1p22.2CNV Type: Deletion-Duplication
Largest CNV size: 219479 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Deletion
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
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-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
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
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
11775
1
0
1
celestino-soper_11_ASD_discovery_cases
ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
99
ASD
87.88% Male
384
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
219478
2
0
2
leblond_12_ASD_replication_cases
Dataset featuring ASD patients from the Autism Genome Project carrying de novo SHANK2 deletions previously identified by Pinto et al. 2010. CNV validation information taken from Pinto report.
2
1 patient diagnosed with autism, 1 patient diagnosed with PDD-NOS.
NA
100% Male
22192
1
0
1
mosca_16_DCD_discovery_cases
Participants recruited as part of a multidisciplinary study at the Alberta Children's Hospital (Calgary, Alberta, Canada)
82
All cases met diagnostic criteria for developmental coordination disorder (DCD) with or without co-occurring ADHD and/or reading disorder.
Range, 8-17 years (Mean, 10.06 2.92 yrs.)
N/A
150854
0
1
1
pinto_10_ASD_discovery_cases
Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
996
ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
219479
1
0
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
217273
2
0
2
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
128414
3
2
5
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
278947
0
1
1
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
127188
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)
7078
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)
217273
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.
130727
9
0
9
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
celestino-soper_11_ASD_discovery_cases
aCGH
Agilent 1M
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
leblond_12_ASD_replication_cases
1 Canadian, 1 French
Solid phase hybridization
Illumina 1M SNP array
QuantiSNP, PennCNV
None
mosca_16_DCD_discovery_cases
Canada
Solid phase hybridization
Illumina HumanOmni2.5-Quad BeadChip
iPattern, PennCNV, QuantiSNP, CNVPartition
qPCR
pinto_10_ASD_discovery_cases
European
Solid phase hybridization
Illumina Infinium 1M SNP microarray
QuantiSNP, iPattern
qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
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
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
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
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
brandler_18_ASD_discovery_cases-caseSSC12959
N/A
M
ASD
Case from SSC cohort
90083939
90095714
11776
GRCh38
Deletion
Yes
celestino-soper_11_ASD_discovery_cases-11076
NA
M
ASD
NA
NA
89058970
89059354
385
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case5256_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
91113291
91157278
43988
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case5394_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
88138111
88357589
219479
GRCh38
Deletion
No
leblond_12_ASD_replication_cases-Pintocase6319_3
NA
M
PDD-NOS
ADI-R domain scores: social, 14; communication, 8; behaviors, 2; age at first symptoms <36 months. Developmental milestones: delayed langauge (1st words at 24 months, 1st sentences at 48 months); no history of regression. Language and communication evaluation: delayed but functional language. Epilepsy/seizures: no history of epilepsy. Neurological examination: normal. Dysmorphic features: large and prominent ears, flat feet. Other comorbid medical conditions: hypermetropia.
Mild intellectual disability (ID). WISC-III IQ scores: full-scale IQ, 60; performance IQ, 60; verbal IQ, 67.
91091100
91113291
22192
GRCh38
Deletion
No
mosca_16_DCD_discovery_cases-case104303
N/A
M
DCD
Ancestry: Admixed. Family history: maternal diagnosis reading disorder; paternal diagnosis reading disorder; sibling diagnosis ADHD.
90063323
90214176
150854
GRCh38
Duplication
Yes
pinto_10_ASD_discovery_cases-case5394_3
NA
M
ASD
NA
NA
88138111
88357589
219479
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case102595
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
91354018
91393614
39597
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case92174L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
88377634
88594906
217273
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-12233.p1
5.5
M
Autism
NA
Full-scale IQ, 106; non-verbal IQ, 108; verbal IQ, 99
91091100
91113291
22192
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12297.p1
15
M
Autism
NA
Full-scale IQ, 97; non-verbal IQ, 102; verbal IQ, 89
89433283
89462631
29349
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12435.p1
11.2
M
Autism
NA
Full-scale IQ, 47; non-verbal IQ, 51; verbal IQ, 40
90087933
90091422
3490
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12566.p1
10.4
M
Autism
NA
Full-scale IQ, 48; non-verbal IQ, 50; verbal IQ, 43
90063323
90191737
128415
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12603.p1
11.7
M
Autism
NA
Full-scale IQ, 23; non-verbal IQ, 26; verbal IQ, 20
88563648
88609013
45366
GRCh38
Duplication
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-controlB741318_1007851257
N/A
N/A
Control
No previous psychiatric history
88588927
88867874
278948
GRCh38
Duplication
No
levy_11_ASD_discovery_controls-11533.s1
NA
M
Control
NA
NA
91294287
91421474
127188
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C39664
N/A
M
Control
NIMH Control (NIMH ID 29934)
88853211
88860288
7078
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11141.s1
5.2
F
Control (matched sibling)
NA
NA
91273205
91403932
130728
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11724.s1
14.5
F
Control (matched sibling)
NA
NA
87893241
87899366
6126
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11905.s1
8.6
F
Control (matched sibling)
NA
NA
87893241
87898771
5531
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12117.s1
12
F
Control (matched sibling)
NA
NA
87893241
87904633
11393
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12228.s1
8.8
F
Control (matched sibling)
NA
NA
87889831
87899366
9536
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12233.s1
6.8
F
Control (matched sibling)
NA
NA
91091100
91113291
22192
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12435.s1
9
F
Control (matched sibling)
NA
NA
90087933
90091422
3490
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12626.s1
16.3
F
Control (matched sibling)
NA
NA
87893241
87898771
5531
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13266.s1
7.9
F
Control (matched sibling)
NA
NA
87893241
87899366
6126
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC12959
SNP VCF
De novo
celestino-soper_11_ASD_discovery_cases-11076
Unknown
Simplex
NA
GBP1
engchuan_15_ASD_discovery_cases-case5256_3
Unknown
engchuan_15_ASD_discovery_cases-case5394_3
Unknown
PKN2-AS1
leblond_12_ASD_replication_cases-Pintocase6319_3
Maternal
mosca_16_DCD_discovery_cases-case104303
qPCR
De novo
Multi-generational
Not segregated
pinto_10_ASD_discovery_cases-case5394_3
Agilent1M
maternal
NA
NA
PKN2-AS1
prasad_12_ASD_discovery_cases-case102595
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case92174L
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-12233.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12297.p1
Both parents
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12435.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12566.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12603.p1
Paternal
Simplex (quad-proband matched)
Segregated
RPL36AP10,PKN2-AS1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB741318_1007851257
Unknown
RNU6-125P,ELOCP19,PKN2,GTF2B,PKN2-AS1
levy_11_ASD_discovery_controls-11533.s1
Maternal
Simplex
NA
FEN1P1,HFM1
poultney_13_ASD_discovery_controls-control05C39664
Unknown
GTF2B
sanders_11_ASD_discovery_controls-11141.s1
Unknown
Simplex (quad)
NA
FEN1P1,HFM1
sanders_11_ASD_discovery_controls-11724.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
sanders_11_ASD_discovery_controls-11905.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
sanders_11_ASD_discovery_controls-12117.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
sanders_11_ASD_discovery_controls-12228.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
sanders_11_ASD_discovery_controls-12233.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12435.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12626.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
sanders_11_ASD_discovery_controls-13266.s1
Unknown
Simplex (quad)
NA
PKN2-AS1
No Animal Model Data Available