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15q25.2CNV Type: Deletion-Duplication


Largest CNV size: 247522 bp

Statistics Box:
Number of Reports: 15



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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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...
Duplication
Phenotypic heterogeneity of genomic disorders and rare copy-number variants.
Deletion-Duplication
An emerging phenotype of interstitial 15q25.2 microdeletions: clinical report and review.
Deletion
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion-Duplication
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Global increases in both common and rare copy number load associated with autism.
Deletion
Identification of candidate intergenic risk loci in autism spectrum disorder.
Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion

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
 895851
 2
 9
 11
 girirajan_12_ASD/DD/ID_discovery_cases
 Samples from affected children submitted to Signature Genomic Laboratories from 2008-2010.
 32587
 Developmental delay with or without congenital malformations
 
 
 1550000
 2
 4
 6
 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
 1050000
 1
 1
 2
 girirajan_13b_ASD_discovery_cases
 Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)
 243
 Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol
 N/A
 N/A
 54065
 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
 1569771
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 533976
 1
 1
 2
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 9713
 1
 0
 1
 palumbo_12_DD/ID_discovery_cases
 Only child of healthy and non-consanguineous parents (with no family history of intellectual disability, congenital anomalies, or stillbirth) referred for investigations regarding suspected congenital encephalopathy.
 1
 Developmental delay/intellectual disability, behavioral problems (autistic features and ADHD), and mild dysmorphic features
 9 yrs.
 Female
 1658802
 1
 0
 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
 
 
 247522
 0
 3
 3
 pinto_14_ASD_discovery_cases
 ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
 1359
 Cases classified according to ADOS and ADI-R
 N/A
 N/A
 895852
 1
 0
 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
 143380
 0
 2
 2
 quintela_17_DD/ID_discovery_cases
 Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
 573
 All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
 Range, 3 months-18 years
 60.38% Male
 460600
 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
 92415
 6
 3
 9
 walker_13_ASD_discovery_cases
 Unrelated ASD probands previously described in Lionel et al., 2011 and Pinto et al., 2010 CNV reports
 1491
 Diagnosis of ASD based on gold-standard instruments including ADI and ADOS.
 N/A
 N/A
 78982
 0
 1
 1
 yin_16_ASD_discovery_cases
 Discovery cohort of ASD cases recruited from the Department of Psychiatry of National Taiwan University Hospital (NTUH), Chang Gung Memorial Hospital (CGMH), Taoyuan, and Taoyuan Mental Hospital (TMH), Taiwan.
 335
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R. Cases' autistic behaviors assessed by Social Responsiveness Scale (SRS), and cognitive functions assessed by the Weschler Intelligence Scale for Children-Third Edition (WISC-III) and the Wisconsin Card Sorting Test (WCST).
 Mean, 9.39 4.04 yrs.
 89.3% Male
 174530
 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
 117182
 1
 6
 7
 girirajan_12_ASD/DD/ID_discovery_controls
 Persons found to have no overt neurological disorders during screening for other studies
 8329
 Control
 
 
 1550000
 0
 0
 0
 girirajan_13a_ASD_discovery_controls3
 Controls assessed for CNVs within 120 SD-mediated hotspots; includes 2090 controls from Wellcome Trust Case-Control Consortium (girirajan_13_ASD_discovery_controls2)
 8329
 Control
 NA
 NA
 0
 0
 0
 0
 girirajan_13b_ASD_discovery_controls
 Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)
 223
 Control
 N/A
 N/A
 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
 583237
 1
 1
 2
 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
 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)
 127831
 1
 0
 1
 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)
 143380
 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.
 
 192415
 3
 6
 9
 walker_13_ASD_discovery_controls
 Control samples from the SAGE cohort (n=1287), from the Ottawa Heart Institute (n=1234), and from the POPGEN collection (n=1123)
 3644
 Control
 N/A
 N/A
 78982
 N/A
 N/A
 N/A
 yin_16_ASD_discovery_controls
 Individuals from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
 1093
 Controls
 Mean, 68.07 10.12 yrs.
 48.0% Male
 174530
 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
 
 
 Yes
 girirajan_12_ASD/DD/ID_discovery_cases
 
 aCGH
  BACs aCGH, SignatureChipOS
 
 
 FISH, aCGH, or confirmation by inheritance
 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)
 girirajan_13b_ASD_discovery_cases
  133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American
 aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
 DNA Copy Number v1.6
 
