A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv1231n67



Internal ID20147743
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr9:112470443..112532456hg38UCSC Ensembl
chr9:115232723..115294736hg19UCSC Ensembl
chr9:114272544..114334557hg18UCSC Ensembl
Cytoband9q32
Allele length
AssemblyAllele length
hg3862014
hg1962014
hg1862014
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv825047, nsv825048
SamplesNA18542, NA18973
Known GenesHSDL2, KIAA1958
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)dgv1231n67
Frequency
Sample Size31
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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