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11p13CNV Type: Deletion-Duplication


Largest CNV size: 416101 bp

Statistics Box:
Number of Reports: 25



Summary Information

Summary statement in development

Additional Locus Information

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References

Major Reports

Title
Author, Year
Report Class
CNV Type
Structural variation of chromosomes in autism spectrum disorder.
Duplication
Characterization of 11p14-p12 deletion in WAGR syndrome by array CGH for identifying genes contributing to mental retardation and autism.
Deletion
Functional impact of global rare copy number variation in autism spectrum disorders.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.
Deletion
Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...
Duplication
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Deletion-Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation.
Deletion-Duplication
Copy number variation in 19 Italian multiplex families with autism spectrum disorder: Importance of synaptic and neurite elongation genes.
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Duplication
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Deletion-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Haploinsufficiency of two histone modifier genes on 6p22.3, ATXN1 and JARID2, is associated with intellectual disability.
Deletion
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion-Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion-Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 addis_15_ASD/DD/ID_discovery_cases
 Cases (children referred to Guy's and St. Thomas NHS Foundation Trust, southeastern UK from pediatricians and regional hospital) from Brain and Body Genetics Research Exchange (BBGRE)
 4092
 Developmental delay, ASD, speech or language delay or congenital defects
 N/A
 63.0% Male
 232686
 8
 1
 9
 addis_15_ASD_replication_cases
 ASD cases from the Autism Genome Project and two Canadian ASD cohorts
 2846
 All cases with a clinical diagnosis of ASD (ADI-R and/or ADOS)
 N/A
 N/A
 194602
 6
 0
 6
 baroy_13_ID/ASD_discovery_cases
 Five unrelated patients with variable degree of cognitive impairment ranging from borderline IQ to severe intellectual disability (University of Olso/Olso University Hospital, Norway).
 5
 Intellectual disability (ID) in four cases (borderline IQ in one case); one case (patient 3) with additional diagnosis of ASD (based on ADOS evaluation).
 Range, 4-17 yrs.
 40% Male
 94000
 1
 0
 1
 brandler_18_ASD_replication_cases
 Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
 1979
 Cases diagnosed with ASD
 N/A
 N/A
 9865
 1
 0
 1
 celestino-soper_11_ASD_discovery_cases
 ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
 99
 ASD
 
 87.88% Male
 291
 2
 0
 2
 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
 196692
 4
 1
 5
 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
 351000
 1
 2
 3
 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
 629604
 5
 3
 8
 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
 229445
 2
 1
 3
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 229445
 4
 1
 5
 kushima_18_SCZ_discovery_cases
 Individuals predominantly recruited from the middle of Honshu Island (Japan)
 2458
 Cases were diagnosed with schizophrenia (SCZ) according to DSM-5 criteria.
 Median age, 44 years
 55.0% Male
 142875
 1
 0
 1
 lesca_12_EP_discovery_cases
 Epilepsy patients collected at four French hospitals from 2009: Strasbourg Univ. Hospital (n=40), Lyons Univ. Hospital (n=18), Henri Gastaut Hospital (St. Paul Centre) in Marseille (n=2), and Reims American Memorial Hospital (n=1).
 61
 Epilepsy/epileptic encephalopathy. 41 patients with continuous spike and wave during slow-wave sleep syndrome (CSWSS), 20 patients with Landau-Kleffner syndrome (LKS). 12 (out of 57) patients displayed autistic features; ADHD features (hyperactivity, attention deficit and/or aggressiveness) reported in 41/58 patients,
 Mean age of diagnosis: 5.6 yrs. (range, 1-14 yrs.)
 61% Male
 159000
 0
 2
 2
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 416101
 1
 1
 2
 lintas_17_ASD_discovery_cases
 ASD cases from 19 Italian ASD multiplex families with either two (N=16) or three (N=3) autistic children
 41
 Cases were assessed with ADOS and ADI-R, Vineland Adaptive Behavior Scales, and either the Wechsler Intelligence Scales for Children (WISC), Griffith Mental Developmental Scales, Colored Raven Matrices, or Leiter International Performance Scale.
 N/A
 87.80% Male
 456110
 0
 1
 1
 lionel_13_ASD/ADHD/DD/ID_discovery_cases
 Individuals referred for postnatal genetic testing across 10 different sites, including 64,114 subjects with neurodevelopmental disorders: 1619 cases from Alberta Children's Hospital; 14,847 cases from Brain and Body Genetic Resource Exchange (BBGRE) database; 7320 cases from Boston Children's Hospital; 3552 cases from Credit Valley Hospital; 7411 cases from the Hospital for Sick Children; 6626 c
 89985
 64,114 cases with neurodevelopmental disorders (including ASD, ADHD, developmental delay, and/or intellectual disability); 25,871 cases with non-neurodevelopmental disorders (multiple congential anomalies, etc.)
 N/A
 N/A
 86917
 0
 1
 1
 marshall_08_ASD_discovery_cases
 Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
 427
 ASD
 
 
 302881
 0
 1
 1
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
 Patients from the Developmental Gene Anatomy Project at Harvard Medical School (DGAP), the Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP), the National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS), the Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database, and DECIPHER
 57365
 Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD
 N/A
 N/A
 2320127
 0
 1
 1
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 46914
 0
 1
 1
 o'roak_12_ASD_discovery_cases
 Autistic probands from the Simons Simplex Collection (SSC), from an initial cohort of 189 autism families
 122
 ASD/autism
 NA
 NA
 251094
 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
 
