9p21.2CNV Type: Deletion
Largest CNV size: 169638 bp
Statistics Box:
Number of Reports: 7
Number of Reports: 7
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
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Refinement and discovery of new hotspots of copy-number variation associated with 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
157203
4
0
4
girirajan_13a_ASD_discovery_cases
1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
2588
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
NA
NA
1017000
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
81047
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
151980
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
98136
0
1
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
106147
1
0
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
169638
15
0
15
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
157203
8
0
8
krumm_13_ASD_discovery_controls
Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
46.47% Male
11545
0
1
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
91583
0
2
2
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)
18889
1
0
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)
98136
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.
157203
11
0
11
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_13a_ASD_discovery_cases
NA
aCGH
Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
ADM-2
Agilent Genomic Workbench
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
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
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
krumm_13_ASD_discovery_controls
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
qPCR
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
engchuan_15_ASD_discovery_cases-case4218_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4340_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
26722738
26789977
67240
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case5072_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case8723_201
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
26265881
26423084
157204
GRCh38
Deletion
No
girirajan_13a_ASD_discovery_cases-13786.p1
N/A
N/A
ASD
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
N/A
25900002
26920002
1020001
GRCh38
Duplication
No
krumm_15_ASD_discovery_cases-case13786.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
26842300
26923347
81048
GRCh38
Duplication
Yes
pinto_10_ASD_discovery_cases-case5072_3
NA
M
ASD
No epilepsy, no dysmorphic features
Average IQ
26265881
26417860
151980
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case111521L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
27733788
27831923
98136
Unknown
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR01-191
N/A
N/A
ACC-CBLH-PMG
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and polymicrogyria (PMG). ASD: N/A. Seizures: yes (onset at 6 wks).
Developmental delay: yes. Intellectual disability: yes.
27247316
27353462
106147
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_cases-11025.p1
4.6
F
ASD
NA
Full-scale IQ, 98; non-verbal IQ, 102; verbal IQ, 92
27799844
27806132
6289
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11030.p1
8.3
M
ASD
NA
Full-scale IQ, 104; non-verbal IQ, 103; verbal IQ, 98
28049520
28050779
1260
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11057.p1
8.7
M
Autism
NA
Full-scale IQ, 89; non-verbal IQ, 89; verbal IQ, 95
28049520
28050779
1260
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11145.p1
5.9
M
Autism
NA
Full-scale IQ, 76; non-verbal IQ, 79; verbal IQ 80
27502988
27508689
5702
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11455.p1
7.6
M
ASD
NA
Full-scale IQ, 68; non-verbal IQ, 73; verbal IQ, 69
26568001
26572238
4238
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11468.p1
10.7
M
Aspergers
NA
Full-scale IQ, 89; non-verbal IQ, 92; verbal IQ, 87
26568001
26576119
8119
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11798.p1
4.8
M
Autism
NA
Full-scale IQ, 114; non-verbal IQ, 111; verbal IQ, 113
27502988
27508689
5702
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11869.p1
10.1
M
Autism
NA
Full-scale IQ, 98; non-verbal IQ, 104; verbal IQ, 86
26953104
26956665
3562
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12093.p1
6
M
ASD
NA
Full-scale IQ, 113; non-verbal IQ, 120; verbal IQ, 97
26953104
26956665
3562
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12121.p1
8.5
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 134; verbal IQ, 110
26265881
26435519
169639
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12212.p1
12.3
M
Autism
NA
Full-scale IQ, 26; non-verbal IQ, 29; verbal IQ, 20
26953104
26956665
3562
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12349.p1
4.9
M
ASD
NA
Full-scale IQ, 81; non-verbal IQ, 81; verbal IQ, 90
26568001
26572238
4238
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12434.p1
5.3
M
Autism
NA
Full-scale IQ, 117; non-verbal IQ, 121; verbal IQ, 106
26953104
26956665
3562
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12852.p1
5.1
M
Autism
NA
Full-scale IQ, 77; non-verbal IQ, 78; verbal IQ, 83
26265881
26423084
157204
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12864.p1
5.8
F
Autism
NA
Full-scale IQ, 67; non-verbal IQ, 65; verbal IQ, 81
27799844
27806132
6289
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-control110036017044_
N/A
N/A
Control
No previous psychiatric history
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-control110036022689_
N/A
N/A
Control
No previous psychiatric history
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB122251_1007842403
N/A
N/A
Control
No previous psychiatric history
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB392747_1007873163
N/A
N/A
Control
No previous psychiatric history
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB666307_1007872266
N/A
N/A
Control
No previous psychiatric history
26265881
26417860
151980
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB697076_1007841045
N/A
N/A
Control
No previous psychiatric history
26978172
27032387
54216
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900131_900131
N/A
N/A
Control
No previous psychiatric history
26265881
26423084
157204
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900935_900935
N/A
N/A
Control
No previous psychiatric history
27998127
28094659
96533
GRCh38
Deletion
No
krumm_13_ASD_discovery_controls-control13926.s1
N/A
F
Control
Unaffected sibling from SSC quad family 13926. SRS score of 41.
