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estd220 (Pettigrew et al. 2015)

Organism:
Human
Study Type:
Case-Control
Submitter:
Kerry Pettigrew
Description:
We screened 86 children with language impairment and/or a family history of dyslexia for copy number variation (CNV). Participants were recruited as part of a longitudinal family study to investigate language and reading development in early childhood, and were assessed over a period of approximately 5 years. DNA was genotyped on an Illumina Human OmniExpress-24 platform, and CNVs predicted using QuantiSNP and PennCNV. Reported CNVs span at least three consecutive genetic variants, have a confidence score > 10, and were predicted by both algorithms. See Variant Summary counts for estd220 in dbVar Variant Summary.
Publication(s):
Pettigrew et al. 2015

Detailed Information: Download 3620 Variant Regions, Download 3585 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr1416411RemappedNC_000001.11
NC_000002.12Chr2178176RemappedNC_000002.12
NC_000003.12Chr38180RemappedNC_000003.12
NC_000004.12Chr4172170RemappedNC_000004.12
NC_000005.10Chr5158154RemappedNC_000005.10
NC_000006.12Chr65555RemappedNC_000006.12
NC_000007.14Chr7204201RemappedNC_000007.14
NC_000008.11Chr8302299RemappedNC_000008.11
NC_000009.12Chr9272268RemappedNC_000009.12
NC_000010.11Chr10252249RemappedNC_000010.11
NC_000011.10Chr11325324RemappedNC_000011.10
NC_000012.12Chr12157157RemappedNC_000012.12
NC_000013.11Chr13129128RemappedNC_000013.11
NC_000014.9Chr14166165RemappedNC_000014.9
NC_000015.10Chr153331RemappedNC_000015.10
NC_000016.10Chr16214214RemappedNC_000016.10
NC_000017.11Chr17108108RemappedNC_000017.11
NC_000018.10Chr183434RemappedNC_000018.10
NC_000019.10Chr19118117RemappedNC_000019.10
NC_000020.11Chr207979RemappedNC_000020.11
NC_000021.9Chr21136135RemappedNC_000021.9
NC_000022.11Chr222828RemappedNC_000022.11
NT_187515.1Chr1|NT_187515.16261RemappedNT_187515.1
NT_187516.1Chr1|NT_187516.122RemappedNT_187516.1
NW_009646196.1Chr1|NW_009646196.122RemappedNW_009646196.1
NW_012132914.1Chr1|NW_012132914.177RemappedNW_012132914.1
NW_017852928.1Chr1|NW_017852928.111RemappedNW_017852928.1
NT_187523.1Chr2|NT_187523.122RemappedNT_187523.1
NT_187527.1Chr2|NT_187527.11615RemappedNT_187527.1
NT_187647.1Chr2|NT_187647.122RemappedNT_187647.1
NW_019805488.1Chr3|NW_019805488.144RemappedNW_019805488.1
NT_187548.1Chr5|NT_187548.111RemappedNT_187548.1
NT_187550.1Chr5|NT_187550.143RemappedNT_187550.1
NT_187555.1Chr6|NT_187555.111RemappedNT_187555.1
NW_004166862.2Chr6|NW_004166862.211RemappedNW_004166862.2
NT_187558.1Chr7|NT_187558.11212RemappedNT_187558.1
NT_187562.1Chr7|NT_187562.11211RemappedNT_187562.1
NT_187653.1Chr7|NT_187653.11212RemappedNT_187653.1
NW_018654714.1Chr7|NW_018654714.111RemappedNW_018654714.1
NT_187571.1Chr8|NT_187571.12626RemappedNT_187571.1
NT_187576.1Chr8|NT_187576.11212RemappedNT_187576.1
