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Xp22.2-p22.13CNV Type: Duplication


Largest CNV size: 100953 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

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References

Major Reports

Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders an...
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.
Duplication
NA
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 100952
 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
 1636999
 1
 0
 1
 kim_18_DD/ID_discovery_cases
  NA NA
 Individuals who had visited Konyang University Hospital for evaluation of unexplained DD/ID in a one year period (September 2013-October 2014)
 50
 All cases presented with developmental delay/intellectual disability (DD/ID); 19 cases (38.0 %) presented with epilepsy, 9 cases (18.0%) presented with autism
 Mean age, 5.4 5.9 yrs. (Range, 0.1-32 yrs.)
 52.0% Male
 743000
 0
 1
 1
 pinto_10_ASD_discovery_cases
 Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
 996
 ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
 
 
 100953
 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
 100499
 0
 1
 1
 willemsen_12_DD/ID_discovery_cases
 Individuals referred between Jan. 2003 and August 2010 to diagnostic center at Dept. of Human Genetics, Radboud Univ. Mijmegen Medical Centre, Nijmegen, The Netherlands for genome-wide array analysis (emphasis on X chromosome CNVs)
 4407
 Majority of cases: indication of developmental delay/intellectual disability [with or without other neuropsychiatric disorders (ASD, ADHD, etc.) and/or congenital anomalies]. Minority of cases: congenital anomalies or behavioral problems without DD/ID.
 2/3 of cases: age range of 1-18 yrs.
 54.5% Male
 470000
 0
 1
 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
 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
 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)
 100499
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 kim_18_DD/ID_discovery_cases
  Korean
 Array SNP
  Affymetrix CytoScan 750K
 
 Affymetrix ChAS
 None
 pinto_10_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium 1M SNP microarray
 QuantiSNP, iPattern
 
 qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 willemsen_12_DD/ID_discovery_cases
  Netherlands
 aCGH, array SNP
  Agilent 32K BAC array, Affymetrix 250K
 
 CNAG V2.0 (SNP array)
 None

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
 
  prasad_12_ASD_discovery_controls
  NA
  aCGH
  Agilent 1M
  ADM-2, DNAcopy (R Bioconductor)
  DNA Analytics v4.0.85 (Agilent), DNAcopy
 

Cases

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_cases-case5282_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 17128573
 17229525
  100953
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005208
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 17167171
 18804175
  1637005
 GRCh38
 Deletion
 Yes
  kim_18_DD/ID_discovery_cases-case12
  NA NA
 1 yr. 11 mos.
 M
 Developmental delay and autistic behavior
 Autistic behavior, absent speech, failure to thrive, microcephaly
 Developmental delay
 16967786
 17710532
  742747
 GRCh38
 Duplication
 No
  pinto_10_ASD_discovery_cases-case5282_3
 NA
 M
 ASD
 NA
 NA
 17128573
 17229525
  100953
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case74887
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 17057335
 17157833
  100499
 Unknown
 Duplication
 No
  willemsen_12_DD/ID_discovery_cases-case25
 
 M
 Intellectual disability
 Multiple congenital anomalies (MCA)
 Intellectual disability
 17071956
 17541957
  470002
 GRCh38
 Duplication
 No

Controls

No Control Data Available

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 engchuan_15_ASD_discovery_cases-case5282_3
 
 
 Unknown
 
 
 REPS2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005208
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 CBX1P4,MIR4768,NHS-AS1,TMSB10P2,GJA6P,PPEF1-AS1,SCML1,RS1,NHS,LINC01456,BEND2,SCML2,CDKL5,PPEF1,RAI2
 
 kim_18_DD/ID_discovery_cases-case12
 
 
 Unknown
 
 
 CBX1P2,CBX1P4,MIR4768,NHS-AS1,REPS2,NHS
 
 pinto_10_ASD_discovery_cases-case5282_3
 Agilent1M
 
 maternal
 NA
 NA
 REPS2
 
 prasad_12_ASD_discovery_cases-case74887
 
 
 Unknown
 Unknown
 Unknown
 REPS2
 
 willemsen_12_DD/ID_discovery_cases-case25
 
 
 Maternal
 
 
 CBX1P2,CBX1P4,MIR4768,REPS2,NHS
 

Controls

No Control Data Available
No Animal Model Data Available
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