A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759219



Internal ID9634678
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:3392617..4349259hg38UCSC Ensembl
Innerchr4:3394344..4350986hg19UCSC Ensembl
Innerchr4:3364142..4401887hg18UCSC Ensembl
Innerchr4:3431313..4469058hg17UCSC Ensembl
Cytoband4p16.2
Allele length
AssemblyAllele length
hg38956643
hg19956643
hg181037746
hg171037746
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757918, esv2757031, esv2757032
SamplesNA19222, NA18969, NA18976, NA19000
Known GenesADRA2C, DOK7, FAM86EP, HGFAC, LINC00955, LOC100133461, LRPAP1, LYAR, OTOP1, RGS12, TMEM128, ZBTB49
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)esv2759219
Frequency
Sample Size270
Observed Gain4
Observed Loss0
Observed Complex0
Frequencyn/a


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