 
 121238
 1
 0
 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)
 42492
 1
 1
 2
 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
 124505
 3
 0
 3
 sajan_13_ACC/CBLH/PMG_discovery_cases
 Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
 487
 Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
 N/A
 N/A
 134699
 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
 251094
 6
 0
 6
 xu_08_WAGR/ASD/DD/ID_discovery_cases
 Patients with WAGR syndrome and de novo deletions in the 11p14-p12 region previously detected by FISH
 31
 All 31 patients diagnosed with WAGR syndrome; neurodevelopmental comorbidities within this cohort include intellectual disability, developmental delay, autism, ADHD, seizures, anxiety, obsessive-compulsive behaviors, and speech delay/speech disorder
 Range, 3-46 yrs.
 45.16% Male
 9600000
 2
 0
 2
 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
 231066
 0
 1
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 addis_15_ASD/DD/ID_discovery_controls
 Controls from the Wellcome Trust Case Control Consortium (WTCCC)
 4783
 Control
 N/A
 N/A
 221753
 1
 0
 1
 addis_15_ASD_replication_controls
 Controls from the Ottawa Heart Institute (n=1234), POPGEN (N=1123), the Ontario Population Genomics Platform (n=416), HapMap3 (n=1056), and the Autism Genome Poject (n=2640)
 6469
 Control
 N/A
 N/A
 0
 0
 0
 0
 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
 143
 1
 0
 1
 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
 327007
 1
 5
 6
 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
 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
 534664
 1
 1
 2
 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
 229445
 1
 1
 2
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 229445
 1
 0
 1
 kushima_18_ASD/SCZ_discovery_controls
 Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
 2095
 Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
 Median age, 37 years
 52.0% Male
 0
 0
 0
 0
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 416101
 1
 1
 2
 marshall_08_ASD_discovery_controls_1
 German PopGen project and entries from Database of Genomic Variants
 500
 Controls
 
 
 0
 0
 0
 0
 marshall_08_ASD_discovery_controls_2
 Non-disease controls from Ontario population
 1152
 Controls
 
 
 0
 0
 0
 0
 nguyen_13_DD/ID/MCA/ASD_discovery_controls
 Control data from the Database of Genomic Variants (DGV, n=12,145) and a published dataset of 8,329 individuals from Moriarty et al., 1998.
 20474
 Control
 N/A
 N/A
 N/A
 N/A
 N/A
 N/A
 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.
 
 9535
 1
 0
 1
 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
 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)
 124505
 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.
 
 255719
 3
 3
 6
 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
 231066
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 addis_15_ASD/DD/ID_discovery_cases
  United Kingdom
 aCGH
  Agilent 60K
 
 
 None
 addis_15_ASD_replication_cases
  Europe and Canada
 Array SNP, solid phase hybridization
  Illumina 1M, Affymetrix 6.0
 PennCNV, iPattern, QuantiSNP, Birdsuite, iPattern, Affymetrix Genotyping Console
 
 qPCR, another method
 baroy_13_ID/ASD_discovery_cases
  Norwegian (n=3), Norwegian/English (n=1), Lebanese (n=1)
 aCGH
  Agilent 4x44K, 2x105A, 4x180K or 244A
 
 Feature Extraction, DNA Analytics v4.0.76
 None
 brandler_18_ASD_replication_cases
  N/A
 WGS
  Illumina HiSeq X10
 ForestSV, Lumpy, Manta, Mobster, SV2
 
 None
 celestino-soper_11_ASD_discovery_cases
 
 aCGH
  Agilent 1M
 ADM-2
 Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
 None
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 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
 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_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
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 kushima_18_SCZ_discovery_cases
  Japanese
 aCGH
  NimbleGen 720K, Agilent 400K
 FASST2
 Nexus Copy Number v.9.0
 N/A
 lesca_12_EP_discovery_cases
  France
 aCGH
  Agilent SurePrint G3 Human CGH Microarray 4x180K
 ADM-2
 Agilent Feature Extraction v10.7.3.1, Agilent Genomic WORKBENCH v5.0.14
 qPCR
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 
 lintas_17_ASD_discovery_cases
  Italy
 aCGH
  Agilent Human Genome CGH SurePrint G3 4x180K
 ADM-2
 Agilent Feature Extraction v10.7, Agilent Cytogenomic Software v2.9
 Validation by visual inspection, RT-PCR, or PCR
 lionel_13_ASD/ADHD/DD/ID_discovery_cases
  N/A
 aCGH, array SNP, solid phase hybridization
  Multiple platforms (Agilent, Affymetrix, Illumina)
 
 
 None
 marshall_08_ASD_discovery_cases
  90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
 Array SNP, karotyping
  Affymetrix 500K
 dChip, CNAG, GEMCA
 
 qPCR, qmPCR
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
  N/A
 aCGH
  SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
 
 
 FISH
 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
 o'roak_12_ASD_discovery_cases
  NA
 WES
  NimbleGen EZ Exome V2.0, Illumina GAIIx or HiSeq2000
 HMM
 mrsFAST aligner
 aCGH, Sanger sequencing
 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)
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 sajan_13_ACC/CBLH/PMG_discovery_cases
  81.31% Caucasian
 Solid phase hybridization
  Illumina InfiniumII HumanHap610
 PennCNV
 
