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19q13.11CNV Type: Deletion-Duplication


Largest CNV size: 318600 bp

Statistics Box:
Number of Reports: 9



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

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
The clinical significance of small copy number variants in neurodevelopmental disorders.
Deletion
Excess of rare, inherited truncating mutations in autism.
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Identifying autism loci and genes by tracing recent shared ancestry.
Deletion
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Duplication
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 asadollahi_14_NDD_discovery_cases
 Patients screened for rare non-polymorphic exonic CNVs sizing 1-500 kb
 714
 Patients with undiagnosed neurodevelopmental disorders (NDD) with or without further congenital anomalies
 N/A
 N/A
 11000
 1
 0
 1
 celestino-soper_11_ASD_discovery_cases
 ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
 99
 ASD
 
 87.88% Male
 8336
 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
 154313
 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
 374118
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 36858
 0
 1
 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)
 
 
 318600
 2
 0
 2
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 24367
 0
 2
 2
 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
 28593
 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
 47115
 2
 1
 3

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
 107334
 1
 0
 1
 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
 kanduri_15_ASD_discovery_controls
 Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
 269
 Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 N/A
 N/A
 334015
 1
 0
 1
 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
 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.
 
 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)
 28593
 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.
 
 0
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 asadollahi_14_NDD_discovery_cases
  Predominantly European
 Array SNP
  Affymetrix 6.0, Affymetrix Cytogenetics 2.7, Affymetrix CytoScan HD
 HMM
 Affymetrix ChAS v.1.0.1
 MLPA
 celestino-soper_11_ASD_discovery_cases
 
 aCGH
  Agilent 1M
 ADM-2
 Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
 None
 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_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
 
 nord_11_ASD_discovery_cases
  29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
 aCGH
  NimbleGen HD2
 Sliding-window algorithm, ~10 kb minumum size threshold
 
 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
 
 

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
 
  kanduri_15_ASD_discovery_controls
  Finnish
  Solid phase hybridization
  Illumina Infinium HD Human610-Quad BeadChip
  QuantiSNP, PennCNV
  Illumina BeadStudio
  None
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  None
  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
  asadollahi_14_NDD_discovery_cases-case61825
 N/A
 F
 NDD
 Case with unspecified neurodevelopmental disorder
 
 34196619
 34207204
  10586
 GRCh38
 Deletion
 Yes
  celestino-soper_11_ASD_discovery_cases-11303
 NA
 M
 ASD
 NA
 NA
 33164142
 33172478
  8337
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case3318_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 32828507
 32907120
  78614
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4320_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 32099284
 32253597
  154314
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002151
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 32469643
 32843761
  374119
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case14236.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 34963629
 35000487
  36859
 GRCh38
 Duplication
 Yes
  morrow_08_ASD_discovery_cases-case3601
 NA
 
 ASD
 NA
 NA
 48071000
 48373000
  302400
 Unknown
 Deletion
 No
  morrow_08_ASD_discovery_cases-case3602
 NA
 
 ASD
 NA
 NA
 48104000
 48423000
  318600
 Unknown
 Deletion
 No
  nord_11_ASD_discovery_cases-226-1
 
 
 ASD
 
 
 38902503
 38925931
  23429
 Unknown
 Duplication
 No
  nord_11_ASD_discovery_cases-255-1
 
 
 ASD
 
 
 38902503
 38926869
  24367
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case53664
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 40008430
 40037022
  28593
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11911.p1
 9.9
 F
 Autism
 NA
 Full-scale IQ, 82; non-verbal IQ, 86; verbal IQ, 79
 33719877
 33741524
  21648
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12001.p1
 5.1
 M
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 104; verbal IQ, 111
 32501287
 32519400
  18114
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12221.p1
 4.1
 M
 Autism
 NA
 Full-scale IQ, 89; non-verbal IQ, 99; verbal IQ, 76
 33408872
 33455987
  47116
 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-controlB910439_1007845334
  N/A
  N/A
  Control
  No previous psychiatric history
 
  32708877
  32816211
  107335
  GRCh38
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split763
  N/A
  N/A
  Control
  Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 
  33690696
  34024710
  334015
  Unknown
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 asadollahi_14_NDD_discovery_cases-case61825
 MLPA
 
 Paternal
 Unknown
 Unknown
 LSM14A
 
 celestino-soper_11_ASD_discovery_cases-11303
 
 
 Unknown
 Simplex
 NA
 WDR88
 
 engchuan_15_ASD_discovery_cases-case3318_3
 
 
 Unknown
 
 
 RN7SKP22,SLC7A9,TDRD12,CEP89
 
 engchuan_15_ASD_discovery_cases-case4320_1
 
 
 Unknown
 
 
 LINC01782,RNA5SP472
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002151
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 PDCD5,SNORA68B,RPS12P31,RN7SL789P,RGS9BP,DPY19L3,NUDT19,SLC7A9,ANKRD27,TDRD12
 
 krumm_15_ASD_discovery_cases-case14236.p1
 Omni2.5-4v1
 
 De novo
 Simplex
 Segregated
 ZNF792,GRAMD1A
 
 morrow_08_ASD_discovery_cases-case3601
 
 
 Maternal
 Multiplex
 NA
 PSG1, PSG2, PSG5, PSG6, PSG11
 
 morrow_08_ASD_discovery_cases-case3602
 
 
 Maternal
 Multiplex
 NA
 PSG6/2/4/5/11
 
 nord_11_ASD_discovery_cases-226-1
 
 
 Paternal
 
 
 CHST8
 
 nord_11_ASD_discovery_cases-255-1
 
 
 Maternal
 
 
 CHST8
 
 prasad_12_ASD_discovery_cases-case53664
 
 
 Unknown
 Unknown
 Unknown
 LOC400685
 
 sanders_11_ASD_discovery_cases-11911.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 CHST8
 
 sanders_11_ASD_discovery_cases-12001.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-12221.p1
 
 
 Paternal
 Simplex (quad-proband unmatched)
 Unknown
 PEPD
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB910439_1007845334
 
 
  Unknown
 
 
  NUDT19,TDRD12
 
kanduri_15_ASD_discovery_controls-control_split763
 
 
  Unknown
 
 
  CEBPA,CEBPG,LRP3,PEPD,SLC7A10
 

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