Variant DetailsVariant: nssv1437828 | Internal ID | 16078568 | | Landmark | | | Location Information | | | Cytoband | 17q25.3 | | Allele length | | Assembly | Allele length | | hg38 | 1077447 | | hg19 | 1070677 | | hg18 | 1066487 |
| | Variant Type | CNV loss | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | S | | Merged Variants | nsv828128 | | Supporting Variants | | | Samples | NA18949 | | Known Genes | AATK, AATK-AS1, ACTG1, ARL16, AZI1, BAHCC1, BAIAP2, BAIAP2-AS1, C17orf70, C17orf89, CCDC137, CHMP6, ENTHD2, FSCN2, HGS, LINC00482, LOC100130370, MIR1250, MIR3065, MIR3186, MIR338, MIR4740, MIR657, MIR6786, MRPL12, NPLOC4, OXLD1, PDE6G, RPTOR, SLC25A10, SLC38A10, TMEM105, TSPAN10 | | 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) | nssv1437828
| | Frequency | | Sample Size | 31 | | Observed Gain | 0 | | Observed Loss | 1 | | Observed Complex | 0 | | Frequency | n/a |
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