 None (not tested or failure to confirm by qPCR)
 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
 
 
 xu_08_WAGR/ASD/DD/ID_discovery_cases
  N/A
 FISH
 
 
 
 aCGH (Agilent)
 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
  addis_15_ASD/DD/ID_discovery_controls
  United Kingdom
  Array SNP
  Affymetrix 6.0
  Birdsuite, iPattern, Affymetrix Genotyping Console
 
  None
  addis_15_ASD_replication_controls
  Primarily European and Canadian
  Array SNP, solid phase hybridization
  Affymetrix 6.0, Illumina 1M
  PennCNV, iPattern, QuantiSNP, Birdsuite, iPattern, Affymetrix Genotyping Console
 
 
  brandler_18_ASD_discovery_controls
  N/A
  WGS
  Illumina HiSeq X10 or HiSeq 2500
  ForestSV, Lumpy, Manta, Mobster, SV2
 
  PCR, array SNP
  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
 
  kanduri_15_ASD_discovery_controls
  Finnish
  Solid phase hybridization
  Illumina Infinium HD Human610-Quad BeadChip
  QuantiSNP, PennCNV
  Illumina BeadStudio
  None
  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
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  kushima_18_ASD/SCZ_discovery_controls
  Japanese
  aCGH
  NimbleGen 720K, Agilent 400K
  FASST2
  Nexus Copy Number v.9.0
  N/A
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  marshall_08_ASD_discovery_controls_1
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  marshall_08_ASD_discovery_controls_2
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  nguyen_13_DD/ID/MCA/ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
  N/A
  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
 
 
  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
 
 
  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
  addis_15_ASD/DD/ID_discovery_cases-BBGRE108970
 5 yrs.
 M
 ASD, ID, epilepsy
 Speech and language disorder, reading and spelling development disorder, autism spectrum disorder, epilepsy >24 months at age of onset
 Severe cognitive delay (IQ 20-34)
 31473713
 31524729
  51017
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE112031
 12 yrs.
 F
 Developmental delay
 Developmental delay, hypotonia
 
 31595342
 31828027
  232686
 GRCh38
 Duplication
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE112601
 1 yr.
 F
 Developmental delay
 Developmental delay, speech and language disorder, microcephaly (<5th %ile), mild cognitive delay, motor skills development disorder
 
 31669722
 31701192
  31471
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE116589
 3 yrs.
 M
 Pervasive developmental disorder (PDD)
 Pervasive developmental disorder (PDD); social interaction difficulties, language disorder, behavioral problems
 
 31562782
 31620778
  57997
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE117003
 8 mos.
 M
 Developmental delay
 Developmental delay, hypotonia, ventriculomegaly
 
 31580221
 31610800
  30580
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE117374
 20 yrs.
 M
 ASD
 Autism
 Learning difficulties
 31683528
 31726083
  42556
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE119460
 2 yrs.
 M
 Autistic features
 Social communication difficulties, speech and language delay
 
 31539673
 31603901
  64229
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE129016
 3 yrs.
 F
 Developmental delay
 Developmental delay (progressing), microcephaly, poor balance
 
 31551875
 31653241
  101367
 GRCh38
 Deletion
 No
  addis_15_ASD/DD/ID_discovery_cases-BBGRE130693
 5 yrs.
 M
 DD and autistic features
 Moderate developmental delay, mainly affecting language; emerging autistic traits
 
 31739356
 31765366
  26011
 GRCh38
 Deletion
 No
  addis_15_ASD_replication_cases-case20130_6005001
 N/A
 M
 ASD
 Strict autism, no seizures, verbal, language delay, delayed first words (at 36 months), delayed first phrases (at 48 months), coordination problems
 Verbal IQ>70
 31555221
 31632021
  76801
 GRCh38
 Deletion
 Yes
  addis_15_ASD_replication_cases-case3617_3
 N/A
 M
 ASD
 Strict autism; no seizures; verbal, language delay; delayed first words (at 24 months), delayed first phrases (at 36 months)
 Verbal IQ>70
 31438959
 31633561
  194603
 GRCh38
 Deletion
 Yes
  addis_15_ASD_replication_cases-case8596_201
 N/A
 M
 ASD
 Strict autism, high functioning; no seizures, verbal, language delay; delayed first words (at 25 months); typical first phrases (at 25 months)
 Verbal IQ>71
 31467343
 31586439
  119097
 GRCh38
 Deletion
 Yes
  addis_15_ASD_replication_cases-caseMM1259-003
 N/A
 F
 ASD
 Autism, langauge delay; delayed first words (at 21 months), mild developmental delay, motor delay, no seizures
 
 31630672
 31742845
  112174
 GRCh38
 Deletion
 Yes
  addis_15_ASD_replication_cases-caseMM1259-004
 N/A
 F
 ASD
 Autism, language delay; delayed first words (at 18 months), delayed first phrases (at 36 months), expressive language problems, mild developmental delay, motor delay, no seizures
 
 31630672
 31742845
  112174
 GRCh38
 Deletion
 Yes
  addis_15_ASD_replication_cases-caseNA-0285
 N/A
 M
 ASD
 Autism, language delay, delayed first words (at 32 months), no seizures
 
