A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv2n30



Internal ID20133244
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chrX:153142213..153228848hg38UCSC Ensembl
chrX:152436538..152541986hg19UCSC Ensembl
chrX:152089732..152195180hg18UCSC Ensembl
CytobandXq28
Allele length
AssemblyAllele length
hg3886636
hg19105449
hg18105449
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv470375, nsv470374
SamplesHGDP00461, HGDP00448
Known GenesMAGEA1
MethodSNP array
AnalysisWe used the previously validated default quality control criteria, excluding samples with a log R ratio standard deviation of >0.28, a median B allele frequency of >0.55 or <0.45, or a B allele frequency drift of >0.002 (for more details see Wang et al. 2007). As the PennCNV algorithm is more sensitive and specific to CNVs covering greater numbers of SNPs in the HumanHap550 array, use of a minimum number of SNPs in CNV detection increases the reliability of CNV calls (with a consequent reduction in calls per individual). We set 10 SNPs as the minimum detection threshold in the algorithm.
PlatformIllumina HumanHap550 Genotyping BeadChip v3
Comments
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)dgv2n30
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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