27217687
27229232
11546
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_controls-control12834.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
27202819
27294402
91584
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control13926.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
27217673
27229247
11575
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_controls-control05C39504A
N/A
M
Control
NIMH Control (NIMH ID 93942)
27548234
27567122
18889
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_controls-11057.s1
5.9
M
Control (matched sibling)
NA
NA
28049520
28050779
1260
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11307.s1
13.1
M
Control (matched sibling)
NA
NA
28049520
28050779
1260
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11584.s1
13.5
M
Control (matched sibling)
NA
NA
25576242
25579844
3603
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11775.s1
12.7
F
Control (matched sibling)
NA
NA
26449876
26453725
3850
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11954.s1
6.8
F
Control (matched sibling)
NA
NA
26568001
26572238
4238
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11981.s1
8.6
F
Control (matched sibling)
NA
NA
26953104
26956665
3562
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12631.s1
18.8
M
Control (matched sibling)
NA
NA
25919853
26051962
132110
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12836.s1
4.2
M
Control (matched sibling)
NA
NA
26265881
26423084
157204
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12864.s1
12.9
F
Control (matched sibling)
NA
NA
27799844
27806132
6289
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13051.s1
9.4
F
Control (matched sibling)
NA
NA
25919853
25929150
9298
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case4218_1
Unknown
engchuan_15_ASD_discovery_cases-case4340_1
Unknown
engchuan_15_ASD_discovery_cases-case5072_3
Unknown
engchuan_15_ASD_discovery_cases-case8723_201
Unknown
girirajan_13a_ASD_discovery_cases-13786.p1
Unknown
Simplex
Unknown
FAM71BP1,RN7SL100P,PLAA,CAAP1
krumm_15_ASD_discovery_cases-case13786.p1
Omni2.5-4v1
Paternal
Simplex
Segregated
RN7SL100P,PLAA,CAAP1
pinto_10_ASD_discovery_cases-case5072_3
Agilent1M
paternal
NA
NA
prasad_12_ASD_discovery_cases-case111521L
Unknown
Unknown
Unknown
0 genes
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR01-191
qPCR
Paternal
Unknown
Unknown
EQTN,MOB3B,LINC00032
sanders_11_ASD_discovery_cases-11025.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11030.p1
Paternal
Simplex (quad-proband matched)
Segregated
LINGO2
sanders_11_ASD_discovery_cases-11057.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINGO2
sanders_11_ASD_discovery_cases-11145.p1
Paternal
Simplex (trio)
NA
MOB3B
sanders_11_ASD_discovery_cases-11455.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11468.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11798.p1
Maternal
Simplex (quad-proband matched)
Not segregated
MOB3B
sanders_11_ASD_discovery_cases-11869.p1
Unknown
Simplex (quad-proband matched)
Segregated
IFT74-AS1,IFT74
sanders_11_ASD_discovery_cases-12093.p1
Maternal
Simplex (trio)
NA
IFT74-AS1,IFT74
sanders_11_ASD_discovery_cases-12121.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12212.p1
Unknown
Simplex (quad-proband matched)
Not segregated
IFT74-AS1,IFT74
sanders_11_ASD_discovery_cases-12349.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12434.p1
Unknown
Simplex (quad-proband matched)
Not segregated
IFT74-AS1,IFT74
sanders_11_ASD_discovery_cases-12852.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12864.p1
Maternal
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-control110036017044_
Unknown
engchuan_15_ASD_discovery_controls-control110036022689_
Unknown
engchuan_15_ASD_discovery_controls-controlB122251_1007842403
Unknown
engchuan_15_ASD_discovery_controls-controlB392747_1007873163
Unknown
engchuan_15_ASD_discovery_controls-controlB666307_1007872266
Unknown
engchuan_15_ASD_discovery_controls-controlB697076_1007841045
Unknown
IFT74,LRRC19
engchuan_15_ASD_discovery_controls-controlHABC_900131_900131
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900935_900935
Unknown
LINGO2
krumm_13_ASD_discovery_controls-control13926.s1
Paternal
Simplex
TEK
krumm_15_ASD_discovery_controls-control12834.s1
Omni2.5-4v1
Paternal
EQTN,TEK,LINC00032
krumm_15_ASD_discovery_controls-control13926.s1
Omni2.5-4v1
Paternal
TEK
poultney_13_ASD_discovery_controls-control05C39504A
qPCR
Unknown
C9orf72
sanders_11_ASD_discovery_controls-11057.s1
Paternal
Simplex (quad)
NA
LINGO2
sanders_11_ASD_discovery_controls-11307.s1
Maternal
Simplex (quad)
NA
LINGO2
sanders_11_ASD_discovery_controls-11584.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11775.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11954.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11981.s1
Unknown
Simplex (quad)
NA
IFT74-AS1,IFT74
sanders_11_ASD_discovery_controls-12631.s1
Maternal
Simplex (quad)
NA
FAM71BP1
sanders_11_ASD_discovery_controls-12836.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12864.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-13051.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available