A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759589



Internal ID9635048
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:6874198..8449233hg38UCSC Ensembl
Innerchr8:6731720..8306743hg19UCSC Ensembl
Innerchr8:6719130..8344153hg18UCSC Ensembl
Innerchr8:6719130..8344153hg17UCSC Ensembl
Cytoband8p23.1
Allele length
AssemblyAllele length
hg381575036
hg191575024
hg181625024
hg171625024
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757255, esv2756808, esv2758147
SamplesNA19142, NA19012, NA10831, NA19207, NA18870, NA18964, NA12154, NA18863, NA19127, NA19194, NA18861, NA12750, NA19192, NA18871, NA19222, NA12801, NA18952, NA19173, NA12875, NA18612, NA18526, NA18550, NA18570, NA19003, NA18859, NA10847, NA18545, NA18603, NA18516, NA12707, NA12813, NA06993, NA18529, NA18969, NA18972, NA18517, NA18573, NA18608, NA18542, NA12005, NA18855, NA19210, NA07348, NA10855, NA18860, NA18524, NA18862, NA18949, NA19143, NA18632, NA19140, NA19161, NA12763, NA18912, NA19211, NA18998, NA18992, NA11839, NA11840, NA18854, NA12155, NA18576, NA18622, NA18960, NA12864, NA18563, NA07357, NA12762, NA12873, NA18991, NA07048, NA18609, NA18547, NA18976, NA11995, NA19100, NA12234, NA12144, NA12239, NA19153, NA12716, NA18515, NA19129, NA18633, NA19094, NA19206, NA18968, NA19102, NA19238, NA18502, NA19119, NA18558, NA18564, NA18858, NA18942, NA18961, NA18997, NA19221, NA18562, NA19159, NA18974, NA19141, NA19145, NA11832, NA10857, NA12146, NA18552, NA19138, NA10860, NA19201, NA06991, NA19193, NA18872, NA19128, NA12156, NA18971, NA18577, NA19099, NA12003, NA10838, NA19160, NA12248, NA18571, NA19171, NA19240, NA18532, NA19204, NA18981, NA06994, NA12760, NA19092, NA19202, NA18980
Known GenesDEFA1, DEFA10P, DEFA11P, DEFA1B, DEFA3, DEFA4, DEFA5, DEFA6, DEFA8P, DEFA9P, DEFB1, DEFB103A, DEFB103B, DEFB104A, DEFB104B, DEFB105A, DEFB105B, DEFB106A, DEFB106B, DEFB107A, DEFB107B, DEFB109P1B, DEFB4A, DEFB4B, DEFT1P, DEFT1P2, FAM66B, FAM66E, FAM86B3P, FAM90A10P, FAM90A7P, LINC00965, MIR548I3, PRR23D1, PRR23D2, SGK223, SPAG11A, SPAG11B, USP17L1P, USP17L3, USP17L4, USP17L8, ZNF705B, ZNF705G
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)esv2759589
Frequency
Sample Size270
Observed Gain85
Observed Loss55
Observed Complex0
Frequencyn/a


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