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22q12.2CNV Type: Deletion-Duplication


Largest CNV size: 800000 bp

Statistics Box:
Number of Reports: 7



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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Excess of rare, inherited truncating mutations in autism.
Duplication
Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Nine patients with a microdeletion 15q11.2 between breakpoints 1 and 2 of the Prader-Willi critical region, possibly associated with behavioural di...
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
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

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 doornbos_09_15q11.2_discovery_cases
 Patients in two genetic centres (University Medical Centre Groningen & Leiden University Medical Centre, Netherlands)
 1576
 Patients originally referred for mental retardation and/or multiple congenital abnormalities; all patients with 15q11.2 microdeletion were clinically re-evaluated.
 
 
 800000
 1
 0
 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
 30135
 1
 0
 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
 596479
 0
 2
 2
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 58052
 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
 718104
 0
 2
 2
 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
 155500
 0
 1
 1
 schmitz-abe_20_ASD_discovery_cases
 ASD probands rom 187 families from the Homozygosity Mapping Collaborative of Autism (HMCA); 22% of families had more than one affected child, and 66% of families were consanguineous.
 255
 Diagnosis of autism or ASD made by a neurologist, child psychiatrist, or psychologist; DSM-IV-R criteria confirmed in all individuals with an Autism diagnosis
 N/A
 N/A
 30301
 2
 0
 2

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
 0
 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_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 111794
 0
 3
 3
 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)
 718104
 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.
 
 153011
 0
 1
 1
 stamouli_18_ASD/NDD_discovery_controls
  NA NA
 Unaffected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
 100 twin pairs
 Control (unaffected) individual following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities and
 N/A
 N/A
 479650
 0
 1
 1

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 doornbos_09_15q11.2_discovery_cases
  Dutch
 aCGH, array SNP, MLPA
  105K oligo array, Affymetrix 262K Nsp1
 
 Feature Extraction V.9., CGH analytics V.3.4.27, CNAG version 2.2
 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)
 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
 
 
 schmitz-abe_20_ASD_discovery_cases
  Middle Eastern
 Array SNP
  Affymetrix 6.0, Affymetrix 500K
 
 
 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_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  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
 
 
  stamouli_18_ASD/NDD_discovery_controls
  Swedish
  Solid phase hybridization
  Illumina Infinium PsychArray-24 v1.1
  PennCNV, QuantiSNP, iPattern, iPsychCNV
 
  None

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  doornbos_09_15q11.2_discovery_cases-case5
 5 yrs.
 M
 ADHD
 Hypotonia & feeding problems as an infant. Delayed motor & speech development. Behavioral difficulties with attention deficit. Convlusions. Normal growth parameters, some dysmorphic features (plagiocephaly, broad forehead, hypertelorism). Genital abnormalities, recurrent infections, 13 pairs of ribs.
 IQ of 70-92 (WISC-III)
 30974014
 31774014
  800001
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case14330_4440
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 29937416
 29967551
  30136
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001133
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 29664957
 29713572
  48616
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001136
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 29281920
 29878399
  596480
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case12695.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 29636750
 29694802
  58053
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case129151L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 27921506
 28639609
  718104
 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
 
 28604129
 28627312
  23184
 Unknown
 Duplication
 No
  sanders_11_ASD_discovery_cases-12695.p1
 12.3
 M
 Autism
 NA
 Full-scale IQ, 49; non-verbal IQ, 56; verbal IQ, 35
 29606451
 29761951
  155501
 GRCh38
 Duplication
 No
  schmitz-abe_20_ASD_discovery_cases-caseAU-2601
 N/A
 M
 ASD
 Proband born to consanguineous parents of Middle Eastern descent from the HMCA cohort. Homozygous deletion segregated with ASD in this family.
 
 29940507
 29970807
  30301
 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
  krumm_15_ASD_discovery_controls-control12695.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  29636750
  29748544
  111795
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control13807.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  29767398
  29769719
  2322
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control14082.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  29767398
  29769719
  2322
  GRCh38
  Duplication
  Yes
  sanders_11_ASD_discovery_controls-12695.s1
  14.1
  M
  Control (matched sibling)
  NA
  NA
  29608940
  29761951
  153012
  GRCh38
  Duplication
  No
  stamouli_18_ASD/NDD_discovery_controls-family21_Twin_2
  N/A
  N/A
  Control
  Control is from a dizygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
 
  29325172
  29804821
  479650
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 doornbos_09_15q11.2_discovery_cases-case5
 
 
 Maternal
 NA
 NA
 TUG1,RN7SL633P,PLA2G3,MIR3928,RNF185-AS1,RNU6-1128P,PIK3IP1,RNA5SP496,LINC01521,RNU6-338P,RNU6-28P,H2AFZP6,MIR7109,RN7SL20P,SMTN,SELENOM,INPP5J,LIMK2,PISD,RNF185,PIK3IP1-AS1,PATZ1,SFI1,PRR14L,DEPDC5,DRG1,EIF4ENIF1
 
 engchuan_15_ASD_discovery_cases-case14330_4440
 
 
 Unknown
 
 
 MTMR3
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001133
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 NF2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001136
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 RASL10A,SNORD125,RFPL4AP6,RPEP4,EWSR1,GAS2L1,RFPL1S,RFPL1,THOC5,NIPSNAP1,CABP7,UQCR10,ASCC2,NEFH,NF2,ZMAT5,AP1B1
 
 krumm_15_ASD_discovery_cases-case12695.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 NF2
 
 prasad_12_ASD_discovery_cases-case129151L
 
 
 Unknown
 Unknown
 Unknown
 NIPSNAP1,GAS2L1,RASL10A,CABP7,MTMR3,RFPL1-AS1,NEFH,EMID1,RFPL1,UQCR10,MIR3653,RHBDD3,ASCC2,ZMAT5,AP1B1,THOC5,EWSR1,SNORD125,NF2
 
 prasad_12_ASD_discovery_cases-case53664
 
 
 Unknown
 Unknown
 Unknown
 MTMR3
 
 sanders_11_ASD_discovery_cases-12695.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 RPEP4,CABP7,NF2,ZMAT5
 
 schmitz-abe_20_ASD_discovery_cases-caseAU-2601
 qPCR
 
 Both parents
 Simplex
 Segregated
 MTMR3
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_15_ASD_discovery_controls-control12695.s1
  Illumina 1MDuo
 
  Paternal
 
 
  CABP7,NF2,ZMAT5
 
krumm_15_ASD_discovery_controls-control13807.s1
  Omni2.5-4v1
 
  De novo
 
 
  UQCR10
 
krumm_15_ASD_discovery_controls-control14082.s1
  Omni2.5-4v1
 
  De novo
 
 
  UQCR10
 
sanders_11_ASD_discovery_controls-12695.s1
 
 
  Paternal
  Simplex (quad)
  NA
  RPEP4,CABP7,NF2,ZMAT5
 
stamouli_18_ASD/NDD_discovery_controls-family21_Twin_2
 
 
  Unknown
  N/A (both twins typically developing)
 
  SNORD125,RFPL4AP6,RPEP4,RFPL1S,RFPL1,THOC5,NIPSNAP1,CABP7,UQCR10,ASCC2,NEFH,NF2,ZMAT5,AP1B1
 

No Animal Model Data Available
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