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3q26.2CNV Type: Deletion


Largest CNV size: 78426 bp

Statistics Box:
Number of Reports: 5



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
NA
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 176
 2
 0
 2
 digregorio_17_DD/ID_discovery_cases
  NA NA
 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
 719000
 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
 1835242
 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
 10633
 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
 78426
 2
 0
 2

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
 126000
 1
 0
 1
 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
 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)
 10633
 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.
 
 87278
 3
 0
 3

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 brandler_18_ASD_discovery_cases
  N/A
 WGS
  Illumina HiSeq X10 or HiSeq 2500
 ForestSV, Lumpy, Manta, Mobster, SV2
 
 PCR, array SNP
 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
 None
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
  N/A
 aCGH
  SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
 
 
 FISH
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 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
 
 

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
  nguyen_13_DD/ID/MCA/ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
  N/A
  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
 
 

Cases

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_cases-caseREACH000555
 N/A
 F
 ASD
 Case from REACH cohort
 
 170095492
 170095668
  177
 GRCh38
 Deletion
 Yes
  brandler_18_ASD_discovery_cases-caseREACH000558
 N/A
 M
 ASD
 Case from REACH cohort
 
 170095492
 170095668
  177
 GRCh38
 Deletion
 Yes
  digregorio_17_DD/ID_discovery_cases-DECIPHER_299885
  NA NA
 N/A
 F
 Developmental delay/intellectual disability
 
 
 168119489
 168838896
  719408
 GRCh38
 Duplication
 No
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC41499
 N/A
 F
 Developmental delay
 Database: Signature. Indication for study: Developmental Delay, Dysmorphic Features, 46,XX,del(10)(p12)
 Developmental delay
 168163838
 169999080
  1835243
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case46685
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 171421331
 171431963
  10633
 Unknown
 Deletion
 Yes
  sanders_11_ASD_discovery_cases-11173.p1
 10.3
 M
 Autism
 NA
 Full-scale IQ, 62; non-verbal IQ, 71; verbal IQ 49
 168325541
 168403967
  78427
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13296.p1
 5.9
 M
 Autism
 NA
 Full-scale IQ, 30; non-verbal IQ, 44; verbal IQ, 15
 170260864
 170281656
  20793
 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-controlREACH000483
  N/A
  M
  Control
  Control from REACH cohort
 
  169550763
  169676762
  126000
  GRCh38
  Deletion
  Yes
  sanders_11_ASD_discovery_controls-11088.s1
  14.5
  F
  Control (matched sibling)
  NA
  NA
  170061606
  170148884
  87279
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11986.s1
  9
  F
  Control (matched sibling)
  NA
  NA
  169685832
  169730964
  45133
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12001.s1
  6.3
  F
  Control (matched sibling)
  NA
  NA
  168993109
  168997845
  4737
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 brandler_18_ASD_discovery_cases-caseREACH000555
 PCR or SNP data validation
 
 Maternal
 
 
 PHC3
 
 brandler_18_ASD_discovery_cases-caseREACH000558
 PCR or SNP data validation
 
 Maternal
 
 
 PHC3
 
 digregorio_17_DD/ID_discovery_cases-DECIPHER_299885
 
 
 Maternal
 
 
 RNU2-20P,MIR551B,RPSAP33,EGFEM1P
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC41499
 FISH
 
 Unknown
 Unknown
 Unknown
 RNU2-20P,MIR551B,RPSAP33,RPL21P43,LINC01997,RPL22P1,RNU6-637P,TERC,ACTRT3,KRT18P43,LINC02082,MYNN,LRRC34,LRRIQ4,SAMD7,SEC62,SEC62-AS1,MECOM,EGFEM1P,LRRC31
 
 prasad_12_ASD_discovery_cases-case46685
 qPCR
 
 Paternal
 Unknown
 Unknown
 PRKCI
 
 sanders_11_ASD_discovery_cases-11173.p1
 
 
 Paternal
 Simplex (trio)
 NA
 EGFEM1P
 
 sanders_11_ASD_discovery_cases-13296.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 PRKCI
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlREACH000483
  PCR or SNP data validation (SNP VCF)
 
  De novo
 
 
  MECOM
 
sanders_11_ASD_discovery_controls-11088.s1
 
 
  Unknown
  Simplex (quad)
  NA
  GPR160,PHC3
 
sanders_11_ASD_discovery_controls-11986.s1
 
 
  Paternal
  Simplex (quad)
  NA
  RNU6-637P
 
sanders_11_ASD_discovery_controls-12001.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 

No Animal Model Data Available
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