12p11.22CNV Type: Deletion-Duplication
Largest CNV size: 211000 bp
Statistics Box:
Number of Reports: 10
Number of Reports: 10
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...
Duplication
Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Clinical genetic testing for patients with autism spectrum disorders.
Deletion
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
ben_mahmoud_23_ASD/ADHD/DD/ID_discovery_cases
Individuals with CNVs affecting the 12p11.22 locus containing at least one ASD candidate gene (from an initial cohort of 7 individuals with 12p11.23-p11.21 CNVs).
2
Both cases presented with developmental delay and intellectual disability; one case also presented with autism, while the another presented with ADHD.
Range, 4-11 yrs.
50% Male
1943263
0
1
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
46166
1
1
2
gai_11_ASD_replication_cases
Replication case samples derived from AGRE sets 1-3
593
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
62040
2
0
2
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
553795
0
2
2
kushima_18_ASD_discovery_cases
Individuals predominantly recruited from the middle of Honshu Island (Japan)
1108
Cases were diagnosed with ASD according to DSM-5 criteria, with diagnostic and screening instruments (ADI-R, ADOS, ASQ, and SRS) used to evaluate ASD-related behaviors and symptoms in the majority of cases.
Median age, 19 years
78.0% Male
105760
1
0
1
kushima_22_ASD_discovery_cases
Japanese ASD probands evaluated for copy number variation from an initial cohort of 1,236 probands before quality control.
1205
Cases diagnosed with autism spectrum disorder (ASD) according to DSM-5 criteria.
Median age, 19 yrs.
77.6% Male
105761
1
0
1
kushima_22_SCZ_discovery_cases
Japanese schizophrenia probands evaluated for copy number variation from an initial cohort of 3,111 probands before quality control.
3014
Cases diagnosed with schizophrenia (SCZ) according to DSM-5 criteria.
Median age, 45 yrs.
53.5% Male
19961
1
0
1
nava_13_ASD_discovery_cases
Subjects recruited in the Centre de Reference deficiences intellectuelles de causes rares', the 'Centre Diagnostic Autisme', Pitie-Salpetriere Hospital (Paris, France) or the Fondation Lejeune over a period of 3 years (20092011).
194
Cases assessed with ADI-R
N/A
83.5% Male
187000
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
102979
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
24798
2
1
3
shen_10_ASD_discovery_cases
Patients from original discovery case cohort that were subsequently used in chromosomal microarray analysis (CMA). Original discovery case cohort (n=933) was 80.9 % male and consisted of 461 patients recruited through Autism Consortium (AC) & 472 patients added through samples from Children's Hospital Boston DNA Diagnostic laboratory (CHB).
848
ASD (initial case cohort of 933 cases consisted of 447 patients diagnosed with autistic disorder, 454 with PDD-NOS, 31 with Asperger disorder, and 1 with CDD. AC Cohort: 54 patients with secondary diagnosis of mental retardation, 36 with seizures, and 16 with multiple congenital anomalies)
211000
1
0
1
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
276822
3
2
5
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
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
189192
1
0
1
kushima_18_ASD/SCZ_discovery_controls
Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
2095
Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
Median age, 37 years
52.0% Male
0
0
0
0
kushima_22_ASD/BPD/SCZ_discovery_controls
Psychiatrically normal control individuals selected from the general population evaluated for copy number variation from an initial cohort of 2,713 control individuals before quality control.
2671
Controls were psychiatrically normal and had no history of mental disorders based on responses to questionnaires or self-reporting.
Median age, 36 yrs.
47.8% Male
0
0
0
0
nord_11_ASD_discovery_controls
Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
123
Controls (no history of psychiatric symptoms by self-report)
30 yrs.
70769
0
2
2
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)
102979
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.
328214
11
2
13
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
ben_mahmoud_23_ASD/ADHD/DD/ID_discovery_cases
Argentina, Portugal
aCGH
Agilent 244K
ADM-2
Agilent Feature Extraction v.9.0, Agilent CGH analytics v.3.4.
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
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
kushima_18_ASD_discovery_cases
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD_discovery_cases
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
kushima_22_SCZ_discovery_cases
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
nava_13_ASD_discovery_cases
France
Solid phase hybridization
Illumina cytoSNP-12, Illumina 660W-Quad, Illumina 370CNV-Quad
GenomeStudio v.2011.1, CNVPartition v.3.1.6
None
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
shen_10_ASD_discovery_cases
aCGH, array SNP
Agilent 244A, Affymetrix NspI, Affymetrix SytI, Affymetrix 5.0
BRLMM, CNAT4, Partek Genomic Suite
CGH Analytics, DNA Analytics software
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
kushima_18_ASD/SCZ_discovery_controls
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD/BPD/SCZ_discovery_controls
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
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
ben_mahmoud_23_ASD/ADHD/DD/ID_discovery_cases-case4
4 yrs.
