A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758972



Internal ID9634431
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:161374465..161711762hg38UCSC Ensembl
Innerchr1:161344255..161681552hg19UCSC Ensembl
Innerchr1:159610879..159948176hg18UCSC Ensembl
Innerchr1:158157328..158413210hg17UCSC Ensembl
Cytoband1q23.3
Allele length
AssemblyAllele length
hg38337298
hg19337298
hg18337298
hg17255883
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757757, esv2756866
SamplesNA10859, NA18503, NA10831, NA18861, NA12750, NA18914, NA19222, NA12801, NA19209, NA18501, NA10839, NA12264, NA19223, NA18603, NA12813, NA19203, NA18529, NA18517, NA18573, NA07019, NA12005, NA18855, NA19144, NA19210, NA18949, NA10863, NA11882, NA18912, NA19211, NA18998, NA18967, NA11840, NA12753, NA18960, NA10846, NA12864, NA12762, NA12814, NA18592, NA07048, NA18956, NA18547, NA12234, NA18970, NA12145, NA18515, NA19129, NA19103, NA19206, NA19102, NA18502, NA18558, NA19154, NA12057, NA18504, NA18564, NA18858, NA18540, NA19131, NA19159, NA18579, NA18974, NA18987, NA10851, NA18582, NA18999, NA19101, NA18995, NA06991, NA18857, NA19132, NA18577, NA07022, NA19205, NA18571, NA18532, NA18853, NA18981, NA06994, NA18913, NA18555
Known GenesFCGR2A, FCGR2B, FCGR2C, FCGR3A, FCGR3B, FCRLA, HSPA6, HSPA7, RPL31P11
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)esv2758972
Frequency
Sample Size270
Observed Gain28
Observed Loss53
Observed Complex0
Frequencyn/a


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