A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758769



Internal ID9634228
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:52907206..53149322hg38UCSC Ensembl
Innerchr19:53410459..53652575hg19UCSC Ensembl
Innerchr19:58102271..58344387hg18UCSC Ensembl
Innerchr19:58102271..58344387hg17UCSC Ensembl
Cytoband19q13.41
Allele length
AssemblyAllele length
hg38242117
hg19242117
hg18242117
hg17242117
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757701, esv2758506
SamplesNA18992, NA12864, NA07048, NA19119, NA19101, NA18913, NA07000
Known GenesERVV-1, ERVV-2, ZNF160, ZNF321P, ZNF347, ZNF415, ZNF702P, ZNF816, ZNF816-ZNF321P
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Agilent
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2758769
Frequency
Sample Size270
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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