15q12CNV Type: Deletion-Duplication
Largest CNV size: 1000000 bp
Statistics Box:
Number of Reports: 12
Number of Reports: 12
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: efficient identification of known microduplica...
Duplication
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
cai_08_ASD_discovery_cases
Unrelated individuals with autism or ASD recruited by SARC and/or AGRE
279
270 cases diagnosed with autism, 2 with Asperger's, 1 with PDD-NOS, 3 with not quite autism (NQA), 3 with broad spectrum autism
Mean 7.94 yrs
79.6% Male
1000000
0
1
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.
943181
0
2
2
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
612134
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
886512
1
1
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
171025
0
1
1
leppa_16_ASD_discovery_cases
Children affected with ASD from 1,464 families from the Autism Genetic Resource Exchange (AGRE)
1764
Diagnosis according to ADOS and ADI-R
N/A
N/A
1348000
0
1
1
miclea_22_DD/ID_discovery_cases
Patients presented in Clinical Emergency Hospital for Children Cluj-Napoca betwwen January 2015 and July 2017.
189
Diagnosis of global developmental delay (DD) or intellectual disability (ID) based on intelligence quotient evaluated by WISC-IV and developmental quotient evaluated by NEPSY.
Range, 1-18 yrs.
51.85% Male
13951
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)
544133
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
805672
2
2
4
sandoval_talamantes_23_ASD_discovery_cases
ASD patients recruited from 2016 to 2019 among patients from the genetic or neuropediatric clinics of La Paz University Hospital (Madrid, Spain).
212
All cases met DSM-5 diagnostic criteria for ASD.
Mean age, 10.73 +/- 6.42 yrs. (median age, 10 yrs.)
87.73% Male
28575
0
1
1
yuan_23_ASD_discovery_cases
ASD probands from 353 pedigrees (338 simplex trios, 15 multiplex families) recruited from the Department of Child and Adolescent Psychiatry, Shanghai Mental Health Center (Shanghai, China).
369
Cases diagnosed with ASD using DSM-IV.
NA
NA
985590
0
1
1
yuen_17_ASD_discovery_cases
ASD genomes (1745 ASD probands, 879 ASD-affected siblings, 1 ASD-affected father, and 1 ASD-affected grandfather) from AGRE (n=730), the AGRE; Autism Treatment Network cohort (n=192) ,the ASD: Genomes to Outcomes Study cohort (n=1421), the Baby Siblings Research Consortium (n=43), the Baby Siblings Research Consortium; The Autism Simplex Collection cohort (n=6), the Infant Sibling Study (n=62), th
2626
ASD diagnosis of research quality when meeting criteria on one (n=437) or both (n=1361) of the diagnostic measures ADI-R and ADOS; clinical diagnosis of ASD (n=819) when given by expert clinician according to DSM-IV or DSM-5
N/A
78.71% Male
145999
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
bacchelli_20_ASD_discovery_controls
Anonymized DNA samples from Italian individuals with no psychiatric disorders
365
Control
N/A
54.52% Male
205632
0
1
1
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
38316
1
0
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.
943181
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
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
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
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
16967
3
0
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
cai_08_ASD_discovery_cases
205 Caucasian, 6 African-American, 24 Hispanic or Latino, 5 Asian, 11 mixed ethnicity, 28 unknown
MLPA
ABI 3130 genetic analyzer (Applied Biosystem)
GeneMarker
Direct DNA sequencing qPCR, FISH
girirajan_11_ASD_discovery_cases
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
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
aCGH (NimbleGen 135K array)
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
Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
leppa_16_ASD_discovery_cases
N/A
Solid phase hybridization
Illumina 550v1 and 550v3, Omni-1.0-B and -H, Omni 2.5
PennCNV, QuantiSNP, GNOSIS
GenomeStudio, CNVision
qPCR
miclea_22_DD/ID_discovery_cases
Romania
Solid phase hybridization
Illumina Infinium OmniExpress-24 BeadChip
NA
Illumina GenomeStudio v.2.0.
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
qPCR
sandoval_talamantes_23_ASD_discovery_cases
Spain
aCGH
KaryoArray v.3.0
NA
Agilent CytoGenomics
None
yuan_23_ASD_discovery_cases
China
WES
Illumina HiSeq
NA
GATK v.4.2.0.0.
None
yuen_17_ASD_discovery_cases
N/A
WGS
Complete Genomics, Illumina HiSeq 2000, HiSeq X
None (CNV validation not available, CNV not detected by validation method, or CNV not detected by WGS but was detected by validation methodology)
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
bacchelli_20_ASD_discovery_controls
Italian
Solid phase hybridization
Illumina Infinium PsychArray
PennCNV, QuantiSNP, CNVPartition
None
cai_08_ASD_discovery_controls
Caucasian
qPCR
ABI Prism 7900 HT (Applied Biosystem)
Sequence Detection
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
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
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
cai_08_ASD_discovery_cases-AU038504
9
M
Autism
Non-verbal language 12, Social 26, Repetitive behavior 8, Onset 4, Raven NA
NA
1000000
Unknown
Duplication
Yes
girirajan_11_ASD_discovery_cases-Si41
10
F
Autism
ADOS score: 10. Vineland composite score: 70.
Mild mental retardation/intellectual disability. Full-scale IQ, 64; Verbal IQ, 83; Non-verbal IQ, 54.
26938237
27341487
403251
GRCh38
Duplication
No
girirajan_11_ASD_discovery_cases-Si41
10
F
Autism
ADOS score: 10. Vineland composite score: 70.
Mild mental retardation/intellectual disability. Full-scale IQ, 64; Verbal IQ, 83; Non-verbal IQ, 54.