NW_018654716.1Chr8|NW_018654716.166RemappedNW_018654716.1
NW_018654717.1Chr8|NW_018654717.133RemappedNW_018654717.1
NW_009646201.1Chr9|NW_009646201.11313RemappedNW_009646201.1
NW_003315935.1Chr10|NW_003315935.122RemappedNW_003315935.1
NT_187681.1Chr11|NT_187681.177RemappedNT_187681.1
NT_187657.1Chr11|NT_187657.111RemappedNT_187657.1
NT_187584.1Chr11|NT_187584.111RemappedNT_187584.1
NT_187585.1Chr11|NT_187585.11010RemappedNT_187585.1
NT_187586.1Chr11|NT_187586.14443RemappedNT_187586.1
NW_015148966.1Chr11|NW_015148966.14140RemappedNW_015148966.1
NT_187587.1Chr12|NT_187587.133RemappedNT_187587.1
NW_011332698.1Chr13|NW_011332698.177RemappedNW_011332698.1
NT_187600.1Chr14|NT_187600.15252RemappedNT_187600.1
NT_187660.1Chr15|NT_187660.154RemappedNT_187660.1
NW_011332701.1Chr15|NW_011332701.154RemappedNW_011332701.1
NT_187607.1Chr16|NT_187607.133RemappedNT_187607.1
NT_187608.1Chr16|NT_187608.122RemappedNT_187608.1
NW_012132921.1Chr16|NW_012132921.111RemappedNW_012132921.1
NT_187661.1Chr17|NT_187661.144RemappedNT_187661.1
NT_187663.1Chr17|NT_187663.11616RemappedNT_187663.1
NT_187664.1Chr17|NT_187664.111RemappedNT_187664.1
NT_187612.1Chr17|NT_187612.122RemappedNT_187612.1
NT_187613.1Chr17|NT_187613.111RemappedNT_187613.1
NT_187614.1Chr17|NT_187614.144RemappedNT_187614.1
NT_187666.1Chr18|NT_187666.133RemappedNT_187666.1
NW_003315961.1Chr18|NW_003315961.133RemappedNW_003315961.1
NW_019805503.1Chr18|NW_019805503.122RemappedNW_019805503.1
NT_187693.1Chr19|NT_187693.111RemappedNT_187693.1
NW_003571060.1Chr19|NW_003571060.111RemappedNW_003571060.1
NT_187622.1Chr19|NT_187622.122RemappedNT_187622.1
NW_003315962.1Chr19|NW_003315962.111RemappedNW_003315962.1
NW_003315964.2Chr19|NW_003315964.266RemappedNW_003315964.2
NW_003571054.1Chr19|NW_003571054.111RemappedNW_003571054.1
NT_187626.1Chr21|NT_187626.199RemappedNT_187626.1
NW_003315968.2Chr21|NW_003315968.211RemappedNW_003315968.2
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr1416411SubmittedNC_000001.10
NC_000002.11Chr2178176SubmittedNC_000002.11
NC_000003.11Chr38180SubmittedNC_000003.11
NC_000004.11Chr4172170SubmittedNC_000004.11
NC_000005.9Chr5158154SubmittedNC_000005.9
NC_000006.11Chr65555SubmittedNC_000006.11
NC_000007.13Chr7204201SubmittedNC_000007.13
NC_000008.10Chr8302299SubmittedNC_000008.10
NC_000009.11Chr9272268SubmittedNC_000009.11
NC_000010.10Chr10252249SubmittedNC_000010.10
NC_000011.9Chr11328326SubmittedNC_000011.9
NC_000012.11Chr12157157SubmittedNC_000012.11
NC_000013.10Chr13129128SubmittedNC_000013.10
NC_000014.8Chr14166165SubmittedNC_000014.8
NC_000015.9Chr153331SubmittedNC_000015.9
NC_000016.9Chr16214214SubmittedNC_000016.9
NC_000017.10Chr17108108SubmittedNC_000017.10
NC_000018.9Chr183434SubmittedNC_000018.9
NC_000019.9Chr19118117SubmittedNC_000019.9
NC_000020.10Chr207979SubmittedNC_000020.10
NC_000021.8Chr21136135SubmittedNC_000021.8
NC_000022.10Chr222828SubmittedNC_000022.10

