Variant DetailsVariant: nsv825478 Internal ID | 16087952 | Landmark | | Location Information | | Cytoband | 10q22.3 | Allele length | Assembly | Allele length | hg38 | 2710 | hg19 | 2710 | hg18 | 2710 |
| Variant Type | CNV loss | Copy Number | | Allele State | | Allele Origin | | Probe Count | | Validation Flag | | Merged Status | M | Merged Variants | dgv164n67 | Supporting Variants | nssv1427684, nssv1440524, nssv1426895, nssv1428492, nssv1422792, nssv1433848, nssv1436867, nssv1431503, nssv1439069, nssv1433036, nssv1429258, nssv1437628, nssv1436040, nssv1438318 | Samples | NA18526, AK10, AK6, NA18949, AK8, NA18973, NA18951, NA18566, NA18542, NA18564, AK18, AK12, NA18972, NA18552 | Known Genes | C10orf11 | 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) | nsv825478
| Frequency | Sample Size | 31 | Observed Gain | 0 | Observed Loss | 14 | Observed Complex | 0 | Frequency | n/a |
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