Variant DetailsVariant: nsv826837 Internal ID | 16089311 | Landmark | | Location Information | | Cytoband | 13q34 | Allele length | Assembly | Allele length | hg38 | 32887 | hg19 | 32887 | hg18 | 32887 |
| Variant Type | CNV loss | Copy Number | | Allele State | | Allele Origin | | Probe Count | | Validation Flag | | Merged Status | M | Merged Variants | | Supporting Variants | nssv1428620, nssv1433160, nssv1441468, nssv1427813, nssv1429396, nssv1430893, nssv1422134, nssv1426098, nssv1429376, nssv1435741, nssv1427028, nssv1435388, nssv1423728, nssv1437734, nssv1439948, nssv1440627, nssv1439255, nssv1432388 | Samples | AK16, NA18592, AK20, NA18999, NA18969, AK10, AK6, NA18942, NA18949, AK8, NA18973, NA18537, NA18564, AK12, AK4, NA18972, NA18968, NA18997 | Known Genes | GAS6, GAS6-AS1, TMEM255B | 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) | nsv826837
| Frequency | Sample Size | 31 | Observed Gain | 0 | Observed Loss | 18 | Observed Complex | 0 | Frequency | n/a |
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