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr1416323172074411319172073
NC_000002.11Chr2178141190018176140190017
NC_000003.11Chr38177000480760004
NC_000004.11Chr417216660001701646000
NC_000005.9Chr51581322100515412921004
NC_000006.11Chr65553000255530002
NC_000007.13Chr7204155240025201153240024
NC_000008.10Chr8302174783047299172773047
NC_000009.11Chr9272208510013268205500013
NC_000010.10Chr1025225000022492470002
NC_000011.9Chr113282215909332622158092
NC_000012.11Chr1215715400031571540003
NC_000013.10Chr1312912002071281190207
NC_000014.8Chr141669851105216597511052
NC_000015.9Chr153327100531261004
NC_000016.9Chr1621419990062141999006
NC_000017.10Chr171086916002310869160023
NC_000018.9Chr183427200534272005
NC_000019.9Chr191181044001011710340010
NC_000020.10Chr207977200079772000
NC_000021.8Chr211366759001013567580010
NC_000022.10Chr22281710100281710100

Samplesets

Number of Samplesets: 2

Sampleset ID:
1
Name:
Case_Dys/LI+
Sampleset Type:
Case
Description:
Children with dyslexia and/or language impairment.
Size:
44
Organisms:
Homo sapiens
Sampleset Phenotype(s):
Dyslexia, language impairment
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDSubject ID Subject Phenotype
    LI-12LI-12Dyslexia, language impairment
    LI-14LI-14Dyslexia, language impairment
    FR-34FR-34Dyslexia, language impairment
    FR-20-SibFR-20-SibDyslexia, language impairment
    FR-20FR-20Dyslexia, language impairment
    LI-02LI-02Dyslexia, language impairment
    LI-05LI-05Dyslexia, language impairment
    FR-08FR-08Dyslexia, language impairment
    FR-39-SibFR-39-SibDyslexia, language impairment
    FR-09-SibAFR-09-SibADyslexia, language impairment
    FR-02-SibFR-02-SibDyslexia, language impairment
    FR-45FR-45Dyslexia, language impairment
    LI-15LI-15Dyslexia, language impairment
    FR-03-SibFR-03-SibDyslexia, language impairment
    LI-08LI-08Dyslexia, language impairment
    FR-37FR-37Dyslexia, language impairment
    FR-23-SibFR-23-SibDyslexia, language impairment
    FR-23FR-23Dyslexia, language impairment
    FR-13FR-13Dyslexia, language impairment
    FR-24FR-24Dyslexia, language impairment
    LI-09LI-09Dyslexia, language impairment
    FR-15FR-15Dyslexia, language impairment
    LI-11LI-11Dyslexia, language impairment
    FR-04FR-04Dyslexia, language impairment
    FR-46FR-46Dyslexia, language impairment
    FR-22-SibFR-22-SibDyslexia, language impairment
    FR-05FR-05Dyslexia, language impairment
    FR-16FR-16Dyslexia, language impairment
    FR-47FR-47Dyslexia, language impairment
    Sib-LI-1Sib-LI-1Dyslexia, language impairment
    FR-36FR-36Dyslexia, language impairment
    FR-39FR-39Dyslexia, language impairment
    LI-13LI-13Dyslexia, language impairment
    TD-04TD-04Dyslexia, language impairment
    LI-16 (proband 62)LI-16 (proband 62)Dyslexia, language impairment
    FR-40FR-40Dyslexia, language impairment
    FR-11FR-11Dyslexia, language impairment
    FR-42FR-42Dyslexia, language impairment
    LI-07LI-07Dyslexia, language impairment
    FR-32FR-32Dyslexia, language impairment
    FR-27FR-27Dyslexia, language impairment
    FR-10FR-10Dyslexia, language impairment
    LI-01LI-01Dyslexia, language impairment
    LI-06LI-06Dyslexia, language impairment
    Sampleset ID:
    2
    Name:
    Control_Dys/LI-
    Sampleset Type:
    Control
    Description:
    Children with normal reading and language ability.
    Size:
    47
    Organisms:
    Homo sapiens
    Sampleset Phenotype(s):
    None reported
  • Download Samples as CSV file
  • Samples for sampleset 2
    Sample IDSubject ID Subject Phenotype
    Sib-LI-2Sib-LI-2Not reported
    LI-14-SibLI-14-SibNot reported
    FR-21FR-21Not reported
    LI-10-Sib(TD-05)LI-10-Sib(TD-05)Not reported
    LI-03LI-03Not reported
    FR-44-SibFR-44-SibNot reported
    LI-04LI-04Not reported
    FR-49FR-49Not reported
    TD-03TD-03Not reported
    FR-01FR-01Not reported
    LI-10LI-10Not reported
    FR-25FR-25Not reported
    FR-10-SibFR-10-SibNot reported
    FR-28FR-28Not reported
    TD-09TD-09Not reported
    FR-33FR-33Not reported
    TD-01TD-01Not reported
    FR-38FR-38Not reported
    FR-12-SibFR-12-SibNot reported
    FR-12FR-12Not reported
    FR-07-SibFR-07-SibNot reported
    FR-14FR-14Not reported
    FR-44FR-44Not reported
    FR-19FR-19Not reported
    TD-10TD-10Not reported
    FR-35FR-35Not reported
    FR-15-SibFR-15-SibNot reported
    FR-07FR-07Not reported
    FR-22FR-22Not reported
    FR-08-SibFR-08-SibNot reported
    FR-18FR-18Not reported
    LI-06-SibLI-06-SibNot reported
    TD-11TD-11Not reported
    FR-09FR-09Not reported
    FR-48FR-48Not reported
    FR-30FR-30Not reported
    FR-17FR-17Not reported
    FR-03FR-03Not reported
    FR-31FR-31Not reported
    FR-06FR-06Not reported
    FR-29FR-29Not reported
    FR-37-SibFR-37-SibNot reported
    FR-02FR-02Not reported
    TD-07TD-07Not reported
    FR-09-SibBFR-09-SibBNot reported
    TD-06TD-06Not reported
    FR-25-SibFR-25-SibNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
    1DiscoverySNP arraySNP genotyping analysisIllumina Human OmniExpress-243,585

    Validations

    No validation data were submitted for this study.

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