 31497377
 31627928
  130552
 GRCh38
 Deletion
 Yes
  baroy_13_ID/ASD_discovery_cases-patient5
 17 yrs.
 F
 Intellectual disability
 Birth/neonatal history: pregnancy complicated by episodes of maternal bleeding, normal delivery, birth weight and length both at 75th %ile (OFC unknown). Developmental milestones: independent walking at 14 months, developed stereotypic habit ot constantly walking around; delayed language and motor development at 3 years and 3 months. Language and communication evaluation: delayed language development. Motor and musculoskeletal evaluation: mild unsteadiness when standing with eyes closed; normal muscle tone. Behavioral/psychiatric evaluation: lack of concentration and impulse control, hyperactivity, episodes of aggression and violent behavior, episdoes of stereotypic and repetitive behavior (not considered to have ASD), psychotic episode at age of 14 years. Dysmorphic features: not noted. Growth parameters: obsese with MBI of 30.6 and height of 162.5 cm (25th %ile). Family history: second of three children of non-consanguineous Norwegian parents; mother had Sjogren syndrome.
 Mild intellectual disability (IQ 50-69) [based on recent testing with WISC-IV (which gave IQ score slightly below 70), Weschler Adult Intelligence Scale-4th edition (WAIS-IV) and other tests]; testing with Bayley-II at age of 3 years 3 months gave Mental Developmental Index of 55 (corresponded to developmental age of ~2 years).
 32675878
 32769906
  94029
 GRCh38
 Deletion
 No
  brandler_18_ASD_replication_cases-caseAU4060306
 N/A
 M
 ASD
 Case from MSSNG cohort
 
 31827194
 31837058
  9865
 GRCh38
 Deletion
 No
  celestino-soper_11_ASD_discovery_cases-11076
 NA
 M
 ASD
 NA
 NA
 34071613
 34071904
  292
 GRCh38
 Deletion
 No
  celestino-soper_11_ASD_discovery_cases-11399
 NA
 M
 ASD
 NA
 NA
 35943661
 35943796
  136
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case14113_2030
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 31259982
 31328261
  68280
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case3617_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 31438959
 31633561
  194603
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case5380_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 31290043
 31411280
  121238
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case5513_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 34100510
 34297202
  196693
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case8596_201
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 31467343
 31586439
  119097
 GRCh38
 Deletion
 No
  girirajan_13a_ASD_discovery_cases-13926.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
 31271877
 31521877
  250001
 GRCh38
 Deletion
 No
  girirajan_13a_ASD_discovery_cases-13948.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
 33161878
 33471878
  310001
 GRCh38
 Duplication
 No
  girirajan_13a_ASD_discovery_cases-AU1230301
 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
 33091878
 33451878
  360001
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000020
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 33031527
 33620145
  588619
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000084
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31780836
 32088303
  307468
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000192
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31634904
 32088303
  453400
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001670
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31765618
 31792086
  26469
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001866
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31528093
 31807593
  279501
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002357
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31500417
 31539732
  39316
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003976
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31096480
 31726083
  629604
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005143
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 31788949
 31800869
  11921
 GRCh38
 Deletion
 Yes
  krumm_13_ASD_discovery_cases-case12810.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 12810. SRS score of 90.
 Full-scale IQ (FSIQ) score of 63.
 32675564
 32760243
  84680
 GRCh38
 Deletion
 Yes
  krumm_13_ASD_discovery_cases-case13296.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 13296. SRS score of 87.
 Full-scale IQ (FSIQ) score of 30.
 32587011
 32602399
  15389
 GRCh38
 Duplication
 No (not tested)
  krumm_13_ASD_discovery_cases-case13926.p1
 N/A
 F
 ASD
 ASD proband from SSC quad family 13926. SRS score of 79.
 Full-scale IQ (FSIQ) score of 62.
 31290646
 31520091
  229446
 GRCh38
 Deletion
 No (not tested)
  krumm_15_ASD_discovery_cases-case12430.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 31263062
 31370859
  107798
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case12810.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 32675564
 32760243
  84680
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case13926.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 31290646
 31520091
  229446
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case13948.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 33161298
 33353568
  192271
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case14134.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 31263062
 31328280
  65219
 GRCh38
 Deletion
 Yes
  kushima_18_SCZ_discovery_cases-caseSCZ1484
 36 yrs.
 F
 Schizophrenia
 No additional clinical information reported for this individual. Family history: unknown.
 
 31405793
 31548667
  142875
 GRCh38
 Deletion
 N/A
  lesca_12_EP_discovery_cases-caseDV42
 NA
 F
 Epilepsy
 Phenotype: s-CSWSS . Seizure Characteristics: Nocturnal. Autistic features: No. ADHD features: No. Other features: Atrophy of the left hemisphere with PMG.
 Initial cognitive development: Normal. Cognitive regression: Yes. Verbal IQ 53, performance IQ 55 (at 7 years of age).
 33227822
 33328161
  100340
 GRCh38
 Duplication
 Yes
  lesca_12_EP_discovery_cases-caseED15
 NA
 F
 Epilepsy
 Phenotype: LKS-woESES. Seizure Characteristics: CPS. Autistic features: No. ADHD features: Yes. Other features: None.
 Initial cognitive development: Delayed. Cognitive regression: No.
 33158415
 33317791
  159377
 GRCh38
 Duplication
 Yes
  levy_11_ASD_discovery_cases-11062.p1
 NA
 M
 ASD
 NA
 NA
 33078709
 33494809
  416101
 GRCh38
 Duplication
 No
  levy_11_ASD_discovery_cases-12430.p1
 NA
 F
 ASD
 NA
 NA
 31153170
 31411095
  257926
 GRCh38
 Deletion
 No
  lintas_17_ASD_discovery_cases-case8.1
 N/A
 N/A
 Asperger syndrome
 No additional clinical information available
 
 33011106
 33467216
  456111
 GRCh38
 Duplication
 Yes
  lionel_13_ASD/ADHD/DD/ID_discovery_cases-case21
 N/A
 M
 ADHD, anxiety disorder, and OCD
 Hyperactivity/ADHD, mild OCD, mild anxiety disorder, sleep disturbance, mild tics, mild oppositional behavior. Deletion present in unaffected brother, paternal DNA not available, but deletion is likely paternal (no neuropsychiatric phenotype except for possible attention deficits in childhood).
 
