A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758759



Internal ID9634218
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:37303948..37560704hg38UCSC Ensembl
Innerchr19:37794850..38051606hg19UCSC Ensembl
Innerchr19:42486690..42743446hg18UCSC Ensembl
Innerchr19:42486690..42743446hg17UCSC Ensembl
Cytoband19q13.12
Allele length
AssemblyAllele length
hg38256757
hg19256757
hg18256757
hg17256757
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757695
SamplesNA07055
Known GenesHKR1, ZNF527, ZNF540, ZNF569, ZNF570, ZNF571-AS1, ZNF793
MethodSNP array
AnalysisThe 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)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2758759
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer