4p16.1CNV Type: Deletion-Duplication
Largest CNV size: 160670 bp
Statistics Box:
Number of Reports: 26
Number of Reports: 26
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Duplication
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.
Duplication
High-resolution SNP genotyping platform identified recurrent and novel CNVs in autism multiplex families.
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Identifying autism loci and genes by tracing recent shared ancestry.
Deletion
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures.
Deletion-Duplication
Global increases in both common and rare copy number load associated with autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion
Large-scale discovery of novel genetic causes of developmental disorders.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
The landscape of copy number variations in Finnish families with autism spectrum disorders.
Deletion-Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Deletion-Duplication
Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
alayadhi_16_ASD_discovery_cases
ASD cases from 11 multiplex families referred to Autism Research and Treatment Center (ART) and Madinah Maternity and Children Hospital (MMCH)
22
All ASD cases met crtieria for autism on one or both diagnostic measures (ADI-R and ADOS), autism severity assessed using CARS-2
N/A
100% Male
114321
0
4
4
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
6275
2
0
2
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
6807
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
45709
0
1
1
costa_21_ASD_discovery_cases
ASD probands referred to the Centro de Estudos sobre o Genoma Humano e Celulas-tronco (CEGH-CEL, Instituto de Biociencias (IB), Universidade de Sao Paulo, USP) between 2009 and 2018.
144
Cases diagnosed with ASD by psychiatrists or neurologists based on the Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV or DSM-5.
Range, 1-34 yrs. (mean, 7.7 yrs.)
77.08% Male
2579287
0
1
1
digregorio_17_DD/ID_discovery_cases
Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
1015
Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
N/A
N/A
2100000
0
2
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
350644
3
4
7
fitzgerald_14_ASD/DD/ID_discovery_cases
Children recruited through all 24 regional genetics services of the UK National Health Service and Republic of Ireland as part of the Deciphering Developmental Disorders Study
1133
Cases affected by severe, undiagnosed developmental disorders; most common phenotypes include developmental delay, intellectual disability, specific learning disability, autism, seizures, microcephaly, and dysmorphic features.
Median age, 5.5 years
N/A
388649
0
2
2
gai_11_ASD_discovery_cases
Discovery case samples derived from AGRE set 4 (most recent patient recruitment)
631
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
88956
1
0
1
gai_11_ASD_replication_cases
Replication case samples derived from AGRE sets 1-3
593
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
117547
3
0
3
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
542000
0
1
1
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
130760
0
2
2
itsara_10_ASD_discovery_cases
ASD probands from multiplex (n=1270) and simplex (n=60) families from AGRE collection
1330
ASD: Autism, broad spectrum autism (Spectrum), or NQA (not quite autism)
31130
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
4742682
2
2
4
kanduri_15_ASD_discovery_cases
Autistic cases from an initial sample of 83 Finnish families comprising 257 family members following quality control
80
Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patients screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and Asperger's Syndrome Diagnostic Interview.
N/A
N/A
80489
1
1
2
krumm_13_ASD_discovery_cases
Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
81.265% Male
18106
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
18106
1
0
1
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
51392
0
1
1
lionel_13_ASD/SCZ/EP_discovery_cases
Patient cohort composed of 1158 Canadian ASD patients, 72 Austrian ASD patients, 450 Canadian schizophrenia patients, and a clinical dataset of 3704 individuals with primary diagnosis of ASD and/or seizure disorder referred for clinical microarray testing at the Mayo Clinic cytogenetics laboratory.
5384
ASD (n=1230), schizophrenia (n=450), and ASD and/or seizure disorder (n=3704). Canadian and Austrian ASD patients met criteria for ASD diagnosis based on ADI-R and/or ADOS.
NA
NA
21113
1
1
2
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
293000
0
3
3
morrow_08_ASD_discovery_cases
Affected individuals from 70 families (52 simplex, 18 multiplex) recruited by Homozygosity Mapping Collaborative for Autism (HMCA) used in CNV analysis. This cohort was selected from an original population of affected individuals from 104 families (79 simplex, 25 multiplex; 82.7% male); 88 of these pedigrees have cousin marriages.
94
ASD (based on DSM-IV-TR diagnoses when research scales not available in native language)
24900
2
0
2
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
42022
0
1
1
poultney_13_ASD_discovery_cases
ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
299
Cases diagnosed with ASD
N/A
79.86% Male (before filtering)
752307
0
1
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
39134
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
92511
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
160670
10
2
12
yap_21_ASD_discovery_cases
ASD probands from the Australian Autism Biobank (AAB) screened for copy number variation after quality control (QC)
723
Cases diagnosed with ASD; additional clinical assessments were adminstered and questionnaries completed, including ADOS-2, ADOS-G, and VABS-II, while cognitive functioning and IQ was assessed using MSEL or WISC-IV.