 35631638
 35718554
  86917
 GRCh38
 Duplication
 No
  marshall_08_ASD_discovery_cases-SK0322-003
 NA
 M
 ASD
 NA
 NA
 33181068
 33483948
  302881
 GRCh38
 Duplication
 Yes
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC37523
 N/A
 F
 Intellectual disability
 Database: Signature. Indication for study: Dysmorphic Features, intellectual disability, karyotype: der(13)t(13;16) w/~3Mb 6q gain
 Intellectual disability
 36093937
 38414064
  2320128
 GRCh38
 Duplication
 Yes
  nord_11_ASD_discovery_cases-275-1
 
 
 ASD
 
 
 32760620
 32807533
  46914
 Unknown
 Duplication
 No
  o'roak_12_ASD_discovery_cases-case12430.p1
 NA
 F
 ASD/Autism
 Case also identified with de novo WNT5A and ITGA2 synonymous mutations. No additional clinical info available.
 High IQ. Non verbal IQ, 110
 31155561
 31406655
  251095
 GRCh38
 Deletion
 Yes
  pinto_10_ASD_discovery_cases-case5380_3
 NA
 M
 ASD
 NA
 NA
 31290043
 31411280
  121238
 GRCh38
 Deletion
 Yes
  poultney_13_ASD_discovery_cases-case00HI1779A
 N/A
 M
 ASD
 ASD case from AGRE (AGRE ID AU0780302; NDAR ID NDAR_INVXV234GU8)
 
 31064469
 31106960
  42492
 GRCh38
 Deletion
 No
  poultney_13_ASD_discovery_cases-case99HI0765
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU054805; NDAR ID NDAR_INVHV388WC3)
 
 34642629
 34658933
  16305
 GRCh38
 Duplication
 No
  prasad_12_ASD_discovery_cases-case117388L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 36246408
 36275250
  28843
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case59983
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 32602414
 32620289
  17876
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case95643
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 31268702
 31393206
  124505
 Unknown
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-case1577-0
 N/A
 N/A
 ACC
 Diagnosis of agenesis of the corpus callosum (ACC). ASD: unknown. Seizures: unknown.
 Developmental delay: yes. Intellectual disability: yes.
 33189644
 33324342
  134699
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11439.p1
 6.8
 M
 Autism
 NA
 Full-scale IQ, 98; non-verbal IQ, 94; verbal IQ, 108
 34437314
 34439222
  1909
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11564.p1
 10.8
 M
 Autism
 NA
 Full-scale IQ, 94; non-verbal IQ, 89; verbal IQ, 106
 34146606
 34166227
  19622
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11998.p1
 5.2
 M
 Autism
 NA
 Full-scale IQ, 107; non-verbal IQ, 103; verbal IQ, 111
 36327846
 36337763
  9918
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12279.p1
 4.1
 M
 Autism
 NA
 Full-scale IQ, 61; non-verbal IQ, 64; verbal IQ, 58
 33761146
 33775862
  14717
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12430.p1
 9.8
 F
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 110; verbal IQ, 106
 31155561
 31406655
  251095
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12810.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 63; non-verbal IQ, 58; verbal IQ, 77
 32678441
 32794034
  115594
 GRCh38
 Deletion
 No
  xu_08_WAGR/ASD/DD/ID_discovery_cases-caseF11a
 11 yrs.
 F
 WAGR syndrome
 Speech delay
 
 31234110
 33881898
  2647789
 GRCh38
 Deletion
 Yes
  xu_08_WAGR/ASD/DD/ID_discovery_cases-caseF22a
 14 yrs.
 M
 WAGR syndrome and DD
 Developmental delay, repetitive behavior, speech disorder
 
 31306291
 36229568
  4923278
 GRCh38
 Deletion
 Yes
  yin_16_ASD_discovery_cases-case408
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 36041419
 36272484
  231066
 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
  addis_15_ASD/DD/ID_discovery_controls-control1
  N/A
  N/A
  Control
  Control from WTCCC
 
  31296288
  31518040
  221753
  GRCh38
  Deletion
  No
  brandler_18_ASD_discovery_controls-controlSSC09260
  N/A
  M
  Control
  Control from SSC cohort
 
  35155569
  35155712
  144
  GRCh38
  Deletion
  Yes
  engchuan_15_ASD_discovery_controls-controlB410426_1007840271
  N/A
  N/A
  Control
  No previous psychiatric history
 
  33085070
  33412077
  327008
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB477091_1007853905
  N/A
  N/A
  Control
  No previous psychiatric history
 
  32969134
  33031561
  62428
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB951788_1007843996
  N/A
  N/A
  Control
  No previous psychiatric history
 
  33361539
  33501067
  139529
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900085_900085
  N/A
  N/A
  Control
  No previous psychiatric history
 
  34515769
  34568721
  52953
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900398_900398
  N/A
  N/A
  Control
  No previous psychiatric history
 
  34621121
  34759389
  138269
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902657_902657
  N/A
  N/A
  Control
  No previous psychiatric history
 
  33111318
  33417589
  306272
  GRCh38
  Duplication
  No
  kanduri_15_ASD_discovery_controls-control_split2059
  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
 
  32775602
  33310265
  534664
  Unknown
  Duplication
  No
  kanduri_15_ASD_discovery_controls-control_split242
  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
 
  32720150
  32782993
  62844
  Unknown
  Deletion
  No
  krumm_13_ASD_discovery_controls-control12445.s1
  N/A
  M
  Control
  Unaffected sibling from SSC quad family 12445. SRS score of 34.
 
