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15q12CNV Type: Deletion-Duplication


Largest CNV size: 1000000 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
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
 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
 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
  NA NA
 Anonymized DNA samples from Italian individuals with no psychiatric disorders
 365
 Control
 N/A
 54.52% Male
 205632
 0
 1
 1
 cai_08_ASD_discovery_controls
 Controls
 248
 Controls
 
 70.2% Male
 1000000
 0
 0
 0
 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
 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
 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
  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
  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
 
 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
 
 
 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
 
 

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