Variant DetailsVariant: nsv822072 | Internal ID | 16084546 | | Landmark | | | Location Information | | | Cytoband | 3p21.31 | | Allele length | | Assembly | Allele length | | hg38 | 2162 | | hg19 | 2162 | | hg18 | 2162 |
| | Variant Type | CNV loss | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | M | | Merged Variants | dgv805n67 | | Supporting Variants | nssv1431206, nssv1424091, nssv1421423, nssv1428159, nssv1427398, nssv1432729, nssv1425287, nssv1424874, nssv1426538, nssv1436484, nssv1438061, nssv1421593, nssv1440256, nssv1423271, nssv1438896, nssv1430473, nssv1437347, nssv1435770, nssv1429691 | | Samples | AK2, NA18947, AK16, NA18592, NA18999, AK10, AK6, NA18547, NA18582, NA18949, AK14, AK8, NA18951, NA18566, NA18542, NA18564, AK18, NA18972, NA18997 | | Known Genes | SCAP | | 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) | nsv822072
| | Frequency | | Sample Size | 31 | | Observed Gain | 0 | | Observed Loss | 19 | | Observed Complex | 0 | | Frequency | n/a |
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