A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv514125



Internal ID6085142
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:234649197..234657965hg19UCSC Ensembl
Innerchr2:234313936..234322704hg18UCSC Ensembl
Cytoband2q37.1
Allele length
AssemblyAllele length
hg19n/a
hg18n/a
Variant TypeCNV Loss
Copy Number
Allele State
Allele OriginNot tested
Probe Count
Merged StatusS
Merged Variants
Supporting Variantsnssv627452
Samples
Known GenesDNAJB3, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9
Method
AnalysisGenotype copy number polymorphisms in known CNP loci. We applied the Agilent ADM2 algorithm to identify potential CNPs in the targeted sites. Boundaries were manually refined. Copy numbers are assigned to each set of sample classes for each interval by simultaneously fitting integer copy number values to the test sample classes and the reference sample using the median signals, log ratios and the estimate of the single copy signal intensity. For potential CNPs that could not be fitted to discrete copy numbers, we use the single channel intensity data to estimate the copy number of the reference sample and the test samples. ADM2 threshold = 5
PlatformAgilent Eichler Human CNP 180K v3.0 + Agilent Eichler Human CNP 180K v2.1
Comments
ReferenceCampbell et al 2011
Pubmed ID21397061
Accession Number(s)nsv514125
Frequency
Sample Size1414
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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