_replication_cases
N/A
WGS
Illumina HiSeq X10
ForestSV, Lumpy, Manta, Mobster, SV2
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_11_ASD_discovery_cases
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
None
kaminsky_11_DD/ID/ASD_discovery_cases
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
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
sanders_11_ASD_discovery_cases
White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
Solid phase hybridization
Illumina 1M v1, Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_11_ASD_discovery_controls
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
bitar_19_ASD_discovery_cases-case117
N/A
M
ASD
Case diagnosed with ASD using DSM-IV criteria and CARS. Additional medical history: deafness. Family history: born to non-consanguineous parents; family history not available.
44809345
44884529
75185
GRCh38
Deletion
Yes
brandler_18_ASD_replication_cases-case1-0400-003
N/A
M
ASD
Case from MSSNG cohort
44759429
44759742
314
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4339_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
43686906
43756501
69596
GRCh38
Deletion
No
girirajan_11_ASD_discovery_cases-Si258
12
M
Autism
ADOS score: 6. Vineland composite score: 69.
No mental retardation/intellectual disability. Full-scale IQ, 74; Verbal IQ, 80; Non-verbal IQ, 74.
45159705
45219474
59770
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004229
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
44193369
46558381
2365013
GRCh38
Deletion
Yes
poultney_13_ASD_discovery_cases-case99HI0807A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU055105; NDAR ID NDAR_INVME794HY9)
44572572
44624567
51996
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case47909
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
45079797
45096230
16434
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case62391L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
45079797
45096230
16434
Unknown
Deletion
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1476-0
N/A
N/A
ACC
Diagnosis of agenesis of the corpus callosum (ACC). ASD: no. Seizures: no.
Developmental delay: no. Intellectual disability: no.
44271346
44387550
116205
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-11665.p1
9.9
M
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 79; verbal IQ, 65
45532387
45535609
3223
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12456.p1
14.3
F
Autism
NA
Full-scale IQ, 40; non-verbal IQ, 45; verbal IQ, 30
46424465
46427422
2958
GRCh38
Deletion
No
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-controlHABC_903002_903002
N/A
N/A
Control
No previous psychiatric history
44271346
44399633
128288
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
bitar_19_ASD_discovery_cases-case117
qPCR
De novo
LINC01952,PURB,MIR4657,PPIA
brandler_18_ASD_replication_cases-case1-0400-003
No validation step reported
Maternal
ZMIZ2
engchuan_15_ASD_discovery_cases-case4339_1
Unknown
COA1
girirajan_11_ASD_discovery_cases-Si258
Unknown
Simplex
RAMP3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004229
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
RNU6-1097P,DDX56,LINC01952,PURB,MIR4657,SNHG15,SNORA9,SNORA5A,SNORA5C,SNORA5B,ELK1P1,RNU6-241P,CICP20,RNU6-326P,IGFBP3,FTLP15,TTC4P1,ZNF619P1,YKT6,NPC1L1,TMED4,ZMIZ2,PPIA,H2AFV,MYO1G,CCM2,TBRG4,RAMP3,GTF2IP13,IGFBP1,GCK,CAMK2B,NUDCD3,OGDH,ADCY1,SEPT7P2,NACAD
poultney_13_ASD_discovery_cases-case99HI0807A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
DDX56,TMED4,OGDH
prasad_12_ASD_discovery_cases-case47909
Unknown
Unknown
Unknown
NACAD,CCM2
prasad_12_ASD_discovery_cases-case62391L
Unknown
Unknown
Unknown
NACAD,CCM2
sajan_13_ACC/CBLH/PMG_discovery_cases-case1476-0
qPCR
Paternal
Unknown
Unknown
CAMK2B,NUDCD3
sanders_11_ASD_discovery_cases-11665.p1
Unknown
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12456.p1
Unknown
Simplex (quad-proband matched)
Not segregated
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_903002_903002
Unknown
CAMK2B,NUDCD3
No Animal Model Data Available