A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv1441239



Internal ID16080388
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:135892081..136495763hg38UCSC Ensembl
Innerchr9:138783927..139390215hg19UCSC Ensembl
Innerchr9:137923748..138510036hg18UCSC Ensembl
Cytoband9q34.3
Allele length
AssemblyAllele length
hg38603683
hg19606289
hg18586289
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv825173
Supporting Variants
SamplesNA18969
Known GenesC9orf163, C9orf69, CAMSAP1, CARD9, DKFZP434A062, DNLZ, GPSM1, INPP5E, LHX3, NACC2, NOTCH1, PMPCA, QSOX2, SDCCAG3, SEC16A, SNAPC4, UBAC1
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)nssv1441239
Frequency
Sample Size31
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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