Range, 2-17 yrs.
NA
1310175
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
243210
1
9
10
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
6275
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
864154
2
5
7
girirajan_11_ASD_discovery_controls
Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
337
Control. Individuals screened specifically for eight mental health disorders.
1285301
0
1
1
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
369410
1
2
3
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
114185
0
1
1
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
18106
1
0
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
111638
1
1
2
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
51392
0
1
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)
39134
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.
37999
4
1
5
stamouli_18_ASD/NDD_discovery_controls
Unaffected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
100 twin pairs
Control (unaffected) individual following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities and
N/A
N/A
187063
1
1
2
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
243210
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
alayadhi_16_ASD_discovery_cases
Saudi
Solid phase hybridization
Illumina HumanOmni 2.5M
CNVPartition v.3.2.0, Penn CNV
Illumina GenomeStudio (Genotyping module v1.9.4, Genome Viewer v.1.9.0)
qPCR
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
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
aCGH (Agilent 4x180K or 8x60K)
costa_21_ASD_discovery_cases
Brazil
aCGH
Agilent 180K
NA
Agilent Genomic Workbench
None
digregorio_17_DD/ID_discovery_cases
Italian
aCGH
Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
ADM-2
Agilent CGH Analytics software ver. 4.0.81
qPCR
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
fitzgerald_14_ASD/DD/ID_discovery_cases
UK and Ireland
aCGH, WES
Agilent 2x1M, Agilent Exome+
Cnsolidate, CoNVex
None
gai_11_ASD_discovery_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
None
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
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
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
itsara_10_ASD_discovery_cases
Solid phase hybridization
Illumina HumanHap550v1 and v3 SNP array
HMM
Illumina GenomeStudio
aCGH (custom NimbleGen 12 X 135)
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
kanduri_15_ASD_discovery_cases
Finnish
Solid phase hybridization
Illumina Human OmniExpress-12v1.0 BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
None
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)
levy_11_ASD_discovery_cases
aCGH
NimbleGen HD2
HMM
lionel_13_ASD/SCZ/EP_discovery_cases
NA
aCGH, array SNP
Agilent ISCA 44K, Agilent 180K, Affymetrix 6.0
Agilent DNA Analytics, Birdsuite, iPattern, Affymetrix Genotyping Console
None
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
morrow_08_ASD_discovery_cases
Arabic Middle East, Turkey, and Pakistan
Array SNP
Affymetrix 500K
BRLMM
dChip
o'roak_12_ASD_discovery_cases
NA
WES
NimbleGen EZ Exome V2.0, Illumina GAIIx or HiSeq2000
HMM
mrsFAST aligner
aCGH, Sanger sequencing
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
yap_21_ASD_discovery_cases
Predominantly European with additional individuals of South Asian, East Asian, African, and other ancestries
Solid phase hybridization
Illumina Global Screening Array v1 and v2
PennCNV, iPattern
GenomeStudio v.2.0.4
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
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
girirajan_11_ASD_discovery_controls
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
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
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
Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
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
stamouli_18_ASD/NDD_discovery_controls
Swedish
Solid phase hybridization
Illumina Infinium PsychArray-24 v1.1
PennCNV, QuantiSNP, iPattern, iPsychCNV
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
alayadhi_16_ASD_discovery_cases-caseAUT4-1
N/A
M
Autism
CARS score of 36.5; Social Responsiveness Scale (SRS) score of 79; Sensory profile score of 123.
9369254
9483653
114400
GRCh38
Duplication
Yes
alayadhi_16_ASD_discovery_cases-caseAUT4-2
N/A
M
Autism
CARS score of 33.5; Social Responsiveness Scale (SRS) score of 80; Sensory profile score of 154.
9369254
9483653
114400
GRCh38
Duplication
Yes
alayadhi_16_ASD_discovery_cases-caseAUT6-1
N/A
M
Autism
CARS score of 34.5; Social Responsiveness Scale (SRS) score N/A; Sensory profile score of 157.
9369254
9483653
114400
GRCh38
Duplication
Yes
alayadhi_16_ASD_discovery_cases-caseAUT6-2
N/A
M
Autism
CARS score of 34.5; Social Responsiveness Scale (SRS) score N/A; Sensory profile score of 125.
