A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758636



Internal ID9634095
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:21293950..21937801hg38UCSC Ensembl
Innerchr16:21305271..21949122hg19UCSC Ensembl
Innerchr16:21212772..21856623hg18UCSC Ensembl
Innerchr16:21212772..21856623hg17UCSC Ensembl
Cytoband16p12.1
Allele length
AssemblyAllele length
hg38643852
hg19643852
hg18643852
hg17643852
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756813, esv2758414
SamplesNA18503, NA19142, NA10831, NA19127, NA19194, NA12802, NA07056, NA18966, NA19173, NA12752, NA18501, NA18500, NA10839, NA19223, NA18545, NA18948, NA12813, NA18517, NA18573, NA12005, NA19144, NA18949, NA19161, NA18912, NA18624, NA18508, NA11840, NA18854, NA18635, NA10846, NA12864, NA07357, NA18623, NA12814, NA18636, NA07048, NA18609, NA18976, NA18637, NA19100, NA12144, NA12006, NA19000, NA19129, NA19094, NA06985, NA19206, NA18558, NA19098, NA19154, NA12057, NA19159, NA18974, NA18945, NA18552, NA19138, NA10860, NA19101, NA06991, NA19128, NA18971, NA19132, NA10830, NA19099, NA19205, NA11993, NA18571, NA11829, NA19171, NA12874, NA19204, NA06994, NA18913, NA12760, NA19202, NA07000
Known GenesCRYM, CRYM-AS1, IGSF6, LOC100190986, LOC100271836, METTL9, NPIPB3, OTOA, RRN3P1, SLC7A5P2, SNX29P1
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)esv2758636
Frequency
Sample Size270
Observed Gain70
Observed Loss6
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer