A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759779



Internal ID9635238
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:100392093..100805979hg38UCSC Ensembl
Innerchr10:102151850..102565736hg19UCSC Ensembl
Innerchr10:102141840..102555726hg18UCSC Ensembl
Innerchr10:102141840..102555726hg17UCSC Ensembl
Cytoband10q24.31
Allele length
AssemblyAllele length
hg38413887
hg19413887
hg18413887
hg17413887
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758238, esv2757407, esv2758237
SamplesNA07029, NA06994, NA19202
Known GenesHIF1AN, NDUFB8, PAX2, SEC31B, WNT8B
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)esv2759779
Frequency
Sample Size270
Observed Gain2
Observed Loss1
Observed Complex0
Frequencyn/a


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