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15q21.2CNV Type: Deletion-Duplication


Largest CNV size: 183904 bp

Statistics Box:
Number of Reports: 9



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
Structural variation of chromosomes in autism spectrum disorder.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
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
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
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-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 brandler_18_ASD_discovery_cases
 Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
 880
 REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
 N/A
 N/A
 21563
 3
 0
 3
 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
 68272
 1
 1
 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
 221793
 2
 0
 2
 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
 
 
 183904
 0
 1
 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
 23454
 0
 1
 1
 quintela_17_DD/ID_discovery_cases
 Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
 573
 All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
 Range, 3 months-18 years
 60.38% Male
 112149
 1
 0
 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
 93119
 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
 84587
 1
 2
 3
 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
 332557
 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
 197431
 0
 5
 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_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
 803839
 0
 1
 1
 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)
 23454
 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.
 
 905624
 2
 2
 4

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 brandler_18_ASD_discovery_cases
  N/A
 WGS
  Illumina HiSeq X10 or HiSeq 2500
 ForestSV, Lumpy, Manta, Mobster, SV2
 
 PCR, array SNP
 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
 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
 quintela_17_DD/ID_discovery_cases
  North West Spain
 Array SNP
  Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
 
 Affymetrix ChAS v.1.2.2
 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
 
 
 wang_18_TS_discovery_cases
  N/A
 WES
  Agilent SureSelect v1.1, Nimblegen EZ v2, Nimblegen EZ v3, IDT xGen
 
 CoNIFER
 qPCR

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
  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
 
  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
  brandler_18_ASD_discovery_cases-case14-591
 N/A
 F
 ASD
 Case from REACH cohort
 
 51972489
 51994052
  21564
 GRCh38
 Deletion
 Yes
  brandler_18_ASD_discovery_cases-caseREACH000319
 N/A
 M
 ASD
 Case from REACH cohort
 
 51972569
 51989334
  16766
 GRCh38
 Deletion
 Yes
  brandler_18_ASD_discovery_cases-caseREACH000322
 N/A
 M
 ASD
 Case from REACH cohort
 
 51972569
 51989334
  16766
 GRCh38
 Deletion
 Yes
  engchuan_15_ASD_discovery_cases-case14415_5240
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 50742924
 50811196
  68273
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case3205_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 50789374
 50822889
  33516
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000623
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 50756382
 50978175
  221794
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001993
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 52005056
 52098273
  93218
 GRCh38
 Deletion
 Yes
  marshall_08_ASD_discovery_cases-SK0300-003
 NA
 M
 ASD
 NA
 NA
 50503638
 50687541
  183904
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case113501L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 49146071
 49169524
  23454
 Unknown
 Duplication
 No
  quintela_17_DD/ID_discovery_cases-caseID_258
 15 yrs.
 M
 Intellectual disability
 Additional clinical information N/A
 Mild intellectual disability
 52014939
 52127087
  112149
 GRCh38
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-260
 N/A
 N/A
 PMG
 Diagnosis of polymicrogyria (PMG).
 
 52099709
 52192827
  93119
 GRCh38
 Deletion
 Yes
  sanders_11_ASD_discovery_cases-11099.p1
 11.4
 M
 Autism
 NA
 Full-scale IQ, 83; non-verbal IQ, 89; verbal IQ, 77
 52709341
 52733495
  24155
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11860.p1
 6
 M
 Autism
 NA
 Full-scale IQ, 86; non-verbal IQ, 95; verbal IQ, 75
 52689677
 52697350
  7674
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12327.p1
 14.6
 M
 Autism
 NA
 Full-scale IQ, 97; non-verbal IQ, 108; verbal IQ, 83
 52530644
 52615231
  84588
 GRCh38
 Duplication
 No
  wang_18_TS_discovery_cases-case25094.p1
 N/A
 N/A
 Tourette syndrome
 Tourette syndrome proband from phase 1 cohort; no additional clinical information available
 
 49235809
 49568365
  332557
 GRCh38
 Deletion
 Yes

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-controlB916582_1007854385
  N/A
  N/A
  Control
  No previous psychiatric history
 
  50675526
  50770936
  95411
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900025_900025
  N/A
  N/A
  Control
  No previous psychiatric history
 
  51424428
  51499362
  74935
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900564_900564
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52706065
  52746291
  40227
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901040_901040
  N/A
  N/A
  Control
  No previous psychiatric history
 
  50510070
  50707501
  197432
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902690_902690
  N/A
  N/A
  Control
  No previous psychiatric history
 
  50593779
  50625910
  32132
  GRCh38
  Duplication
  No
  krumm_13_ASD_discovery_controls-control13216.s1
  N/A
  M
  Control
  Unaffected sibling from SSC quad family 13216. SRS score of 50.
 