  32966299
  33092340
  126042
  GRCh38
  Duplication
  No (not tested)
  krumm_13_ASD_discovery_controls-control13926.s1
  N/A
  F
  Control
  Unaffected sibling from SSC quad family 13926. SRS score of 41.
 
  31290646
  31520091
  229446
  GRCh38
  Deletion
  No (not tested)
  krumm_15_ASD_discovery_controls-control13926.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  31290646
  31520091
  229446
  GRCh38
  Deletion
  Yes
  levy_11_ASD_discovery_controls-11062.s1
  NA
  F
  Control
  NA
  NA
  33078709
  33494809
  416101
  GRCh38
  Duplication
  No
  levy_11_ASD_discovery_controls-12430.s1
  NA
  M
  Control
  NA
  NA
  31153170
  31411095
  257926
  GRCh38
  Deletion
  No
  nord_11_ASD_discovery_controls-04C27853
 
 
  Control
 
 
  33779529
  33789063
  9535
  Unknown
  Deletion
 
  sanders_11_ASD_discovery_controls-11339.s1
  11.2
  M
  Control (matched sibling)
  NA
  NA
  35223027
  35235769
  12743
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11542.s1
  14.6
  F
  Control (matched sibling)
  NA
  NA
  31112219
  31127396
  15178
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11557.s1
  6.8
  M
  Control (matched sibling)
  NA
  NA
  35228123
  35239827
  11705
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12430.s1
  8.3
  M
  Control (matched sibling)
  NA
  NA
  31155561
  31411280
  255720
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12445.s1
  6.6
  M
  Control (matched sibling)
  NA
  NA
  32969134
  33094508
  125375
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12741.s1
  5.9
  M
  Control (matched sibling)
  NA
  NA
  36331921
  36337763
  5843
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 addis_15_ASD/DD/ID_discovery_cases-BBGRE108970
 
 
 Paternal
 Unknown
 Unknown
 ELP4,IMMP1L
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE112031
 
 
 Unknown
 Unknown
 Unknown
 PAX6,ELP4,PAUPAR
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE112601
 
 
 Paternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE116589
 
 
 Maternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE117003
 
 
 Maternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE117374
 
 
 Maternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE119460
 
 
 Maternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE129016
 
 
 Unknown
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD/DD/ID_discovery_cases-BBGRE130693
 
 
 De novo
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD_replication_cases-case20130_6005001
 qPCR or another method
 
 Maternal
 Unknown
 Unknown
 ELP4
 
 addis_15_ASD_replication_cases-case3617_3
 qPCR or another method
 
 Paternal
 Unknown
 Unknown
 ELP4,IMMP1L
 
 addis_15_ASD_replication_cases-case8596_201
 qPCR or another method
 
 Maternal
 Unknown
 Unknown
 ELP4,IMMP1L
 
 addis_15_ASD_replication_cases-caseMM1259-003
 qPCR or another method
 
 Unknown
 Multiplex
 Possibly segregated
 ELP4
 
 addis_15_ASD_replication_cases-caseMM1259-004
 qPCR or another method
 
 Unknown
 Multiplex
 Possibly segregated
 ELP4
 
 addis_15_ASD_replication_cases-caseNA-0285
 qPCR or another method
 
 Maternal
 Unknown
 Unknown
 ELP4,IMMP1L
 
 baroy_13_ID/ASD_discovery_cases-patient5
 
 
 Unknown
 Likely simplex
 Unknown
 CCDC73
 
 brandler_18_ASD_replication_cases-caseAU4060306
 No validation step reported
 
 Paternal
 
 
 PAUPAR
 
 celestino-soper_11_ASD_discovery_cases-11076
 
 
 Unknown
 Simplex
 NA
 CAPRIN1
 
 celestino-soper_11_ASD_discovery_cases-11399
 
 
 Unknown
 Simplex
 NA
 
 
 engchuan_15_ASD_discovery_cases-case14113_2030
 
 
 Unknown
 
 
 CYCSP25,DCDC1
 
 engchuan_15_ASD_discovery_cases-case3617_3
 
 
 Unknown
 
 
 ELP4,IMMP1L
 
 engchuan_15_ASD_discovery_cases-case5380_3
 
 
 Unknown
 
 
 DNAJC24,DCDC1
 
 engchuan_15_ASD_discovery_cases-case5513_3
 
 
 Unknown
 
 
 NAT10,CAPRIN1,ABTB2
 
 engchuan_15_ASD_discovery_cases-case8596_201
 
 
 Unknown
 
 
 ELP4,IMMP1L
 
 girirajan_13a_ASD_discovery_cases-13926.p1
 
 
 Unknown
 Simplex
 Unknown
 CYCSP25,DNAJC24,DCDC1,ELP4,IMMP1L
 
 girirajan_13a_ASD_discovery_cases-13948.p1
 
 
 Unknown
 Simplex
 Unknown
 RPL29P23,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
 girirajan_13a_ASD_discovery_cases-AU1230301
 
