A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759608



Internal ID9635067
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:39316760..39740120hg38UCSC Ensembl
Innerchr8:39174279..39597639hg19UCSC Ensembl
Innerchr8:39293436..39716796hg18UCSC Ensembl
Innerchr8:39293436..39716796hg17UCSC Ensembl
Cytoband8p11.22
Allele length
AssemblyAllele length
hg38423361
hg19423361
hg18423361
hg17423361
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758154, esv2757269
SamplesNA10859, NA18503, NA11881, NA18621, NA19207, NA18870, NA18964, NA12154, NA18863, NA19127, NA12043, NA19152, NA19194, NA12249, NA18861, NA18605, NA12750, NA18594, NA18951, NA19192, NA18914, NA18871, NA12802, NA19222, NA18561, NA12801, NA18523, NA18952, NA18975, NA07056, NA18966, NA19173, NA12752, NA12875, NA18612, NA19209, NA18501, NA19093, NA19120, NA18500, NA18526, NA10839, NA18550, NA18570, NA12264, NA18859, NA19223, NA12815, NA10847, NA18545, NA18603, NA18948, NA18516, NA12813, NA06993, NA19203, NA18521, NA18529, NA18953, NA18969, NA18972, NA18517, NA18947, NA18573, NA18608, NA18542, NA07019, NA12005, NA18855, NA19144, NA19210, NA07348, NA18507, NA10855, NA18860, NA18994, NA07029, NA18524, NA18965, NA18505, NA12044, NA19208, NA18506, NA18862, NA18943, NA18949, NA19143, NA18632, NA12865, NA19140, NA11882, NA19161, NA12763, NA18912, NA19211, NA18998, NA18624, NA18508, NA18967, NA19239, NA18992, NA11839, NA11840, NA12753, NA07034, NA12004, NA18854, NA18566, NA11994, NA18635, NA12155, NA18576, NA18622, NA18960, NA10846, NA12864, NA18563, NA07357, NA18623, NA12762, NA12873, NA18990, NA18991, NA12814, NA18636, NA12740, NA18592, NA18856, NA07048, NA12761, NA18956, NA18959, NA18609, NA18547, NA11831, NA18976, NA18637, NA18973, NA11995, NA18593, NA19100, NA12234, NA12144, NA18970, NA12751, NA12006, NA19000, NA12239, NA12145, NA19153, NA12716, NA18537, NA18620, NA18515, NA19129, NA19172, NA12892, NA18633, NA18572, NA19094, NA19103, NA06985, NA19206, NA18968, NA19102, NA18522, NA19238, NA19005, NA18502, NA19119, NA18558, NA19098, NA19154, NA12057, NA10856, NA19139, NA12872, NA18504, NA18978, NA18564, NA18858, NA18942, NA18961, NA18540, NA18997, NA19221, NA18562, NA19131, NA19159, NA18579, NA18974, NA18945, NA19141, NA18940, NA19145, NA11832, NA12891, NA18987, NA10851, NA18582, NA18999, NA10857, NA12146, NA07055, NA18552, NA19138, NA10860, NA19101, NA19201, NA18995, NA06991, NA19193, NA18872, NA19128, NA12812, NA18857, NA12156, NA19116, NA10835, NA19132, NA10830, NA18577, NA19099, NA07022, NA12878, NA11830, NA11992, NA12003, NA18944, NA19205, NA10838, NA18852, NA11993, NA19160, NA12248, NA18571, NA18611, NA11829, NA12236, NA19130, NA19171, NA19240, NA12717, NA18532, NA18853, NA19204, NA18981, NA06994, NA18913, NA19092, NA18555, NA19200, NA19007, NA19202, NA07000, NA18980, NA10854, NA10861, NA19142, NA19137, NA10831
Known GenesADAM18, ADAM3A, ADAM5, LOC100130964
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)esv2759608
Frequency
Sample Size270
Observed Gain169
Observed Loss92
Observed Complex0
Frequencyn/a


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