A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757255



Internal ID9632714
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:7063882..8288409hg38UCSC Ensembl
Innerchr8:6921404..8145931hg19UCSC Ensembl
Innerchr8:6908814..8183341hg18UCSC Ensembl
Innerchr8:6908814..8183341hg17UCSC Ensembl
Cytoband8p23.1
Allele length
AssemblyAllele length
hg381224528
hg191224528
hg181274528
hg171274528
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759589
Supporting Variantsessv14023, essv8885, essv16580, essv18055, essv971, essv1578, essv11387, essv737, essv12055, essv18524, essv10504, essv15434, essv17370, essv21604, essv13110, essv8030, essv13398, essv14017, essv24014, essv21894, essv15948, essv1677, essv1003
SamplesNA19222, NA18862, NA12155, NA19127, NA19171, NA18964, NA06993, NA19238, NA18859, NA18515, NA18871, NA18981, NA19003, NA19206, NA06991, NA18517, NA12873, NA18992, NA19193, NA12763, NA19143, NA18872, NA18997
Known GenesDEFB103A, DEFB103B, DEFB104A, DEFB104B, DEFB105A, DEFB105B, DEFB106A, DEFB106B, DEFB107A, DEFB107B, DEFB109P1B, DEFB4A, DEFB4B, FAM66B, FAM66E, FAM86B3P, FAM90A10P, FAM90A7P, LINC00965, MIR548I3, PRR23D1, PRR23D2, SPAG11A, SPAG11B, USP17L1P, USP17L3, USP17L4, USP17L8, ZNF705B, ZNF705G
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)esv2757255
Frequency
Sample Size270
Observed Gain9
Observed Loss14
Observed Complex0
Frequencyn/a


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