A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759539



Internal ID9981684
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr7:79172072..79258609hg38UCSC Ensembl
Innerchr7:78801388..78887925hg19UCSC Ensembl
Innerchr7:78639324..78725861hg18UCSC Ensembl
Innerchr7:78446039..78532576hg17UCSC Ensembl
Cytoband7q21.11
Allele length
AssemblyAllele length
hg3886538
hg1986538
hg1886538
hg1786538
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757230
SamplesNA19092, NA18870, NA19130, NA19172, NA19128, NA19132, NA19094, NA19173, NA18872, NA19129
Known GenesMAGI2
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)esv2759539
Frequency
Sample Size270
Observed Gain0
Observed Loss10
Observed Complex0
Frequencyn/a


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