A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759214



Internal ID9634673
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:197128182..197770997hg38UCSC Ensembl
Innerchr3:196855053..197497868hg19UCSC Ensembl
Innerchr3:198339450..198982265hg18UCSC Ensembl
Innerchr3:198343363..198986178hg17UCSC Ensembl
Cytoband3q29
Allele length
AssemblyAllele length
hg38642816
hg19642816
hg18642816
hg17642816
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757029, esv2757914
SamplesNA10859, NA18503, NA10831, NA19194, NA12249, NA12750, NA18914, NA18871, NA12875, NA18501, NA19093, NA18500, NA10839, NA19223, NA10847, NA18948, NA12813, NA18521, NA18517, NA18608, NA07019, NA12005, NA19144, NA07348, NA10855, NA18505, NA18506, NA18949, NA12865, NA11882, NA19161, NA12763, NA18912, NA18508, NA19239, NA12753, NA07034, NA12004, NA18854, NA11994, NA18960, NA10846, NA07357, NA18991, NA12740, NA07048, NA18959, NA12751, NA12239, NA12145, NA18620, NA19206, NA19102, NA19119, NA18504, NA19159, NA19145, NA12891, NA18987, NA19101, NA19193, NA19128, NA12812, NA19099, NA11830, NA12003, NA10838, NA19160, NA11829, NA19130, NA12874, NA18532, NA18981, NA18913, NA19200, NA19202, NA07000, NA18980, NA10854
Known GenesBDH1, DLG1, DLG1-AS1, FYTTD1, KIAA0226, LOC220729, MIR4797, MIR922
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)esv2759214
Frequency
Sample Size270
Observed Gain30
Observed Loss56
Observed Complex0
Frequencyn/a


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