12q15CNV Type: Deletion-Duplication
Largest CNV size: 85536 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...
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Identifying autism loci and genes by tracing recent shared ancestry.
Duplication
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Using extended pedigrees to identify novel autism spectrum disorder (ASD) candidate genes.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
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
35856
0
1
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
1064890
2
0
2
krumm_13_ASD_discovery_cases
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
Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
81.265% Male
1864
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
1864
1
0
1
morrow_08_ASD_discovery_cases
Affected individuals from 70 families (52 simplex, 18 multiplex) recruited by Homozygosity Mapping Collaborative for Autism (HMCA) used in CNV analysis. This cohort was selected from an original population of affected individuals from 104 families (79 simplex, 25 multiplex; 82.7% male); 88 of these pedigrees have cousin marriages.
94
ASD (based on DSM-IV-TR diagnoses when research scales not available in native language)
1000
0
1
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)
105640
0
3
3
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
9279
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
85536
5
3
8
wang_18_TS_discovery_cases
Probands from 789 trio families (582 simplex trios, 103 multi-generational trios, and 104 trios with insufficient parental phenotypic data) from TIC Genetics, TAAICG, UTC, and TSGENESEE cohorts
789
Probands diagnosed with Tourette syndrome
N/A
80.57% Male
503490
1
0
1
woodbury-smith_14_ASD_discovery_cases
Probands from 19 extended ASD pedigrees (defined as at least three ASD cases spread across at least two nuclear families); 6 families recruited in Canada, 13 families recruited in the United States
19
Diagnosis of ASD made using combination of ADI-R, ADOS, and clinical judgment in conjunction with DSM-IV criteria.
N/A
N/A
518552
0
1
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
80743
0
2
2
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_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
0
0
0
0
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
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)
27685
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)
9279
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.
84806
3
3
6
woodbury-smith_14_ASD_discovery_controls
Platform-matched controls from the KORA and COGEND datasets
2988
Control
N/A
N/A
0
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
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
krumm_13_ASD_discovery_cases
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_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
morrow_08_ASD_discovery_cases
Arabic Middle East, Turkey, and Pakistan
Array SNP
Affymetrix 500K
BRLMM
dChip
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
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
wang_18_TS_discovery_cases
N/A
WES
Agilent SureSelect v1.1, Nimblegen EZ v2, Nimblegen EZ v3, IDT xGen
CoNIFER
None
woodbury-smith_14_ASD_discovery_cases
US and Canada
Solid phase hybridization
Illumina HumanOmni2.5 BeadChip
PennCNV, QuantiSNP, iPattern
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_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
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
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
woodbury-smith_14_ASD_discovery_controls
Predominantly European
Solid phase hybridization
Illumina HumanOmni2.5 BeadChip
PennCNV, QuantiSNP, iPattern
None
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-case13003_43
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
68763920
68799776
35857
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001810
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
70051305
71116195
1064891
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002629
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
70029314
70599455
570142
GRCh38
Deletion
Yes
krumm_13_ASD_discovery_cases-case12334.p1
N/A
M
ASD
ASD proband from SSC quad family 12334. SRS score of 61.
Full-scale IQ (FSIQ) score of 84.
69348408
69350272
1865
GRCh38
Deletion
No (not tested)
krumm_15_ASD_discovery_cases-case12334.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
69348408
69350272
1865
GRCh38
Deletion
Yes
morrow_08_ASD_discovery_cases-case10401
NA
ASD
NA
NA
67884000
67884000
1000
Unknown
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
69571274
69671581
100308
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
68225584
68331223
105640
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
68690629
68759241
68613
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case59794L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
67309307
67318585
9279
Unknown
Deletion
Yes
sanders_11_ASD_discovery_cases-11245.p1
10.9
M
Autism
NA
Full-scale IQ, 111; non-verbal IQ, 107; verbal IQ, 117
68049471
68055051
5581
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11262.p1
6.2
M
Autism
NA
Full-scale IQ, 84; non-verbal IQ, 85; verbal IQ, 89
70478078
70490716
12639
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11472.p1
13.7
F
Autism
NA
Full-scale IQ, 30; non-verbal IQ, 30; verbal IQ, 31
67917841
68003377
85537
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12083.p1
7.9
M
Autism
NA
Full-scale IQ, 114; non-verbal IQ, 111; verbal IQ, 117
71105359
71116475
11117
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12150.p1
8.7
M
Autism
NA
Full-scale IQ, 109; non-verbal IQ, 95; verbal IQ, 133
70117766
70124056
6291
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12334.p1
8.9
M
Autism
NA
Full-scale IQ, 84; non-verbal IQ, 92; verbal IQ, 75
69347451
69350324
2874
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12552.p1
8.7
M
Autism
NA
Full-scale IQ, 104; non-verbal IQ, 107; verbal IQ, 98
70117766
70124056
6291
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12691.p1
10.9
F
Autism
NA
Full-scale IQ, 34; non-verbal IQ, 32; verbal IQ, 39
68049471
68064101
14631
GRCh38
Deletion
No
wang_18_TS_discovery_cases-case25095.p1
N/A
N/A
Tourette syndrome
Tourette syndrome proband from phase 1 cohort; no additional clinical information available
68747883
69251372
503490
GRCh38
Deletion
No
woodbury-smith_14_ASD_discovery_cases-case12
N/A
M
ASD
Family history: broad autism phenotype (BAP)-defined mother.