  50439073
  51242912
  803840
  GRCh38
  Duplication
  No (not tested)
  sanders_11_ASD_discovery_controls-11316.s1
  13.3
  F
  Control (matched sibling)
  NA
  NA
  51350687
  51354172
  3486
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11860.s1
  14.1
  M
  Control (matched sibling)
  NA
  NA
  52689677
  52697350
  7674
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12327.s1
  16.3
  F
  Control (matched sibling)
  NA
  NA
  52560413
  52615231
  54819
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13216.s1
  6
  M
  Control (matched sibling)
  NA
  NA
  50437077
  51342701
  905625
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 brandler_18_ASD_discovery_cases-case14-591
 PCR or SNP data validation
 
 Paternal
 
 
 MAPK6
 
 brandler_18_ASD_discovery_cases-caseREACH000319
 PCR or SNP data validation
 
 Paternal
 
 
 MAPK6
 
 brandler_18_ASD_discovery_cases-caseREACH000322
 PCR or SNP data validation
 
 Paternal
 
 
 MAPK6
 
 engchuan_15_ASD_discovery_cases-case14415_5240
 
 
 Unknown
 
 
 SPPL2A
 
 engchuan_15_ASD_discovery_cases-case3205_3
 
 
 Unknown
 
 
 
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000623
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 DCAF13P3,SPPL2A,AP4E1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001993
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 MAPK6-DT,MAPK6
 
 marshall_08_ASD_discovery_cases-SK0300-003
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 USP50,USP8,TRPM7
 
 prasad_12_ASD_discovery_cases-case113501L
 
 
 Unknown
 Unknown
 Unknown
 TNFAIP8L3
 
 quintela_17_DD/ID_discovery_cases-caseID_258
 
 
 Unknown
 
 Unknown
 MAPK6-DT,BCL2L10,MAPK6,GNB5
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-260
 qPCR
 
 Unknown
 Unknown
 Unknown
 BCL2L10,CERNA1,MYO5C,GNB5
 
 sanders_11_ASD_discovery_cases-11099.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 FAM214A
 
 sanders_11_ASD_discovery_cases-11860.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 FAM214A
 
 sanders_11_ASD_discovery_cases-12327.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 ARPP19,FAM214A
 
 wang_18_TS_discovery_cases-case25094.p1
 qPCR
 
 De novo
 
 
 FGF7,FAM227B,GALK2
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB916582_1007854385
 
 
  Unknown
 
 
  RN7SL354P,TRPM7,SPPL2A
 
engchuan_15_ASD_discovery_controls-controlHABC_900025_900025
 
 
  Unknown
 
 
  DMXL2
 
engchuan_15_ASD_discovery_controls-controlHABC_900564_900564
 
 
  Unknown
 
 
  FAM214A
 
engchuan_15_ASD_discovery_controls-controlHABC_901040_901040
 
 
  Unknown
 
 
  RN7SL354P,USP50,USP8,TRPM7,SPPL2A
 
engchuan_15_ASD_discovery_controls-controlHABC_902690_902690
 
 
  Unknown
 
 
  TRPM7
 
krumm_13_ASD_discovery_controls-control13216.s1
 
 
  Paternal
  Simplex
 
  RNA5SP395,RN7SL354P,DCAF13P3,MIR4713,USP50,TNFAIP8L3,USP8,TRPM7,SPPL2A,AP4E1,MIR4713HG,CYP19A1
 
sanders_11_ASD_discovery_controls-11316.s1
 
 
  Paternal
  Simplex (quad)
  NA
  GLDN
 
sanders_11_ASD_discovery_controls-11860.s1
 
 
  Paternal
  Simplex (quad)
  NA
  FAM214A
 
sanders_11_ASD_discovery_controls-12327.s1
 
 
  Maternal
  Simplex (quad)
  NA
  ARPP19,FAM214A
 
sanders_11_ASD_discovery_controls-13216.s1
 
 
  Paternal
  Simplex (quad)
  NA
  RNA5SP395,RN7SL354P,DCAF13P3,MIR4713,MIR7973-2,MIR7973-1,USP50,TNFAIP8L3,USP8,TRPM7,SPPL2A,AP4E1,MIR4713HG,CYP19A1,GLDN
 

No Animal Model Data Available
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