9369254
9483653
114400
GRCh38
Duplication
Yes
brandler_18_ASD_discovery_cases-caseSSC08732
N/A
M
ASD
Case from SSC_phase1 cohort
8055724
8061998
6275
GRCh38
Deletion
Yes
brandler_18_ASD_discovery_cases-caseSSC09546
N/A
M
ASD
Case from SSC cohort
8201395
8202797
1403
GRCh38
Deletion
Yes
brandler_18_ASD_replication_cases-caseSSC03573
N/A
M
ASD
Case from SSC_phase2 cohort
6784665
6791471
6807
GRCh38
Deletion
No
celestino-soper_11_ASD_discovery_cases-11533
NA
M
ASD
NA
NA
9323365
9369074
45710
GRCh38
Duplication
Yes
costa_21_ASD_discovery_cases-caseP68
NA
M
ASD, developmental delay, and intellectual disability
Case diagnosed with ASD based on DSM-IV or DSM-5 criteria. Additional clinical features: cardiac alterations, absent speech, intellectual disability, facial dysmorphisms, hypotonia.
Intellectual disability
7320201
9899487
2579287
GRCh38
Duplication
No
digregorio_17_DD/ID_discovery_cases-DECIPHER_299797
N/A
F
Intellectual disability
Father is affected with a similar or milder phenotype.
Intellectual disability
9765062
10120385
355324
GRCh38
Duplication
Yes
digregorio_17_DD/ID_discovery_cases-DECIPHER_300097
N/A
M
Cognitive impairment
Cognitive impairment
8279332
10415824
2136493
GRCh38
Duplication
Yes
engchuan_15_ASD_discovery_cases-case14134_2320
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
5592474
5627571
35098
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case14403_5120
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
7307932
7360327
52396
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case16090_1571122001
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
7727977
7800959
72983
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case3268_4
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
8782230
9097760
315530
NCBI36
Deletion
No
engchuan_15_ASD_discovery_cases-case3489_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
8356196
8417478
61283
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4230_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
9541140
9891779
350640
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4428_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
8677895
8979912
302017
NCBI36
Duplication
No
fitzgerald_14_ASD/DD/ID_discovery_cases-case000033
N/A
N/A
N/A
Clinical profile N/A; CNV from Supplementary Table S39
N/A
9869037
10257686
388650
GRCh38
Duplication
No
fitzgerald_14_ASD/DD/ID_discovery_cases-case000034
N/A
N/A
N/A
Clinical profile N/A; CNV from Supplementary Table S40
N/A
10429742
10712070
282329
GRCh38
Duplication
No
gai_11_ASD_discovery_cases-AU1521302
Autism
8573121
8662076
88956
Unknown
Deletion
No
gai_11_ASD_replication_cases-AU017504
Autism
10678363
10753898
75536
Unknown
Deletion
No
gai_11_ASD_replication_cases-AU068903
Autism
8980214
9097760
117547
Unknown
Deletion
No
gai_11_ASD_replication_cases-AU0745301
Autism
8980214
9097760
117547
Unknown
Deletion
No
girirajan_13a_ASD_discovery_cases-13603.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
9919278
10459278
540001
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_cases-25807108397
N/A
N/A
Autism
Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Asian
N/A
7495067
7565126
70060
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_cases-709110652
N/A
N/A
Autism
Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Hispanic
N/A
8120730
8251490
130761
GRCh38
Duplication
No
itsara_10_ASD_discovery_cases-HI1977
NA
NA
Autism
NA
NA
8200484
8231614
31131
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002303
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
9381969
10163409
781441
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004241
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
9946394
10449826
503433
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004790
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
5455628
10640216
5184589
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005118
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
9946194
10938417
992224
GRCh38
Duplication
Yes
kanduri_15_ASD_discovery_cases-case3051
N/A
N/A
ASD
Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patient screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and/or Asperger's Syndrome Diagnostic Interview.
9404812
9485300
80489
Unknown
Duplication
No
kanduri_15_ASD_discovery_cases-case3070
N/A
N/A
ASD
Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patient screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and/or Asperger's Syndrome Diagnostic Interview.
9371116
9446843
75728
Unknown
Deletion
No
krumm_13_ASD_discovery_cases-case12161.p1
N/A
F
ASD
ASD proband from SSC quad family 12161. SRS score of 55.
Full-scale IQ (FSIQ) score of 106.
6593172
6611278
18107
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case12161.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
6593172
6611278
18107
GRCh38
Deletion
Yes
levy_11_ASD_discovery_cases-11224.p1
NA
M
ASD
NA
NA
5721152
5772543
51392
GRCh38
Duplication
No
lionel_13_ASD/SCZ/EP_discovery_cases-proband1
13 yrs.
