A curated catalogue of human genomic structural variation

Variant Details

Variant: nsv829420

Internal ID16091894
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:155563604..155567654hg38UCSC Ensembl
InnerchrX:154793265..154797315hg19UCSC Ensembl
InnerchrX:154446459..154450509hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv1437474, nssv1423916
SamplesNA18592, NA18547
Known GenesTMLHE
MethodOligo aCGH
AnalysisTo select parameters for calling CNVs (that is, the statistical threshold of the ADM2 algorithm, the minimum +/- log2 ratio and the minimum number of consecutive probes in a CNV interval), we calculated the sensitivity and positive predictive value based on the comparison of aCGH-based CNV calls (using our high-resolution Agilent 24M platform) with read-depth sequence data for two samples from Korean individuals (AK1 and AK2). We attempted to obtain `absolute' copy number status of the sample from NA10851, which was used as the reference sample for aCGH experiments in this study. For this, we used read-depth data for NA10851 obtained from massively parallel sequencing by the Illumina GA II data. The read-depth data represent the copy number status of NA10851 as compared to the human reference genome (hg18) because the short read sequences were aligned to hg18.
PlatformAgilent 24M aCGH
Pubmed ID20364138
Accession Number(s)nsv829420
Sample Size31
Observed Gain0
Observed Loss2
Observed Complex0

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