A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv823469



Internal ID16085943
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29847053..29955498hg38UCSC Ensembl
Innerchr6:29814830..29923275hg19UCSC Ensembl
Innerchr6:29922809..30031254hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg38108446
hg19108446
hg18108446
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv1433673, nssv1428305, nssv1441087, nssv1437465, nssv1438861, nssv1421740, nssv1423431, nssv1435113, nssv1426743, nssv1432919, nssv1424242
SamplesNA18947, NA18592, NA18999, NA18526, NA18969, AK10, NA18942, NA18582, NA18949, NA18973, NA18997
Known GenesHCG4B, HLA-A, HLA-H
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
Comments
ReferencePark_et_al_2010
Pubmed ID20364138
Accession Number(s)nsv823469
Frequency
Sample Size31
Observed Gain0
Observed Loss11
Observed Complex0
Frequencyn/a


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