F
ASD
Diagnosis of high-functioning ASD made following assessment at 13 years of age using ADOS and ADI-R. Birth/neonatal history: uncomplicated pregnancy; delivery at 38 weeks of gestation. Developmental milestones: walking at 12 months, otherwise had slow motor development and gait issues, which prompted ergotherapy; language delay with no speech at 2 yrs., followed by gradual speech development by 4 yrs. Language and communication evaluation: episodes of echolalia. Behavioral/psychiatric evaluation: up to 6 years of age, case continued to desire swaddling and had hypersensitivty to light and sound associated with self-injury (head banging, tearing hair). Dysmorphic features: none reported. Family history: non-consanguineous parents; no reported medical or neuropsychiatric conditions in parents or two older siblings.
Completed secondary school degree with exception of mathematics
10212536
10233644
21109
GRCh38
Deletion
No
lionel_13_ASD/SCZ/EP_discovery_cases-proband5
24 yrs.
M
Schizophrenia
Diagnosis of chronic schizophrenia confirmed through use of detailed psychiatric assessment, including use of a modified version of Strructed Clinical Interviews for DSM-III-R for Axis I disorder. Developmental milestones: no evidence of developmental delay. Behavioral/psychiatric evaluation: increasing anxiety, preoccupation, and paranoia at 23 years (responded well ti a few months of treatment with chloropromazine); admitted to hospital for schizophrenia at 24 years of age; improved with electroconvulsive therapy and was discharged for two months; following two additional hospitalizations, case has been relatively stable on standard antipsychotic medication regiment with an adjuvant antidepressant for many years. no evidence of autistic features. Epilepsy/seizures: no history of seizures. Dysmorphic features: no significant dysmorphology. Family history: non-consanguineous parents; no known history of neuropsychiatric illness or seizures in parents or siblings; significant history of schizophrenia in paternal extended family.
Full Scale IQ of 92 (Wechsler Adult Intelligence Scale/WAIS) at 24 years of age.
10212532
10233644
21113
GRCh38
Duplication
No
maini_18_ASD/DD/ID_discovery_cases-case_unknown157
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
7879230
8144281
265052
GRCh38
Tetrasomy
No
maini_18_ASD/DD/ID_discovery_cases-case_unknown158
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
9957004
10250666
293663
GRCh38
Duplication
No
morrow_08_ASD_discovery_cases-case1802
NA
ASD
NA
NA
9885000
9887000
1500
Unknown
Deletion
No
morrow_08_ASD_discovery_cases-case9101
NA
ASD
NA
NA
5855000
5879000
24900
Unknown
Deletion
No
o'roak_12_ASD_discovery_cases-case11224.p1
NA
M
ASD/Autism
Case also identified with de novo AP3B2 missense mutation. No additional clinical info available.
High IQ. Non verbal IQ, 112
5729306
5771328
42023
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case99HI1083A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU060303; NDAR ID NDAR_INVFG744LPG)
7723697
8476003
752307
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case64129L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
9456413
9471112
14700
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case64378L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
10394148
10433281
39134
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case93736
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
5821920
5830445
8526
Unknown
Deletion
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1051-0
N/A
N/A
ACC
Diagnosis of agenesis of the corpus callosum (ACC). ASD: yes. Seizures: no.
Developmental delay: yes. Intellectual disability: yes.
7829736
7922246
92511
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11114.p1
8.8
F
Autism
NA
Full-scale IQ, 40; non-verbal IQ, 45; verbal IQ, 30
7336474
7336892
419
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11202.p1
11.8
M
Autism
NA
Full-scale IQ, 81; non-verbal IQ, 85; verbal IQ 71
7182257
7184549
2293
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11206.p1
6.1
M
Autism
NA
Full-scale IQ, 36; non-verbal IQ, 40; verbal IQ, 32
5768100
5777590
9491
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11224.p1
8.9
M
Autism
NA