27351931
28295112
943182
GRCh38
Duplication
No
girirajan_13a_ASD_discovery_cases-13355.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
26724830
27305311
580482
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003769
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
26575931
27051075
475145
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004542
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
26856856
27620867
764012
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case13355.p1
N/A
M
ASD
ASD proband from SSC quad family 13355. SRS score of 90.
Full-scale IQ (FSIQ) score of 30.
26772401
26943426
171026
GRCh38
Duplication
Yes
leppa_16_ASD_discovery_cases-AU038504
N/A
N/A
ASD
25502430
26850173
1347744
GRCh38
Duplication
Yes
miclea_22_DD/ID_discovery_cases-case65
NA
NA
Developmental delay and intellectual disability
Global developmental delay
Intellectual disability
26629247
26643197
13951
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-caseHI4731
N/A
F
ASD
ASD case from AGRE (AGRE ID AU1607307; NDAR ID NDAR_INVLT002PME)
27755386
28299518
544133
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12007.p1
8.7
F
Autism
NA
Full-scale IQ, 64; non-verbal IQ, 54; verbal IQ, 83
25583558
26345683
762126
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-12007.p1
8.7
F
Autism
NA
Full-scale IQ, 64; non-verbal IQ, 54; verbal IQ, 83
26353773
27127792
774020
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-12370.p1
8.2
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 127; verbal IQ, 123
27615301
27629529
14229
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13162.p1
9.8
M
Autism
NA
Full-scale IQ, 74; non-verbal IQ, 78; verbal IQ, 72
25873763
25881990
8228
GRCh38
Deletion
No
sandoval_talamantes_23_ASD_discovery_cases-caseAUT146
NA
NA
ASD
Case met DSM-5 diagnostic criteria for ASD.
27066765
27095339
28575
GRCh38
Duplication
No
yuan_23_ASD_discovery_cases-qma01716s000
NA
NA
ASD
Case diagnosed with ASD according to DSM-IV criteria.
26547542
27533131
985590
GRCh38
Duplication
No
yuen_17_ASD_discovery_cases-caseAU3930302
N/A
N/A
ASD
Case cohort: AGRE. Clinical description: N/A
26414854
26560853
146000
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
bacchelli_20_ASD_discovery_controls-control20029
N/A
M
Control
Control
26242318
26447949
205632
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900151_900151
N/A
N/A
Control
No previous psychiatric history
26280628
26318944
38317
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11285.s1
16.4
M
Control (matched sibling)
NA
NA
25984646
25988385
3740
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12370.s1
6.3
F
Control (matched sibling)
NA
NA
27612562
27629529
16968
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13162.s1
6.7
F
Control (matched sibling)
NA
NA
25873763
25881990
8228
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
cai_08_ASD_discovery_cases-AU038504
FISH
De novo
Multiplex
Not segregated
ATP10A, GABRB3
girirajan_11_ASD_discovery_cases-Si41
De novo
Simplex
GABRG3-AS1,RNA5SP391,SERPINE4P,TVP23BP1,GABRB3,GABRA5,GABRG3
girirajan_11_ASD_discovery_cases-Si41
De novo
Simplex
RPL5P32,OCA2,GABRG3,HERC2
girirajan_13a_ASD_discovery_cases-13355.p1
aCGH (NimbleGen 135K array)
De novo
Simplex
Possibly segregated
GABRG3-AS1,RNA5SP391,TVP23BP1,GABRB3,GABRA5,GABRG3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003769
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
TVP23BP1,GABRB3,GABRA5,GABRG3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004542
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
GABRG3-AS1,RNA5SP391,SERPINE4P,TVP23BP1,GABRB3,GABRA5,GABRG3
krumm_13_ASD_discovery_cases-case13355.p1
Solid phase hybridization (Illumina 1M) or aCGH (Agilent SurePrint G3 4x180K)
De novo
Simplex
Segregated
GABRB3,GABRA5
leppa_16_ASD_discovery_cases-AU038504
qPCR
De novo
Multiplex
Not segregated (CNV not present in affected sibling)
RNA5SP390,MIR4715,LINC00929,LINC02248,LINC02250,ATP10A,LINC02346,GABRB3
miclea_22_DD/ID_discovery_cases-case65
Unknown
GABRB3
poultney_13_ASD_discovery_cases-caseHI4731
Unknown
Unknown (likely multiplex/AGRE)
Unknown
RPL5P32,OCA2,HERC2
sanders_11_ASD_discovery_cases-12007.p1
qPCR
De Novo
Simplex (quad-proband matched)
Segregated
RNA5SP390,MIR4715,LINC00929,ATP10A,LINC02346
sanders_11_ASD_discovery_cases-12007.p1
qPCR
De Novo
Simplex (quad-proband matched)
Segregated
LINC02248,TVP23BP1,GABRB3,GABRA5,GABRG3
sanders_11_ASD_discovery_cases-12370.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-13162.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sandoval_talamantes_23_ASD_discovery_cases-caseAUT146
Unknown
GABRG3,GABRG3-AS1
yuan_23_ASD_discovery_cases-qma01716s000
De novo
GABRA5,GABRB3,GABRG3,TVP23BP1,RNA5SP391,GABRG3-AS1,SERPINE4P
yuen_17_ASD_discovery_cases-caseAU3930302
Not available
Unknown
Multiplex
Unknown
LINC02248,GABRB3
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
bacchelli_20_ASD_discovery_controls-control20029
Unknown
LINC02248
engchuan_15_ASD_discovery_controls-controlHABC_900151_900151
Unknown
sanders_11_ASD_discovery_controls-11285.s1
Paternal
Simplex (quad)
NA
LINC02346
sanders_11_ASD_discovery_controls-12370.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-13162.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available