Variant DetailsVariant: dgv2n67 | Internal ID | 20146514 | | Landmark | | | Location Information | | | Cytoband | 1p36.33 | | Allele length | | Assembly | Allele length | | hg38 | 548883 | | hg19 | 548883 | | hg18 | 548883 |
| | Variant Type | CNV gain | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | M | | Merged Variants | | | Supporting Variants | nsv826141, nsv825030 | | Samples | NA18969, NA18968 | | Known Genes | ACAP3, AGRN, ANKRD65, AURKAIP1, B3GALT6, C1orf159, C1orf170, CCNL2, CPSF3L, DVL1, FAM132A, GLTPD1, HES4, ISG15, KLHL17, LOC100130417, LOC148413, LOC254099, MIR200A, MIR200B, MIR429, MIR6726, MIR6727, MIR6808, MRPL20, MXRA8, NOC2L, PLEKHN1, PUSL1, RNF223, SAMD11, SCNN1D, SDF4, TAS1R3, TMEM88B, TNFRSF18, TNFRSF4, TTLL10, UBE2J2 | | 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) | dgv2n67
| | Frequency | | Sample Size | 31 | | Observed Gain | 2 | | Observed Loss | 0 | | Observed Complex | 0 | | Frequency | n/a |
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