Full-scale IQ, 127; non-verbal IQ, 112; verbal IQ, 136
5733576
5771328
37753
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11348.p1
7.8
M
Autism
NA
Full-scale IQ, 77; non-verbal IQ, 84; verbal IQ, 64
7182257
7184549
2293
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11444.p1
16.3
F
Aspergers
NA
Full-scale IQ, 120; non-verbal IQ, 125; verbal IQ, 121
8356196
8369827
13632
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11568.p1
13.5
F
Autism
NA
Full-scale IQ, 51; non-verbal IQ, 72; verbal IQ, 28
5768100
5777590
9491
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11657.p1
4.9
M
Autism
NA
Full-scale IQ, 71; non-verbal IQ, 75; verbal IQ, 73
5768916
5777590
8675
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12161.p1
6.3
F
Autism
NA
Full-scale IQ, 106; non-verbal IQ, 95; verbal IQ, 122
6593220
6610086
16867
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12301.p1
13.9
M
Autism
NA
Full-scale IQ, 119; non-verbal IQ, 115; verbal IQ, 122
6746153
6755457
9305
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12323.p1
10.1
M
Autism
NA
Full-scale IQ, 90; non-verbal IQ, 90; verbal IQ, 92
5346091
5506761
160671
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12617.p1
10.8
F
Autism
NA
Full-scale IQ, 109; non-verbal IQ, 112; verbal IQ, 106
5768100
5777590
9491
GRCh38
Deletion
No
yap_21_ASD_discovery_cases-case1101240
NA
M
ASD
Sleep disturbances (CSHQ 44)
WISC-IV composite score 78
6103137
7413311
1310175
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case179
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
7568631
7589339
20709
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case180
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case181
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case182
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case183
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case184
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case185
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case186
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case187
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9484428
9679665
195238
GRCh38
Duplication
No
yin_16_ASD_discovery_cases-case188
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
9499738
9742967
243230
GRCh38
Deletion
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
brandler_18_ASD_discovery_controls-controlSSC08738
N/A
M
Control
Control from SSC_phase1 cohort
8055724
8061998
6275
GRCh38
Deletion
Yes
engchuan_15_ASD_discovery_controls-controlB287525_1007875241
N/A
N/A
Control
No previous psychiatric history
8724839
9699920
975082
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB351918_1007875243
N/A
N/A
Control
No previous psychiatric history
9369088
9587803
218716
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB452714_1007872596
N/A
N/A
Control
No previous psychiatric history
9671044
9870851
199808
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB452714_1007872596
N/A
N/A
Control
No previous psychiatric history
10006681
10823687
817007
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB481649_1007874870
N/A
N/A
Control
No previous psychiatric history
9506565
9726975
220411
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB779950_1007875276
N/A
N/A
Control
No previous psychiatric history
5248217
5331364
83148
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_902676_902676
N/A
N/A
Control
No previous psychiatric history
9992214
10856368
864155
GRCh38
Duplication
No
girirajan_11_ASD_discovery_controls-NIMH_220
NA
NA
Control
NA
NA
9472989
10758395
1285407
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-54104102012
N/A
N/A
Control
Ethnicity: Hispanic
N/A
6273577
6378687
105111
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-56305104466
N/A
N/A
Control
Ethnicity: Hispanic
N/A
6886350
6956840
70491
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-9409110993
N/A
N/A
Control
Ethnicity: Caucasian
N/A
10220646
10590056
369411
GRCh38
Deletion
No
kanduri_15_ASD_discovery_controls-control_split870
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
9371116
9485300
114185
Unknown
Duplication
No
krumm_13_ASD_discovery_controls-control12161.s1
N/A
F
Control
Unaffected sibling from SSC quad family 12161. SRS score of 44.
