Variant DetailsVariant: nsv827709 | Internal ID | 16090183 | | Landmark | | | Location Information | | | Cytoband | 1q44 | | Allele length | | Assembly | Allele length | | hg38 | 7027 | | hg19 | 7027 | | hg18 | 7027 |
| | Variant Type | CNV loss | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | M | | Merged Variants | dgv114n67 | | Supporting Variants | nssv1431134, nssv1434231 | | Samples | NA18570, AK18 | | Known Genes | SMYD3 | | Method | Oligo aCGH | | Analysis | To 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. | | Platform | Agilent 24M aCGH | | Comments | | | Reference | Park_et_al_2010 | | Pubmed ID | 20364138 | | Accession Number(s) | nsv827709
| | Frequency | | Sample Size | 31 | | Observed Gain | 0 | | Observed Loss | 2 | | Observed Complex | 0 | | Frequency | n/a |
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