A curated catalogue of human genomic structural variation




Variant Details

Variant: essv11350



Internal ID9608504
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:148853549..148928116hg38UCSC Ensembl
Outerchr1:146056907..148933491hg38UCSC Ensembl
Innerchr1:144956373..145030865hg19UCSC Ensembl
Outerchr1:144950998..145378096hg19UCSC Ensembl
Innerchr1:143667730..143742222hg18UCSC Ensembl
Outerchr1:143662355..144089453hg18UCSC Ensembl
Innerchr1:142445417..142519909hg17UCSC Ensembl
Outerchr1:142440042..142867140hg17UCSC Ensembl
Cytoband1q21.1
Allele length
AssemblyAllele length
hg382876585
hg19427099
hg18427099
hg17427099
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2756861
Supporting Variants
SamplesNA19128
Known GenesLOC100288142, LOC101929780, NBPF10, NBPF12, NBPF9, NOTCH2NL, PDE4DIP, SEC22B
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)essv11350
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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