6593172
6611278
18107
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control12161.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
6593172
6611278
18107
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control12854.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
7855465
7967103
111639
GRCh38
Duplication
Yes
levy_11_ASD_discovery_controls-11224.s1
NA
F
Control
NA
NA
5721152
5772543
51392
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11224.s1
7.1
F
Control (matched sibling)
NA
NA
5733329
5771328
38000
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11348.s1
9.2
F
Control (matched sibling)
NA
NA
7182257
7184549
2293
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11444.s1
19.5
F
Control (matched sibling)
NA
NA
8356196
8369827
13632
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11564.s1
6.3
F
Control (matched sibling)
NA
NA
5255637
5278069
22433
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12161.s1
7.7
F
Control (matched sibling)
NA
NA
6593220
6610086
16867
GRCh38
Deletion
No
stamouli_18_ASD/NDD_discovery_controls-family13_Twin_2
N/A
N/A
Control
Control is from a monozygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
9622447
9809509
187063
GRCh38
Duplication
No
stamouli_18_ASD/NDD_discovery_controls-family31_Twin_1
N/A
N/A
Control
Control is from a dizygotic twin pair from the Discordant ASD/Discordant NDD diagnostic subgroup
6301834
6314227
12394
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
alayadhi_16_ASD_discovery_cases-caseAUT4-1
qPCR
De novo (CNV not observed in either parent)
Multiplex
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E84P
alayadhi_16_ASD_discovery_cases-caseAUT4-2
qPCR
De novo (CNV not observed in either parent)
Multiplex
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E84P
alayadhi_16_ASD_discovery_cases-caseAUT6-1
qPCR
De novo (CNV not observed in either parent)
Multiplex
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E84P
alayadhi_16_ASD_discovery_cases-caseAUT6-2
qPCR
De novo (CNV not observed in either parent)
Multiplex
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E84P
brandler_18_ASD_discovery_cases-caseSSC08732
PCR or SNP data validation
Paternal
ABLIM2
brandler_18_ASD_discovery_cases-caseSSC09546
SNP VCF
De novo
SH3TC1
brandler_18_ASD_replication_cases-caseSSC03573
No validation step reported
Maternal
KIAA0232
celestino-soper_11_ASD_discovery_cases-11533
aCGH (Agilent 4x180K or 8x60K)
Inherited
Simplex
NA
USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P
costa_21_ASD_discovery_cases-caseP68
Unknown
DRD5,GPR78,SH3TC1,SLC2A9,AFAP1,SORCS2,ABLIM2,AFAP1-AS1,HTRA3,TRMT44,HMX1,OR7E83P,OR7E35P,USP17L9P,OR7E84P,USP17L6P,MIR95,OR7E86P,OR7E85P,DEFB131A,FAM86MP,USP17L27,RPS3AP19,USP17L30,USP17L25,USP17L28,OR7E85BP,GMPSP1,USP17L29,USP17L5,USP17L26,USP17L24,PSAPL1,DEFB108F,ALG1L3P,USP17L15,USP17L10,USP17L20,OR7E111FP,USP17L11,USP17L21,USP17L12,USP17L22,USP17L16P,USP17L14P,FAM90A26,USP17L19,FAM86KP,USP17L17,USP17L18,USP17L13,MIR548I2,ENPP7P10,ENPP7P11,MIR4274,RNA5SP152,RNA5SP153,RNA5SP154,UNC93B8,ALG1L14P,UNC93B7,USP17L23,LINC02517,SNRPCP16,SNRPCP13,DEFB130D,ACOX3,CPZ
digregorio_17_DD/ID_discovery_cases-DECIPHER_299797
qPCR
Paternal
Paternal
Multi-generational
DRD5,RNA5SP154,MIR3138,RNA5SP155,SLC2A9,WDR1
digregorio_17_DD/ID_discovery_cases-DECIPHER_300097
qPCR
Maternal
RNA5SP152,SNRPCP16,ALG1L14P,USP17L10,USP17L11,USP17L12,USP17L13,USP17L14P,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L23,USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P,DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,HTRA3,LINC02517,TRMT44,GPR78,CPZ,HMX1,UNC93B8,ENPP7P10,FAM86KP,USP17L16P,OR7E84P,RAF1P1,FAM90A26,FAM86MP,SLC2A9,WDR1,ACOX3
engchuan_15_ASD_discovery_cases-case14134_2320
Unknown
EVC2
engchuan_15_ASD_discovery_cases-case14403_5120
Unknown
MIR4798,SORCS2
engchuan_15_ASD_discovery_cases-case16090_1571122001
Unknown
AFAP1-AS1,AFAP1,SORCS2
engchuan_15_ASD_discovery_cases-case3268_4
Unknown
DEFB131;LOC650293;LOC728373;LOC728379;LOC728393;LOC728400;LOC728405;USP17;USP17L5;USP17L6P
engchuan_15_ASD_discovery_cases-case3489_3
Unknown
RNA5SP152,ACOX3
engchuan_15_ASD_discovery_cases-case4230_1
Unknown
MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,FAM86MP,SLC2A9