M
ASD, developmental delay, and intellectual disability
Alternate patient ID 022821. Developmental delay, autism, microcephaly, language/speech delay, moderate hearing loss in the right ear and mild hearing loss in the left ear, hand/finger/feet/toe anomalies (syndactyly, tapering fingers), skeletal anomalies, hypotonia, impaired motor skills, delayed ability to walk (unassisted walking at 2 years), short stature, some visual asymmetry detected by VEP testing at 2 years, toe walking, repetitive movements, obsession with spinning objects. Patient was of Argentinian ethnicity.
Intellectual disability, learning disability, dyslexia
28047313
29990575
1943263
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case14128_2240
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
28546231
28592397
46167
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case8639_201
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
29891999
29931069
39071
GRCh38
Deletion
No
gai_11_ASD_replication_cases-AU028503
Autism
28890940
28952979
62040
Unknown
Deletion
No
gai_11_ASD_replication_cases-AU028504
Autism
28890940
28952979
62040
Unknown
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000573
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
29539481
30093276
553796
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004395
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
28856455
29343246
486792
GRCh38
Duplication
Yes
kushima_18_ASD_discovery_cases-caseASD1005
23 yrs.
M
ASD, DD
Developmental milestones: language delay, motor delay. Family history: positive for intellectual disability (ID).
IQ > 70
28125337
28231096
105760
GRCh38
Deletion
N/A
kushima_22_ASD_discovery_cases-caseASD1005
NA
NA
ASD
Diagnosis of ASD according to DSM-5 criteria.
28125336
28231096
105761
GRCh38
Deletion
Yes
kushima_22_SCZ_discovery_cases-caseSCZ2935
NA
NA
Schizophrenia
Diagnosis of schizophrenia according to DSM-5 criteria.
28243256
28263216
19961
GRCh38
Deletion
Yes
nava_13_ASD_discovery_cases-Fam643Proband7565
N/A
M
ASD
Additional clinical profile info N/A
ID
28303065
28490280
187216
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case138150L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
30273218
30376196
102979
Unknown
Duplication
No
sanders_11_ASD_discovery_cases-11552.p1
9.6
M
Autism
NA
Full-scale IQ, 87; non-verbal IQ, 85; verbal IQ, 92
28120979
28124405
3427
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11625.p1
11.6
M
Autism
NA
Full-scale IQ, 34; non-verbal IQ, 44; verbal IQ, 14
28731859
28756657
24799
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-13083.p1
7.5
M
Autism
NA
Full-scale IQ, 52; non-verbal IQ, 67; verbal IQ, 23
27946399
27963178
16780
GRCh38
Deletion
No
shen_10_ASD_discovery_cases-ASD-09-051
NA
F
PDD-NOS
NA
NA
28320320
28531166
210847
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-controlB355344_1007874659
N/A
N/A
Control
No previous psychiatric history
28323914
28442760
118847
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB420588_1007854321
N/A
N/A
Control
No previous psychiatric history
28350789
28447311
96523
GRCh38
Homozygous deletion
No
engchuan_15_ASD_discovery_controls-controlB917455_1007854021
N/A
N/A
Control
No previous psychiatric history
28546231
28592397
46167
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900990_900990
N/A
N/A
Control
No previous psychiatric history
29440999
29717821
276823
GRCh38
Duplication
No
krumm_15_ASD_discovery_controls-control12786.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
29444144
29633336
189193
GRCh38
Deletion
Yes
nord_11_ASD_discovery_controls-04C25914
Control
29098234
29118001
19768
Unknown
Duplication
nord_11_ASD_discovery_controls-04C27513
Control
28575144
28645912
70769
Unknown
Duplication
sanders_11_ASD_discovery_controls-11227.s1
14.5
M
Control (matched sibling)
NA
NA
28428169
28447311
19143
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11432.s1
8.1
F
Control (matched sibling)
NA
NA
28410948
28447311
36364
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11479.s1
4.2
F
Control (matched sibling)
NA
NA
28428169
28447311
19143
