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3q13.11CNV Type: Deletion-Duplication


Largest CNV size: 79887 bp

Statistics Box:
Number of Reports: 5



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
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Duplication
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 gai_11_ASD_discovery_cases
 Discovery case samples derived from AGRE set 4 (most recent patient recruitment)
 631
 Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
 
 
 107135
 0
 1
 1
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 79887
 1
 0
 1
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 14785
 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
 44855
 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
 79440
 4
 1
 5

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 brandler_18_ASD_discovery_controls
 Unaffected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (112 individuals from 311 families) and the Simons Simplex 1 (SSC1) cohort (518 controls from simplex quad families)
 630
 Control
 N/A
 N/A
 20677
 1
 0
 1
 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
 58558
 1
 0
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 5437
 1
 0
 1
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 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.
 
 24972
 2
 0
 2
 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)
 44855
 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.
 
 86518
 4
 0
 4

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 gai_11_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 None
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 aCGH (Agilent 244K)
 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
 
 qPCR

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  brandler_18_ASD_discovery_controls
  N/A
  WGS
  Illumina HiSeq X10 or HiSeq 2500
  ForestSV, Lumpy, Manta, Mobster, SV2
 
  PCR, array SNP
  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
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  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
  gai_11_ASD_discovery_cases-AU1407302
 
 
 Autism
 
 
 107474046
 107581180
  107135
 Unknown
 Duplication
 No
  levy_11_ASD_discovery_cases-11227.p1
 NA
 M
 ASD
 NA
 NA
 105250532
 105330418
  79887
 GRCh38
 Deletion
 Yes
  nord_11_ASD_discovery_cases-301-1
 
 
 ASD
 
 
 107778992
 107793776
  14785
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case82921L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 106505099
 106549953
  44855
 Unknown
 Duplication
 No
  sanders_11_ASD_discovery_cases-11227.p1
 9.7
 M
 Autism
 NA
 Full-scale IQ, 80; non-verbal IQ, 93; verbal IQ, 63
 105254492
 105333932
  79441
 GRCh38
 Deletion
 Yes
  sanders_11_ASD_discovery_cases-11324.p1
 11.4
 F
 Autism
 NA
 Full-scale IQ, 30; non-verbal IQ, 34; verbal IQ, 21
 103226498
 103232017
  5520
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12597.p1
 6.4
 M
 Autism
 NA
 Full-scale IQ, 70; non-verbal IQ, 77; verbal IQ, 66
 103226498
 103232017
  5520
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13010.p1
 7.9
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 122; verbal IQ, 99
 105245771
 105260842
  15072
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13322.p1
 16.9
 M
 Autism
 NA
 Full-scale IQ, 59; non-verbal IQ, 62; verbal IQ, 56
 105163092
 105189217
  26126
 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
  brandler_18_ASD_discovery_controls-controlSSC06338
  N/A
  F
  Control
  Control from SSC_phase1 cohort
 
  105546484
  105567161
  20678
  GRCh38
  Deletion
  Yes
  kanduri_15_ASD_discovery_controls-control_split1532
  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
 
  102892138
  102950695
  58558
  Unknown
  Deletion
  No
  krumm_15_ASD_discovery_controls-control13034.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  105547148
  105552585
  5438
  GRCh38
  Deletion
  Yes
  nord_11_ASD_discovery_controls-04C27079
 
 
  Control
 
 
  106181509
  106206480
  24972
  Unknown
  Deletion
 
  nord_11_ASD_discovery_controls-04C27708
 
 
  Control
 
 
  104828586
  104846282
  17697
  Unknown
  Deletion
 
  sanders_11_ASD_discovery_controls-11324.s1
  13
  F
  Control (matched sibling)
  NA
  NA
  103226498
  103232017
  5520
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11334.s1
  12.7
  M
  Control (matched sibling)
  NA
  NA
  103746208
  103746456
  249
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11367.s1
  4.6
  F
  Control (matched sibling)
  NA
  NA
  103763171
  103849689
  86519
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11512.s1
  4.3
  F
  Control (matched sibling)
  NA
  NA
  104382261
  104403830
  21570
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gai_11_ASD_discovery_cases-AU1407302
 
 
 Inherited
 
 
 0 genes
 
 levy_11_ASD_discovery_cases-11227.p1
 aCGH (Agilent 244K)
 
 De novo
 Simplex
 Segregated
 
 
 nord_11_ASD_discovery_cases-301-1
 
 
 Paternal
 
 
 0 genes
 
 prasad_12_ASD_discovery_cases-case82921L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11227.p1
 qPCR
 
 De Novo
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-11324.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12597.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-13010.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-13322.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC06338
  PCR or SNP data validation
 
  Maternal
 
 
  ALCAM
 
kanduri_15_ASD_discovery_controls-control_split1532
 
 
  Unknown
 
 
  Intergenic CNV: nearest genes, ZPLD1(dist=693453),MIR548A3(dist=952781)
 
krumm_15_ASD_discovery_controls-control13034.s1
  1M-Duov3
 
  Maternal
 
 
  ALCAM
 
nord_11_ASD_discovery_controls-04C27079
 
 
 
 
 
  0 genes
 
nord_11_ASD_discovery_controls-04C27708
 
 
 
 
 
  0 genes
 
sanders_11_ASD_discovery_controls-11324.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11334.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11367.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11512.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 

No Animal Model Data Available
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