 
 Unknown
 Multiplex
 Unknown
 RPL29P23,TCP11L1,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000020
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 PIGCP1,RPL29P23,TCP11L1,LINC00294,CSTF3-DT,DEPDC7,CSTF3,HIPK3,KIAA1549L
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000084
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 EIF4A2P5,PAX6,ELP4,PAUPAR
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000192
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 EIF4A2P5,PAX6,ELP4,PAUPAR
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001670
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 PAX6,ELP4
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001866
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 PAX6,ELP4
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002357
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ELP4,IMMP1L
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003976
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 CYCSP25,DNAJC24,DCDC1,ELP4,IMMP1L
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005143
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 PAX6,ELP4
 
 krumm_13_ASD_discovery_cases-case12810.p1
 Solid phase hybridization (Illumina 1M) and aCGH (Agilent SurePrint G3 4x180K)
 
 Maternal
 Simplex
 Segregated
 CCDC73
 
 krumm_13_ASD_discovery_cases-case13296.p1
 
 
 Maternal
 Simplex
 Segregated
 HNRNPA3P9,EIF3M,CCDC73
 
 krumm_13_ASD_discovery_cases-case13926.p1
 
 
 Maternal
 Simplex
 Not segregated
 DNAJC24,DCDC1,ELP4,IMMP1L
 
 krumm_15_ASD_discovery_cases-case12430.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Segregated
 CYCSP25,DNAJC24,DCDC1
 
 krumm_15_ASD_discovery_cases-case12810.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Segregated
 CCDC73
 
 krumm_15_ASD_discovery_cases-case13926.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 DNAJC24,DCDC1,ELP4,IMMP1L
 
 krumm_15_ASD_discovery_cases-case13948.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Segregated
 RPL29P23,CSTF3-DT,CSTF3,HIPK3
 
 krumm_15_ASD_discovery_cases-case14134.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Segregated
 CYCSP25,DCDC1
 
 kushima_18_SCZ_discovery_cases-caseSCZ1484
 While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
 
 Unknown
 Unknown
 Unknown
 DNAJC24,ELP4,IMMP1L
 
 lesca_12_EP_discovery_cases-caseDV42
 qPCR
 
 Maternal
 Unknown
 Unknown
 HIPK3
 
 lesca_12_EP_discovery_cases-caseED15
 qPCR
 
 Paternal
 Unknown
 Unknown
 RPL29P23,CSTF3-DT,CSTF3,HIPK3
 
 levy_11_ASD_discovery_cases-11062.p1
 
 
 Maternal
 Simplex
 Not segregated
 RPL29P23,TCP11L1,LINC00294,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
 levy_11_ASD_discovery_cases-12430.p1
 
 
 Maternal
 Simplex
 Not segregated
 CYCSP25,DNAJC24,DCDC1
 
 lintas_17_ASD_discovery_cases-case8.1
 Validation by visual inspection, RT-PCR, or PCR
 
 De novo
 Multiplex
 Not segregated (CNV only observed in 1/2 affected siblings)
 PIGCP1,RPL29P23,TCP11L1,LINC00294,CSTF3-DT,DEPDC7,CSTF3,HIPK3,KIAA1549L
 
 lionel_13_ASD/ADHD/DD/ID_discovery_cases-case21
 
 
 Unknown
 Simplex
 Unknown
 TRIM44
 
 marshall_08_ASD_discovery_cases-SK0322-003
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 RPL29P23,CSTF3-DT,HIPK3,KIAA1549L
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC37523
 FISH
 
 Unknown
 Unknown
 Unknown
 RPL7AP56,LRRC6P1,COMMD9,TRAF6,RAG2,C11orf74,LDLRAD3,PRR5L,RAG1
 
 nord_11_ASD_discovery_cases-275-1
 
 
 Paternal
 
 
 CCDC73
 
 o'roak_12_ASD_discovery_cases-case12430.p1
 aCGH, Sanger sequencing
 
 Maternal
 Simplex (quad)
 Unknown
 CYCSP25,DNAJC24,DCDC1
 
 pinto_10_ASD_discovery_cases-case5380_3
 Agilent1M
 
 maternal
 NA
 NA
 DNAJC24,DCDC1
 
 poultney_13_ASD_discovery_cases-case00HI1779A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 DCDC1
 
 poultney_13_ASD_discovery_cases-case99HI0765
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 EHF
 
 prasad_12_ASD_discovery_cases-case117388L
 
 
 Unknown
 Unknown
 Unknown
 PRR5L,COMMD9
 
 prasad_12_ASD_discovery_cases-case59983
 
 
 Unknown
 Unknown
 Unknown
 CCDC73
 
 prasad_12_ASD_discovery_cases-case95643
 
 
 Unknown
 Unknown
 Unknown
 DNAJC24,DCDC1
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-case1577-0
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 RPL29P23,CSTF3-DT,HIPK3
 
 sanders_11_ASD_discovery_cases-11439.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 CAT
 
 sanders_11_ASD_discovery_cases-11564.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 NAT10,ABTB2
 
 sanders_11_ASD_discovery_cases-11998.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 PRR5L
 
 sanders_11_ASD_discovery_cases-12279.p1
 
 
 Paternal
 Simplex (quad-proband unmatched)
 Unknown
 FBXO3-DT,FBXO3
 
 sanders_11_ASD_discovery_cases-12430.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 CYCSP25,DNAJC24,DCDC1
 
 sanders_11_ASD_discovery_cases-12810.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 CCDC73
 
 xu_08_WAGR/ASD/DD/ID_discovery_cases-caseF11a
 aCGH (Agilent)
 
