A curated catalogue of human genomic structural variation




Variant Details

Variant: essv18917



Internal ID5595
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr4:9521611..9790712hg19UCSC Ensembl
chr4:9130709..9399810hg18UCSC Ensembl
chr4:9197880..9466981hg17UCSC Ensembl
Cytoband4p16.1
Allele length
AssemblyAllele length
hg19n/a
hg18n/a
hg17n/a
Variant TypeCNV CNV
Copy Number
Allele State
Allele Origin
Probe Count
Merged StatusS
Merged Variants
Supporting Variants
SamplesNA12717
Known GenesDRD5, MIR548I2
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 Mapping 500K Early Access Array (250K_Sty_SNP + 250K_Nsp_SNP)
Comments
ReferenceRedon et al 2006
Pubmed ID17122850
Accession Number(s)essv18917
Frequency
Sample Size271
Observed Gain0
Observed Loss0
Observed Complex0
Frequencyn/a


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