engchuan_15_ASD_discovery_cases-case4428_1
Unknown
LOC728373;LOC728379;LOC728393;LOC728400;LOC728405;USP17;USP17L5;USP17L6P
fitzgerald_14_ASD/DD/ID_discovery_cases-case000033
De novo
Unknown
Unknown
MIR3138,RNA5SP155,RAF1P1,SLC2A9,WDR1
fitzgerald_14_ASD/DD/ID_discovery_cases-case000034
De novo
Unknown
Unknown
ZNF518B,CLNK
gai_11_ASD_discovery_cases-AU1521302
Inherited
GPR78, CPZ
gai_11_ASD_replication_cases-AU017504
Inherited
0 genes
gai_11_ASD_replication_cases-AU068903
Inherited
DEFB131, LOC650293
gai_11_ASD_replication_cases-AU0745301
Inherited
DEFB131, LOC650293
girirajan_13a_ASD_discovery_cases-13603.p1
Unknown
Simplex
Unknown
MIR3138,RNA5SP155,RAF1P1,ZNF518B,SLC2A9,WDR1
girirajan_13b_ASD_discovery_cases-25807108397
Unknown
Unknown
Unknown
SORCS2
girirajan_13b_ASD_discovery_cases-709110652
Unknown
Unknown
Unknown
GMPSP1,SH3TC1,ABLIM2
itsara_10_ASD_discovery_cases-HI1977
aCGH (custom NimbleGen 12 X 135)
De novo
Multiplex
SH3TC1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002303
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,OR7E84P,FAM86MP,SLC2A9,WDR1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004241
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR3138,RNA5SP155,RAF1P1,ZNF518B,SLC2A9,WDR1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004790
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SKP275,LINC01587,MIR378D1,MRFAP1,LINC002481,S100P,MRFAP1L1,RN7SKP292,CCDC96,LINC02447,RN7SKP36,MIR4798,PSAPL1,MIR4274,MIR95,GMPSP1,RNA5SP152,SNRPCP16,ALG1L14P,USP17L10,USP17L11,USP17L12,USP17L13,USP17L14P,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L23,USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P,DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,LINC02495,MAN2B2,LINC02482,BLOC1S4,TADA2B,GRPEL1,AFAP1-AS1,SH3TC1,HTRA3,LINC02517,TRMT44,GPR78,CPZ,HMX1,UNC93B8,ENPP7P10,FAM86KP,USP17L16P,OR7E84P,RAF1P1,ZNF518B,EVC2,EVC,CRMP1,C4orf50,JAKMIP1,PPP2R2C,KIAA0232,TBC1D14,AFAP1,ABLIM2,FAM90A26,FAM86MP,SLC2A9,WDR1,CLNK,STK32B,WFS1,SORCS2,ACOX3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005118
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR3138,RNA5SP155,RAF1P1,ZNF518B,SLC2A9,WDR1,CLNK,LINC02498
kanduri_15_ASD_discovery_cases-case3051
Maternal
Unknown
Unknown
DEFB131
kanduri_15_ASD_discovery_cases-case3070
Paternal
Unknown
Unknown
DEFB131
krumm_13_ASD_discovery_cases-case12161.p1
Solid phase hybridization (Illumina 1M) and aCGH (Agilent SurePrint G3 4x180K)
Maternal
Simplex
Not segregated
MAN2B2
krumm_15_ASD_discovery_cases-case12161.p1
Illumina 1MDuo
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
MAN2B2
levy_11_ASD_discovery_cases-11224.p1
Paternal
Simplex
Not segregated
EVC,CRMP1
lionel_13_ASD/SCZ/EP_discovery_cases-proband1
Unknown
Simplex
Unknown
lionel_13_ASD/SCZ/EP_discovery_cases-proband5
Unknown
Simplex
Unknown
maini_18_ASD/DD/ID_discovery_cases-case_unknown157
Paternal
Unknown
Unknown
MIR95,AFAP1,ABLIM2
maini_18_ASD/DD/ID_discovery_cases-case_unknown158
Paternal
Unknown
Unknown
MIR3138,RNA5SP155,SLC2A9,WDR1
morrow_08_ASD_discovery_cases-case1802
Maternal
NA
NA
0 genes
morrow_08_ASD_discovery_cases-case9101
Paternal
NA
NA
EVC
o'roak_12_ASD_discovery_cases-case11224.p1
aCGH, Sanger sequencing
Paternal
Simplex (quad)
Unknown
EVC,CRMP1
poultney_13_ASD_discovery_cases-case99HI1083A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
MIR95,GMPSP1,RNA5SP152,AFAP1-AS1,SH3TC1,HTRA3,LINC02517,TRMT44,AFAP1,ABLIM2,SORCS2,ACOX3
prasad_12_ASD_discovery_cases-case64129L
Unknown
Unknown
Unknown
SLC2A9
prasad_12_ASD_discovery_cases-case64378L
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case93736
Unknown
Unknown
Unknown
EVC
sajan_13_ACC/CBLH/PMG_discovery_cases-case1051-0
qPCR (CNV not detected)
Biparental/Diploid copy number
Unknown
Unknown
AFAP1
sanders_11_ASD_discovery_cases-11114.p1
Maternal
Simplex (quad-proband matched)
Segregated
SORCS2
sanders_11_ASD_discovery_cases-11202.p1
Both parents
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11206.p1
Maternal
Simplex (quad-proband matched)
Not segregated
EVC,CRMP1
sanders_11_ASD_discovery_cases-11224.p1
Paternal
Simplex (quad-proband matched)
Not segregated
EVC,CRMP1
sanders_11_ASD_discovery_cases-11348.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11444.p1
Maternal
Simplex (quad-proband matched)
Not segregated
ACOX3
sanders_11_ASD_discovery_cases-11568.p1
Maternal
Simplex (quad-proband matched)
Not segregated
EVC,CRMP1
sanders_11_ASD_discovery_cases-11657.p1
Paternal
Simplex (quad-proband matched)
Not segregated
EVC,CRMP1
sanders_11_ASD_discovery_cases-12161.p1
Maternal
Simplex (quad-proband matched)
Not segregated
MAN2B2
sanders_11_ASD_discovery_cases-12301.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12323.p1
Paternal
Simplex (quad-proband matched)
Not segregated
RN7SKP275,STK32B
sanders_11_ASD_discovery_cases-12617.p1
Paternal
Simplex (quad-proband matched)
Not segregated
EVC,CRMP1
yap_21_ASD_discovery_cases-case1101240
Unknown
BLOC1S4,TBC1D14,SORCS2,GRPEL1,TADA2B,MRFAP1,MRFAP1L1,JAKMIP1,CCDC96,LINC02495,LINC02481,C4orf50,LINC02447,MIR4798,S100P,PPP2R2C,LINC02482,RN7SKP292,WFS1,RN7SKP36,KIAA0232,MAN2B2
yin_16_ASD_discovery_cases-case179
Unknown
Unknown
Unknown
SORCS2
yin_16_ASD_discovery_cases-case180
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case181
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case182
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case183
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case184
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case185
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case186
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case187
Unknown
Unknown
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11
yin_16_ASD_discovery_cases-case188
Unknown
Unknown
Unknown
OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,FAM86MP
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC08738
PCR or SNP data validation
Paternal
ABLIM2
engchuan_15_ASD_discovery_controls-controlB287525_1007875241
Unknown
SNRPCP16,ALG1L14P,USP17L10,USP17L11,USP17L12,USP17L13,USP17L14P,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L23,USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P,DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,HMX1,UNC93B8,ENPP7P10,FAM86KP,USP17L16P,OR7E84P,FAM90A26,FAM86MP
engchuan_15_ASD_discovery_controls-controlB351918_1007875243
Unknown
DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,OR7E84P
engchuan_15_ASD_discovery_controls-controlB452714_1007872596
Unknown
ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,FAM86MP,SLC2A9
engchuan_15_ASD_discovery_controls-controlB452714_1007872596
Unknown
MIR3138,RNA5SP155,RAF1P1,ZNF518B,SLC2A9,WDR1,CLNK,LINC02498
engchuan_15_ASD_discovery_controls-controlB481649_1007874870
Unknown
OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,FAM86MP
engchuan_15_ASD_discovery_controls-controlB779950_1007875276
Unknown
STK32B
engchuan_15_ASD_discovery_controls-controlHABC_902676_902676
Unknown
MIR3138,RNA5SP155,RAF1P1,ZNF518B,SLC2A9,WDR1,CLNK,LINC02498
girirajan_11_ASD_discovery_controls-NIMH_220
Unknown
OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,RAF1P1,ZNF518B,FAM86MP,SLC2A9,WDR1,CLNK,LINC02498
girirajan_13b_ASD_discovery_controls-54104102012
Unknown
PPP2R2C,WFS1
girirajan_13b_ASD_discovery_controls-56305104466
Unknown
TBC1D14
girirajan_13b_ASD_discovery_controls-9409110993
Unknown
RAF1P1,ZNF518B,CLNK
kanduri_15_ASD_discovery_controls-control_split870
Unknown
DEFB131
krumm_13_ASD_discovery_controls-control12161.s1
Solid phase hybridization (Illumina 1M) and aCGH (Agilent SurePrint G3 4x180K)
Maternal
Simplex
MAN2B2
krumm_15_ASD_discovery_controls-control12161.s1
Illumina 1MDuo
Maternal
MAN2B2
krumm_15_ASD_discovery_controls-control12854.s1
1M-Duov3
Paternal
AFAP1,ABLIM2
levy_11_ASD_discovery_controls-11224.s1
Paternal
Simplex
NA
EVC,CRMP1
sanders_11_ASD_discovery_controls-11224.s1
Paternal
Simplex (quad)
NA
EVC,CRMP1
sanders_11_ASD_discovery_controls-11348.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11444.s1
Maternal
Simplex (quad)
NA
ACOX3
sanders_11_ASD_discovery_controls-11564.s1
Both parents
Simplex (quad)
NA
STK32B
sanders_11_ASD_discovery_controls-12161.s1
Maternal
Simplex (quad)
NA
MAN2B2
stamouli_18_ASD/NDD_discovery_controls-family13_Twin_2
Unknown
N/A (both twins typically developing)
ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,FAM86MP,SLC2A9
stamouli_18_ASD/NDD_discovery_controls-family31_Twin_1
Unknown
Simplex
WFS1
No Animal Model Data Available