 De novo
 
 Likely segregated
 CYCSP25,EIF4A2P5,HNRNPA3P9,PIGCP1,RPL29P23,C11orf91,FBXO3-DT,DNAJC24,PAX6,RCN1,WT1,WT1-AS,EIF3M,PRRG4,TCP11L1,LINC00294,CSTF3-DT,CD59,FBXO3,LMO2,DCDC1,ELP4,PAUPAR,THEM7P,CCDC73,QSER1,DEPDC7,CSTF3,HIPK3,IMMP1L,KIAA1549L
 
 xu_08_WAGR/ASD/DD/ID_discovery_cases-caseF22a
 aCGH (Agilent)
 
 De novo
 
 Likely segregated
 EIF4A2P5,HNRNPA3P9,PIGCP1,RPL29P23,C11orf91,FBXO3-DT,CIR1P3,MIR1343,CD44-AS1,KRT18P14,RPL12P31,MIR3973,DNAJC24,PAX6,RCN1,WT1,WT1-AS,EIF3M,PRRG4,TCP11L1,LINC00294,CSTF3-DT,CD59,FBXO3,LMO2,NAT10,ELF5,EHF,CD44,FJX1,DCDC1,ELP4,PAUPAR,THEM7P,CCDC73,QSER1,DEPDC7,CSTF3,HIPK3,CAPRIN1,ABTB2,CAT,APIP,PDHX,SLC1A2,PAMR1,TRIM44,LDLRAD3,IMMP1L,KIAA1549L
 
 yin_16_ASD_discovery_cases-case408
 
 
 Unknown
 Unknown
 Unknown
 COMMD9,LDLRAD3
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
addis_15_ASD/DD/ID_discovery_controls-control1
 
 
  Unknown
  Unknown
  Unknown
  DNAJC24,DCDC1,ELP4,IMMP1L
 
brandler_18_ASD_discovery_controls-controlSSC09260
  PCR
 
  De novo
 
 
  CD44
 
engchuan_15_ASD_discovery_controls-controlB410426_1007840271
 
 
  Unknown
 
 
  RPL29P23,TCP11L1,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
engchuan_15_ASD_discovery_controls-controlB477091_1007853905
 
 
  Unknown
 
 
  QSER1,DEPDC7
 
engchuan_15_ASD_discovery_controls-controlB951788_1007843996
 
 
  Unknown
 
 
  KIAA1549L
 
engchuan_15_ASD_discovery_controls-controlHABC_900085_900085
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_900398_900398
 
 
  Unknown
 
 
  EHF
 
engchuan_15_ASD_discovery_controls-controlHABC_902657_902657
 
 
  Unknown
 
 
  RPL29P23,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
kanduri_15_ASD_discovery_controls-control_split2059
 
 
  Unknown
 
 
  CCDC73,CSTF3,DEPDC7,HIPK3,PRRG4,QSER1,TCP11L1
 
kanduri_15_ASD_discovery_controls-control_split242
 
 
  Unknown
 
 
  CCDC73
 
krumm_13_ASD_discovery_controls-control12445.s1
 
 
  Paternal
  Simplex
 
  PIGCP1,TCP11L1,LINC00294,QSER1,DEPDC7,CSTF3
 
krumm_13_ASD_discovery_controls-control13926.s1
 
 
  Maternal
  Simplex
 
  DNAJC24,DCDC1,ELP4,IMMP1L
 
krumm_15_ASD_discovery_controls-control13926.s1
  Omni2.5-4v1
 
  Maternal
 
 
  DNAJC24,DCDC1,ELP4,IMMP1L
 
levy_11_ASD_discovery_controls-11062.s1
 
 
  Maternal
  Simplex
  NA
  RPL29P23,TCP11L1,LINC00294,CSTF3-DT,CSTF3,HIPK3,KIAA1549L
 
levy_11_ASD_discovery_controls-12430.s1
 
 
  Maternal
  Simplex
  NA
  CYCSP25,DNAJC24,DCDC1
 
nord_11_ASD_discovery_controls-04C27853
 
 
 
 
 
  0 genes
 
sanders_11_ASD_discovery_controls-11339.s1
 
 
  Paternal
  Simplex (quad)
  NA
  CD44
 
sanders_11_ASD_discovery_controls-11542.s1
 
 
  Maternal
  Simplex (quad)
  NA
  DCDC1
 
sanders_11_ASD_discovery_controls-11557.s1
 
 
  Maternal
  Simplex (quad)
  NA
  CD44
 
sanders_11_ASD_discovery_controls-12430.s1
 
 
  Maternal
  Simplex (quad)
  NA
  CYCSP25,DNAJC24,DCDC1
 
sanders_11_ASD_discovery_controls-12445.s1
 
 
  Paternal
  Simplex (quad)
  NA
  PIGCP1,TCP11L1,LINC00294,QSER1,DEPDC7,CSTF3
 
sanders_11_ASD_discovery_controls-12741.s1
 
 
  Unknown
  Simplex (quad)
  NA
  PRR5L
 

No Animal Model Data Available
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