A curated catalogue of human genomic structural variation




Variant Details

Variant: essv1661



Internal ID9614347
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Outerchr7:142722674..142804120hg38UCSC Ensembl
Innerchr7:142135045..142176424hg18UCSC Ensembl
Outerchr7:142110079..142211931hg18UCSC Ensembl
Innerchr7:141941760..141983139hg17UCSC Ensembl
Outerchr7:141916794..142018646hg17UCSC Ensembl
Cytoband7q34
Allele length
AssemblyAllele length
hg3881447
hg18101853
hg17101853
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757241
Supporting Variants
SamplesNA18961
Known GenesPRSS1, PRSS2, PRSS3P2
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)essv1661
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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