 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)
 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
 palumbo_12_DD/ID_discovery_cases
  Caucasian
 Array SNP
  Affymetrix GeneChip Genome Wide Human SNP 6.0
 
 Genotyping Console Software V4.1
 Array SNP, microsatellite analysis
 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)
 pinto_14_ASD_discovery_cases
  Predominantly European
 Solid phase hybridization
  Illumina 1M (v.1 and v.3)
 
 
 qPCR, MLPA, long-range PCR
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 quintela_17_DD/ID_discovery_cases
  North West Spain
 Array SNP
  Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
 
 Affymetrix ChAS v.1.2.2
 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
 
 
 walker_13_ASD_discovery_cases
  N/A
 Array SNP, solid phase hybridization
  Illumina 1M, Affymetrix 6.0
 
 QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
 None
 yin_16_ASD_discovery_cases
  Han Chinese
 Array SNP
  Affymetrix 6.0
 
 Affymetrix Genotyping Console v.4.1
 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
  girirajan_12_ASD/DD/ID_discovery_controls
 
  aCGH
  BACs ACGH (SignatureChipoWG) or oligoarray (SignatureChipOS)
 
 
 
  girirajan_13a_ASD_discovery_controls3
  NA
  Array SNP
  N/A
 
 
  None
  girirajan_13b_ASD_discovery_controls
  116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American
  aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
  DNA Copy Number v1.6
 
 
  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)
  nord_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  Sliding-window algorithm, ~10 kb minumum size threshold
 
  None
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  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
 
 
  walker_13_ASD_discovery_controls
  N/A
  Array SNP, solid phase hybridization
  Illumina 1M, Affymetrix 6.0
 
  QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
  None
  yin_16_ASD_discovery_controls
  Han Chinese
  Array SNP
  Affymetrix 6.0
 
  Affymetrix Genotyping Console v.4.1
  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
  engchuan_15_ASD_discovery_cases-case1260_10
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 81704532
 81806048
  101517
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case13086_1013
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 81704532
 81796947
  92416
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case14181_2940
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 84562030
 84641012
  78983
 GRCh38
 Duplication
 Yes
  engchuan_15_ASD_discovery_cases-case2159_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 83819884
 84164180
  344297
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case3145_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 84056335
 84390814
  334480
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case4432_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 81704532
 81796947
  92416
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case5205_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 81704532
 81806048
  101517
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case5357_4
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 82151598
 82399249
  247652
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case5537_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 84262270
 85185603
  923334
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case8605_202
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 81696852
 81796947
  100096
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case8695_201
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 83268329
 84164180
  895852
 GRCh38
 Deletion
 Yes
  girirajan_12_ASD/DD/ID_discovery_cases-case0836
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Deletion
 NA
  girirajan_12_ASD/DD/ID_discovery_cases-case0837
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Deletion
 NA
  girirajan_12_ASD/DD/ID_discovery_cases-case0838
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Duplication
 NA
  girirajan_12_ASD/DD/ID_discovery_cases-case0839
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Duplication
 NA
  girirajan_12_ASD/DD/ID_discovery_cases-case0840
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Duplication
 NA
  girirajan_12_ASD/DD/ID_discovery_cases-case0841
 NA
 NA
 Developmental delay
 NA
 NA
 82558402
 84070244
  1511843
 GRCh38
 Duplication
 NA
  girirajan_13a_ASD_discovery_cases-11348.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
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 Yes
  girirajan_13a_ASD_discovery_cases-14252.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
 84165244
 85330765
  1165522
 GRCh38
 Duplication
 Yes
  girirajan_13b_ASD_discovery_cases-60705104612
 N/A
 N/A
 Autism
 Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Caucasian
 N/A
 82696769
 82750834
  54066
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002611
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 82558402
 84121082
  1562681
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case11348.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 84603927
 85137903
  533977
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case14252.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 84603927
 85137903
  533977
 GRCh38
 Duplication
 Yes
  nord_11_ASD_discovery_cases-255-1
 
