A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757450



Internal ID9632909
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:67705434..68123822hg38UCSC Ensembl
Innerchr11:67472905..67891289hg19UCSC Ensembl
Innerchr11:67229481..67647865hg18UCSC Ensembl
Innerchr11:67229481..67647865hg17UCSC Ensembl
Cytoband11q13.2
Allele length
AssemblyAllele length
hg38418389
hg19418385
hg18418385
hg17418385
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759835
Supporting Variantsessv6442, essv4346, essv5774, essv3266, essv7059, essv6544, essv605, essv6928
SamplesNA18947, NA18592, NA18967, NA18608, NA18540, NA18624, NA18612, NA18622
Known GenesALDH3B1, CHKA, FAM86C2P, MIR4691, MIR6753, MIR7113, NDUFS8, TCIRG1, UNC93B1
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)esv2757450
Frequency
Sample Size270
Observed Gain0
Observed Loss8
Observed Complex0
Frequencyn/a


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