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11536.s1
4.2
F
Control (matched sibling)
NA
NA
29279548
29282742
3195
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11572.s1
14.3
F
Control (matched sibling)
NA
NA
28421892
28452300
30409
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11625.s1
17.3
M
Control (matched sibling)
NA
NA
28724365
28756657
32293
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12153.s1
16.5
F
Control (matched sibling)
NA
NA
29847455
29862561
15107
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12299.s1
9.7
F
Control (matched sibling)
NA
NA
29053391
29073147
19757
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12674.s1
4.6
F
Control (matched sibling)
NA
NA
27940181
27963178
22998
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12786.s1
4.9
M
Control (matched sibling)
NA
NA
29403406
29731620
328215
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13053.s1
6.6
M
Control (matched sibling)
NA
NA
28172916
28210856
37941
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13083.s1
9.8
F
Control (matched sibling)
NA
NA
27946399
27963178
16780
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13175.s1
13.7
F
Control (matched sibling)
NA
NA
27940181
27963178
22998
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
ben_mahmoud_23_ASD/ADHD/DD/ID_discovery_cases-case4
De novo
ERGIC2,FAR2,CCDC91,TMTC1,OVCH1,RPL21P99,OVCH1-AS1,RNA5SP355,RNU4-54P
engchuan_15_ASD_discovery_cases-case14128_2240
Unknown
CCDC91
engchuan_15_ASD_discovery_cases-case8639_201
Unknown
gai_11_ASD_replication_cases-AU028503
Inherited
0 genes
gai_11_ASD_replication_cases-AU028504
Inherited
0 genes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000573
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPL21P99,TMTC1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004395
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
FAR2,ERGIC2
kushima_18_ASD_discovery_cases-caseASD1005
While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
Unknown
Not simplex
Unknown
CCDC91
kushima_22_ASD_discovery_cases-caseASD1005
qRT-PCR
Unknown
CCDC91
kushima_22_SCZ_discovery_cases-caseSCZ2935
qRT-PCR
Unknown
CCDC91
nava_13_ASD_discovery_cases-Fam643Proband7565
Maternal
Simplex
Unknown
RNU4-54P,CCDC91
prasad_12_ASD_discovery_cases-case138150L
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-11552.p1
Paternal
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-11625.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-13083.p1
Unknown
Simplex (quad-proband matched)
Not segregated
PTHLH
shen_10_ASD_discovery_cases-ASD-09-051
De novo
NA
NA
RNA5SP355,CCDC91
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB355344_1007874659
Unknown
CCDC91
engchuan_15_ASD_discovery_controls-controlB420588_1007854321
Unknown
CCDC91
engchuan_15_ASD_discovery_controls-controlB917455_1007854021
Unknown
CCDC91
engchuan_15_ASD_discovery_controls-controlHABC_900990_900990
Unknown
RPL21P99,OVCH1-AS1,OVCH1,TMTC1
krumm_15_ASD_discovery_controls-control12786.s1
Illumina 1MDuo
Maternal
OVCH1-AS1,OVCH1,TMTC1
nord_11_ASD_discovery_controls-04C25914
0 genes
nord_11_ASD_discovery_controls-04C27513
CCDC91
sanders_11_ASD_discovery_controls-11227.s1
Unknown
Simplex (quad)
NA
CCDC91
sanders_11_ASD_discovery_controls-11432.s1
Unknown
Simplex (quad)
NA
CCDC91
sanders_11_ASD_discovery_controls-11479.s1
Maternal
Simplex (quad)
NA
CCDC91
sanders_11_ASD_discovery_controls-11536.s1
Maternal
Simplex (quad)
NA
FAR2
sanders_11_ASD_discovery_controls-11572.s1
Unknown
Simplex (quad)
NA
CCDC91
sanders_11_ASD_discovery_controls-11625.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12153.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12299.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12674.s1
Unknown
Simplex (quad)
NA
PTHLH
sanders_11_ASD_discovery_controls-12786.s1
Maternal
Simplex (quad)
NA
RPL21P99,OVCH1-AS1,OVCH1,TMTC1
sanders_11_ASD_discovery_controls-13053.s1
Maternal
Simplex (quad)
NA
CCDC91
sanders_11_ASD_discovery_controls-13083.s1
Maternal
Simplex (quad)
NA
PTHLH
sanders_11_ASD_discovery_controls-13175.s1
Unknown
Simplex (quad)
NA
PTHLH
No Animal Model Data Available