68431953
68950504
518552
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-controlB201628_1007841172
N/A
N/A
Control
No previous psychiatric history
69531915
69601546
69632
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900881_900881
N/A
N/A
Control
No previous psychiatric history
71011650
71092393
80744
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
68225147
68252831
27685
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11010.s1
7.7
M
Control (matched sibling)
NA
NA
71105359
71116475
11117
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11472.s1
10.6
F
Control (matched sibling)
NA
NA
67908968
67993774
84807
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12051.s1
7.5
M
Control (matched sibling)
NA
NA
70411418
70437576
26159
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12073.s1
7.3
F
Control (matched sibling)
NA
NA
71105359
71116475
11117
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12083.s1
5.5
F
Control (matched sibling)
NA
NA
71105359
71116475
11117
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12691.s1
23.8
M
Control (matched sibling)
NA
NA
68049471
68055051
5581
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-case13003_43
Unknown
SLC35E3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001810
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNU4-65P,FAHD2P1,LINC01481,KCNMB4,PTPRB,PTPRR,CNOT2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002629
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
RNU4-65P,LINC01481,KCNMB4,PTPRB,CNOT2
krumm_13_ASD_discovery_cases-case12334.p1
Paternal
Simplex
Segregated
LYZ
krumm_15_ASD_discovery_cases-case12334.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
LYZ
morrow_08_ASD_discovery_cases-case10401
Maternal
NA
NA
0 genes
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
MIR3913-1,MIR3913-2,LRRC10,FRS2,BEST3,CCT2
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
IL22,IL26,MDM1,IFNG-AS1
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
KRT8P39,NUP107,SLC35E3
prasad_12_ASD_discovery_cases-case59794L
qPCR
Maternal
Unknown
Unknown
RAP1B
sanders_11_ASD_discovery_cases-11245.p1
Paternal
Simplex (quad-proband matched)
Segregated
IFNG-AS1
sanders_11_ASD_discovery_cases-11262.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11472.p1
Maternal
Simplex (quad-proband matched)
Not segregated
RPL39P28,LINC01479,IFNG-AS1
sanders_11_ASD_discovery_cases-12083.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12150.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC01481
sanders_11_ASD_discovery_cases-12334.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LYZ
sanders_11_ASD_discovery_cases-12552.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC01481
sanders_11_ASD_discovery_cases-12691.p1
Paternal
Simplex (quad-proband matched)
Not segregated
IFNG-AS1
wang_18_TS_discovery_cases-case25095.p1
Validation failed
De novo
RNU7-4P,PRELID2P1,SLC35E3,CPSF6,MDM2,CPM
woodbury-smith_14_ASD_discovery_cases-case12
Maternal
Possible multi-generational (CNV transmitted from BAP-defined parent to ASD diagnosed offspring)
Unknown
RPSAP12,RPL10P12,SNORA70G,ATP5PDP4,RPL7P42,KRT8P39,RNU7-4P,RAP1B,NUP107,SLC35E3,LINC02384,MDM2,CPM
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB201628_1007841172
Unknown
MIR3913-1,MIR3913-2,FRS2,CCT2
engchuan_15_ASD_discovery_controls-controlHABC_900881_900881
Unknown
poultney_13_ASD_discovery_controls-control05C44621
Unknown
IL22,IL26,IFNG-AS1
sanders_11_ASD_discovery_controls-11010.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11472.s1
Maternal
Simplex (quad)
NA
LINC01479,IFNG-AS1
sanders_11_ASD_discovery_controls-12051.s1
Paternal
Simplex (quad)
NA
KCNMB4
sanders_11_ASD_discovery_controls-12073.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12083.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12691.s1
Paternal
Simplex (quad)
NA
IFNG-AS1
No Animal Model Data Available