A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759695



Internal ID9635154
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:69485653..69519460hg38UCSC Ensembl
Innerchr9:72100569..72134376hg19UCSC Ensembl
Innerchr9:71290389..71324196hg18UCSC Ensembl
Innerchr9:69330123..69363930hg17UCSC Ensembl
Cytoband9q21.11
Allele length
AssemblyAllele length
hg3833808
hg1933808
hg1833808
hg1733808
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757341
SamplesNA10831, NA18863, NA18952, NA18953, NA18862, NA12155
Known GenesAPBA1
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)esv2759695
Frequency
Sample Size270
Observed Gain3
Observed Loss3
Observed Complex0
Frequencyn/a


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