 
 ASD
 
 
 81101576
 81111288
  9713
 Unknown
 Deletion
 No
  palumbo_12_DD/ID_discovery_cases-case1
 9 yrs.
 F
 Developmental delay/intellectual disability, autistic features, and ADHD
 Case referred for investigations regarding suspected congenital encephalopathy. Developmental milestones: psychomotor delay observed during first months of life; delays in both receptive and expressive language; learned to walk at 3 yrs. 9 mos. of age. Langauge and communication evaluation: used some syllabic sounds and two approximations of sign language words, but they were not specific. Motor and musculoskeletal evaluation: general hypotonia, scoliosis, pectus excavatum. Behavioral/psychiatric evaluation: autistic features (stereotypies), anxiety, hyperactivity, attention deficits, oppositional behavior. EEG: normal. Brain imaging: normal cerebral MRI. Auditory evaluation: normal auditory evoked potential. Dysmorphic features: high hairline, round eyes, flat nasal bridge, thin upper lip vermillion, delayed teeth eruption, diastema of teeth, long fingers, 5th finger clinodactyly. Growth parameters (at 7 yrs.): height, 120 cm (<50th %ile); weight, 22 kg (25th-50th %ile); OFC, 50.9 cm (<25th %ile). Karyotype: normal (46, XX). Family history: only child of healthy, non-consanguineous parents; no family history of intellectual disability, congenital anomalies, or stillborn children.
 Global developmental delays. Moderate-to-severe cognitive delay (social behavior Q 37, locomotor Q 25, language Q 21, eye and hand coordination Q 34).
 82641775
 84159587
  1517813
 GRCh38
 Deletion
 Yes
  pinto_10_ASD_discovery_cases-case1260_10
 NA
 M
 ASD
 NA
 NA
 81704532
 81806048
  101517
 GRCh38
 Duplication
 Yes
  pinto_10_ASD_discovery_cases-case5205_3
 NA
 M
 ASD
 NA
 NA
 81704532
 81806048
  101517
 GRCh38
 Duplication
 Yes
  pinto_10_ASD_discovery_cases-case5357_4
 NA
 M
 ASD
 NA
 NA
 82151598
 82399249
  247652
 GRCh38
 Duplication
 Yes
  pinto_14_ASD_discovery_cases2-case8695_201
 6 yrs.
 M
 ASD
 Autism (ADI-R and ADOS positive), language delay (first words 42 mo, first phrases 48 mo), verbal. Family history: N/A.
 Mild ID (Differential Ability Scales at 6 y: FSIQ 58)
 83268329
 84164180
  895852
 GRCh38
 Deletion
 Yes
  prasad_12_ASD_discovery_cases-case103953
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 80221809
 80365188
  143380
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case52401
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 82561076
 82603838
  42763
 Unknown
 Duplication
 No
  quintela_17_DD/ID_discovery_cases-caseID_505
 6 yrs.
 F
 Intellectual disability and epilepsy
 Epilepsy. Incomplete parental clinical history.
 Intellectual disability
 81682787
 82143386
  460600
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11088.p1
 5.7
 M
 Autism
 NA
 Full-scale IQ, 92; non-verbal IQ, 102; verbal IQ, 80
 83931900
 83938174
  6275
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11142.p1
 7.9
 M
 Autism
 NA
 Full-scale IQ, 44; non-verbal IQ, 53; verbal IQ, 31
 84148033
 84167478
  19446
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11393.p1
 8.2
 M
 Autism
 NA
 Full-scale IQ, 28; non-verbal IQ, 37; verbal IQ, 17
 81668068
 81706050
  37983
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11532.p1
 9.1
 M
 Autism
 NA
 Full-scale IQ, 59; non-verbal IQ, 65; verbal IQ, 60
 81704532
 81796947
  92416
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11568.p1
 13.5
 F
 Autism
 NA
 Full-scale IQ, 51; non-verbal IQ, 72; verbal IQ, 28
 84396135
 84403620
  7486
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11734.p1
 13.8
 F
 Autism
 NA
 Full-scale IQ, 84; non-verbal IQ, 81; verbal IQ, 95
 81564197
 81606076
  41880
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11984.p1
 5
 M
 Autism
 NA
 Full-scale IQ, 94; non-verbal IQ, 100; verbal IQ, 88
 81668068
 81706050
  37983
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12150.p1
 8.7
 M
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 95; verbal IQ, 133
 82052627
 82062993
  10367
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12201.p1
 13.3
 M
 Autism
 NA
 Full-scale IQ, 130; non-verbal IQ, 131; verbal IQ, 116
 84393201
 84403620
  10420
 GRCh38
 Deletion
 No
  walker_13_ASD_discovery_cases-case8-14181-2940
 N/A
 M
 ASD
 N/A
 N/A
 84562030
 84641012
  78983
 GRCh38
 Duplication
 No
  yin_16_ASD_discovery_cases-case482
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 84246328
 84546378
  300051
 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
  engchuan_15_ASD_discovery_controls-controlB269904_1007853875
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81704532
  81796947
  92416
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB427661_1007840422
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81696852
  81796947
  100096
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB428806_1007853319
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81668068
  81706050
  37983
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB649933_1007874697
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81704532
  81796947
  92416
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900500_900500
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81704532
  81758338
  53807
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901095_901095
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81855966
  81973148
  117183
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
  N/A
  N/A
  Control
  No previous psychiatric history
 
