Variant DetailsVariant: nsv824940 Internal ID | 16087414 | Landmark | | Location Information | | Cytoband | 9q21.11 | Allele length | Assembly | Allele length | hg38 | 5245 | hg19 | 5245 | hg18 | 5245 |
| Variant Type | CNV loss | Copy Number | | Allele State | | Allele Origin | | Probe Count | | Validation Flag | | Merged Status | M | Merged Variants | | Supporting Variants | nssv1432226, nssv1434555, nssv1426852, nssv1425924, nssv1421974, nssv1436816, nssv1423577, nssv1440488, nssv1438291, nssv1429224, nssv1427829, nssv1422754, nssv1428175, nssv1421877, nssv1427647, nssv1439817, nssv1429970 | Samples | NA18947, AK20, NA18999, AK6, NA18547, AK14, AK8, NA18951, NA18537, NA18570, NA18542, NA18564, AK12, AK4, NA18552, NA18968, NA18997 | Known Genes | TJP2 | 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) | nsv824940
| Frequency | Sample Size | 31 | Observed Gain | 0 | Observed Loss | 17 | Observed Complex | 0 | Frequency | n/a |
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