15q23-q24.2CNV Type: Deletion
Largest CNV size: 4289500 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Structural variation of chromosomes in autism spectrum disorder.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
5269115
1
0
1
marshall_08_ASD_discovery_cases
Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
427
ASD
4289500
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
4300440
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
marshall_08_ASD_discovery_controls_1
German PopGen project and entries from Database of Genomic Variants
500
Controls
0
0
0
0
marshall_08_ASD_discovery_controls_2
Non-disease controls from Ontario population
1152
Controls
0
0
0
0
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)
4300440
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
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
marshall_08_ASD_discovery_cases
90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
qPCR, qmPCR
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
marshall_08_ASD_discovery_controls_1
European
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
marshall_08_ASD_discovery_controls_2
European
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003860
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
70788624
76057736
5269113
GRCh38
Deletion
Yes
marshall_08_ASD_discovery_cases-SK0243-003
NA
M
ASD
Severe language delay and dysmorphism, moderate repetitive behavior
LOF severely impaired
71521907
75811404
4289498
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case67941
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
69592164
73892603
4300440
Unknown
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003860
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,DNM1P33,RN7SL429P,ISLR,PPIAP46,MIR6881,CYP1A1,CYP1A2,MIR4513,CPLX3,MIR6882,FAM219B,RPL36AP45,NIFKP4,RN7SL489P,RN7SL327P,ANP32BP1,COMMD4,MIR631,RPL13P4,DNM1P35,PPIAP47,MIR4313,RN7SL319P,RN7SL510P,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,TBC1D21,LOXL1,STOML1,PML,GOLGA6A,ISLR2,CYP11A1,LINC02255,SEMA7A,UBL7-AS1,CLK3,EDC3,CSK,LMAN1L,SCAMP2,MPI,COX5A,RPP25,C15orf39,GOLGA6C,GOLGA6D,DNM1P34,NEIL1,SIN3A,SNUPN,IMP3,SNX33,CSPG4,ODF3L1,DNM1P49,FBXO22,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,LOXL1-AS1,STRA6,CCDC33,ARID3B,ULK3,SCAMP5,PPCDC,MAN2C1,UBE2Q2,NRG4,THSD4,HEXA,UBL7,PTPN9
marshall_08_ASD_discovery_cases-SK0243-003
qPCR, qmPCR
De novo
Simplex-CHR
NA
RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,DNM1P33,RN7SL429P,ISLR,PPIAP46,MIR6881,CYP1A1,CYP1A2,MIR4513,CPLX3,MIR6882,FAM219B,RPL36AP45,NIFKP4,RN7SL489P,RN7SL327P,ANP32BP1,COMMD4,MIR631,RPL13P4,DNM1P35,PPIAP47,MIR4313,RN7SL319P,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,TBC1D21,LOXL1,STOML1,PML,GOLGA6A,ISLR2,CYP11A1,LINC02255,SEMA7A,UBL7-AS1,CLK3,EDC3,CSK,LMAN1L,SCAMP2,MPI,COX5A,RPP25,C15orf39,GOLGA6C,GOLGA6D,DNM1P34,NEIL1,SIN3A,SNUPN,IMP3,SNX33,CSPG4,ODF3L1,DNM1P49,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,LOXL1-AS1,STRA6,CCDC33,ARID3B,ULK3,SCAMP5,PPCDC,MAN2C1,THSD4,HEXA,UBL7,PTPN9
prasad_12_ASD_discovery_cases-case67941
Unknown
Unknown
Unknown
PKM2,C15orf59,PPCDC,CELF6,UBL7,HCN4,C15orf39,EDC3,ADPGK,MAN2C1,C15orf34,COX5A,LOXL1,CYP11A1,NPTN,CSK,TBC1D21,MIR631,MIR630,COMMD4,GRAMD2,TMEM202,NEO1,CCDC33,PML,SNX33,PARP6,SIN3A,ULK3,SCAMP5,SCAMP2,ARIH1,SENP8,PTPN9,STRA6,THSD4,SNUPN,RPP25,CPLX3,C15orf60,GOLGA6D,GOLGA6C,GOLGA6B,GOLGA6A,NR2E3,MIR4313,C15orf17,DNM1P35,SEMA7A,LOC283731,IMP3,CYP1A1,CYP1A2,ARID3B,ISLR,CSPG4,HEXA,HIGD2B,CD276,BBS4,STOML1,MPI,ODF3L1,NEIL1,MYO9A,LMAN1L,CLK3,ISLR2
Controls
No Control Data Available
No Animal Model Data Available