  81704532
  81811598
  107067
  GRCh38
  Duplication
  No
  krumm_15_ASD_discovery_controls-control11348.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  84554666
  85137903
  583238
  GRCh38
  Deletion
  Yes
  krumm_15_ASD_discovery_controls-control14252.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  84603927
  85137903
  533977
  GRCh38
  Duplication
  Yes
  poultney_13_ASD_discovery_controls-controlNA12891
  N/A
  M
  Control
  Control from CEPH
 
  82659560
  82787390
  127831
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11041.s1
  15.7
  M
  Control (matched sibling)
  NA
  NA
  81668068
  81706050
  37983
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11216.s1
  6.4
  M
  Control (matched sibling)
  NA
  NA
  82206704
  82399249
  192546
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11393.s1
  9.1
  M
  Control (matched sibling)
  NA
  NA
  81659718
  81706050
  46333
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11532.s1
  13.5
  F
  Control (matched sibling)
  NA
  NA
  81704532
  81796947
  92416
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11981.s1
  8.6
  F
  Control (matched sibling)
  NA
  NA
  84118883
  84164180
  45298
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11984.s1
  7.7
  F
  Control (matched sibling)
  NA
  NA
  81659718
  81704532
  44815
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12150.s1
  10.3
  F
  Control (matched sibling)
  NA
  NA
  82052627
  82062993
  10367
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12507.s1
  26.1
  F
  Control (matched sibling)
  NA
  NA
  83936368
  83938174
  1807
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12701.s1
  10.4
  M
  Control (matched sibling)
  NA
  NA
  82711432
  82765864
  54432
  NCBI36
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 engchuan_15_ASD_discovery_cases-case1260_10
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case13086_1013
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case14181_2940
 
 
 De novo
 
 
 EGLN1P1,LINC00933,ZSCAN2,SCAND2P,WDR73,UBE2Q2P1
 
 engchuan_15_ASD_discovery_cases-case2159_1
 
 
 Unknown
 
 
 RNU6-1339P,EFL1P1,ADAMTSL3
 
 engchuan_15_ASD_discovery_cases-case3145_3
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,EFL1P1,UBE2Q2L,CSPG4P11,GOLGA2P7
 
 engchuan_15_ASD_discovery_cases-case4432_1
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case5205_3
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case5357_4
 
 
 Unknown
 
 
 RNU1-77P,SAXO2,GOLGA6L10,UBE2Q2P2,EFL1,ADAMTS7P1
 
 engchuan_15_ASD_discovery_cases-case5537_3
 
 
 Unknown
 
 
 RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
 engchuan_15_ASD_discovery_cases-case8605_202
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case8695_201
 
 
 De novo
 
 
 RNU6-401P,TUBAP4,RNU6-1339P,BNC1,EFL1P1,SH3GL3,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0836
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0837
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0838
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0839
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0840
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_12_ASD/DD/ID_discovery_cases-case0841
 NA
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 girirajan_13a_ASD_discovery_cases-11348.p1
 aCGH (NimbleGen 135K array)
 
 Maternal
 Simplex
 Unknown
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_ASD_discovery_cases-14252.p1
 aCGH (NimbleGen 135K array)
 
 Paternal
 Simplex
 Unknown
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13b_ASD_discovery_cases-60705104612
 
