Variant DetailsVariant: nsv822720 Internal ID | 16085194 | Landmark | | Location Information | | Cytoband | 1p32.3 | Allele length | Assembly | Allele length | hg38 | 3646 | hg19 | 3646 | hg18 | 3646 |
| Variant Type | CNV loss | Copy Number | | Allele State | | Allele Origin | | Probe Count | | Validation Flag | | Merged Status | M | Merged Variants | | Supporting Variants | nssv1437936, nssv1429560, nssv1427254, nssv1438586, nssv1431069, nssv1423115, nssv1437607, nssv1423958, nssv1436337, nssv1426389, nssv1439457, nssv1421451, nssv1434167, nssv1440810, nssv1432097, nssv1424736, nssv1435653, nssv1428023, nssv1425494, nssv1428824, nssv1440406, nssv1430343, nssv1437222, nssv1423485, nssv1422370, nssv1424053, nssv1433417, nssv1440122, nssv1434865, nssv1431811 | Samples | AK2, NA18947, AK16, NA18592, AK20, NA18999, NA18526, NA18969, AK10, AK6, NA18547, NA18942, NA18582, NA18949, AK14, AK8, NA18973, NA18951, NA18537, NA18566, NA18570, NA18542, NA18564, AK18, AK12, AK4, NA18972, NA18552, NA18968, NA18997 | Known Genes | ACOT11 | 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) | nsv822720
| Frequency | Sample Size | 31 | Observed Gain | 0 | Observed Loss | 30 | Observed Complex | 0 | Frequency | n/a |
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