A curated catalogue of human genomic structural variation




Variant Details

Variant: essv22621



Internal ID9621027
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:8215617..8225603hg38UCSC Ensembl
Outerchr12:8215617..8239767hg38UCSC Ensembl
Innerchr12:8368213..8378199hg19UCSC Ensembl
Outerchr12:8368213..8392363hg19UCSC Ensembl
Innerchr12:8259480..8269466hg18UCSC Ensembl
Outerchr12:8259480..8283630hg18UCSC Ensembl
Innerchr12:8259480..8269466hg17UCSC Ensembl
Outerchr12:8259480..8283630hg17UCSC Ensembl
Cytoband12p13.31
Allele length
AssemblyAllele length
hg3824151
hg1924151
hg1824151
hg1724151
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757488
Supporting Variants
SamplesNA12154
Known GenesFAM86FP, FAM90A1
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)essv22621
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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