 
 Unknown
 Unknown
 Unknown
 ACTG1P17,SNHG21,AP3B2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002611
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,EFL1P1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 krumm_15_ASD_discovery_cases-case11348.p1
 Illumina 1M
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 EGLN1P1,RNU6-339P,RNU6-796P,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,SEC11A,ZNF592,PDE8A,SLC28A1
 
 krumm_15_ASD_discovery_cases-case14252.p1
 Omni2.5-4v1
 
 Paternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 EGLN1P1,RNU6-339P,RNU6-796P,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,SEC11A,ZNF592,PDE8A,SLC28A1
 
 nord_11_ASD_discovery_cases-255-1
 
 
 Maternal
 
 
 CPEB1
 
 palumbo_12_DD/ID_discovery_cases-case1
 Array SNP, microsatellite analysis
 
 De novo
 Simplex
 Likely segregated
 ACTG1P17,SCARNA15,RAMAC,MIR4515,RNU6-401P,TUBAP4,RNU6-1339P,CPEB1-AS1,SNHG21,FSD2,WHAMM,C15orf40,BTBD1,TM6SF1,HDGFL3,BNC1,EFL1P1,CPEB1,AP3B2,SH3GL3,HOMER2,ADAMTSL3
 
 pinto_10_ASD_discovery_cases-case1260_10
 Illumina550
 
 maternal
 NA
 NA
 
 
 pinto_10_ASD_discovery_cases-case5205_3
 Agilent1M
 
 maternal
 NA
 NA
 
 
 pinto_10_ASD_discovery_cases-case5357_4
 Agilent1M
 
 maternal
 NA
 NA
 RNU1-77P,SAXO2,GOLGA6L10,UBE2Q2P2,EFL1,ADAMTS7P1
 
 pinto_14_ASD_discovery_cases2-case8695_201
 qPCR
 
 De novo
 Simplex
 (not tested)
 RNU6-401P,TUBAP4,RNU6-1339P,BNC1,EFL1P1,SH3GL3,ADAMTSL3
 
 prasad_12_ASD_discovery_cases-case103953
 
 
 Unknown
 Unknown
 Unknown
 EFTUD1,FAM154B
 
 prasad_12_ASD_discovery_cases-case52401
 
 
 Unknown
 Unknown
 Unknown
 LOC648809
 
 quintela_17_DD/ID_discovery_cases-caseID_505
 
 
 Maternal
 
 Unknown
 MEX3B,LINC01583,EFL1
 
 sanders_11_ASD_discovery_cases-11088.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 ADAMTSL3
 
 sanders_11_ASD_discovery_cases-11142.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 DNM1P41
 
 sanders_11_ASD_discovery_cases-11393.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11532.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11568.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 CSPG4P5,DNM1P51
 
 sanders_11_ASD_discovery_cases-11734.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-11984.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12150.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12201.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 RN7SL417P,CSPG4P5,DNM1P51
 
 walker_13_ASD_discovery_cases-case8-14181-2940
 
 
 Unknown
 Simplex
 Unknown
 EGLN1P1,LINC00933,ZSCAN2,SCAND2P,WDR73,UBE2Q2P1
 
 yin_16_ASD_discovery_cases-case482
 
 
 Unknown
 Unknown
 Unknown
 UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,UBE2Q2P12,GOLGA6L5P,DNM1P51,UBE2Q2P1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB269904_1007853875
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlB427661_1007840422
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlB428806_1007853319
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlB649933_1007874697
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_900500_900500
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_901095_901095
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
 
 
  Unknown
 
 
 
 
krumm_15_ASD_discovery_controls-control11348.s1
  Illumina 1M
 
  Maternal
 
 
  EGLN1P1,RNU6-339P,RNU6-796P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
krumm_15_ASD_discovery_controls-control14252.s1
  Omni2.5-4v1
 
  Paternal
 
 
  EGLN1P1,RNU6-339P,RNU6-796P,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,SEC11A,ZNF592,PDE8A,SLC28A1
 
poultney_13_ASD_discovery_controls-controlNA12891
 
 
  Unknown
 
 
  ACTG1P17,SCARNA15,CPEB1-AS1,SNHG21,FSD2,AP3B2
 
sanders_11_ASD_discovery_controls-11041.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11216.s1
 
 
  Maternal
  Simplex (quad)
  NA
  SAXO2,GOLGA6L10,UBE2Q2P2,EFL1,ADAMTS7P1
 
sanders_11_ASD_discovery_controls-11393.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11532.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11981.s1
 
 
  Paternal
  Simplex (quad)
  NA
  EFL1P1
 
sanders_11_ASD_discovery_controls-11984.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12150.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12507.s1
 
 
  Maternal
  Simplex (quad)
  NA
  ADAMTSL3
 
sanders_11_ASD_discovery_controls-12701.s1
 
 
  Paternal
  Simplex (quad)
  NA
  0 genes
 

No Animal Model Data Available
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