Table 4 Comparison of the performances of DeviCNV and previous tools using cell lines with known CNVs
Sample | Known CNV | DeviCNV | VisCap | XHMM | CODEX | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Panel | Cell line | Median read depth | Gene | NM | CNV | CNV size (kb) | Find?a | #CNVb | Find? | #CNV | Find? | #CNV | Find? | #CNV |
IMD_HYB | GM14603 | 81.99 | GAA | NM_000152 | EX18 DEL | 0.16 | O | 24 | X | 7 | X | 0 | X | 56 |
GM14734 | 249.4 | CYP21A2 | NM_000500 | 30 KB DEL, Entire gene DEL | 3.35 | O | 2 | O | 37 | O | 1 | X | 2 | |
GM24007 | 142.84 | OTC | NM_000531 | Entire gene DEL | 68.97 | O | 7 | O | 14 | O | 3 | O | 46 | |
NA01741 | 164.4 | GALT | NM_000155 | Entire gene DEL | 4.01 | O | 6 | O | 40 | O | 1 | O | 37 | |
NA06804 | 261.98 | HPRT1 | NM_000194 | EX2–3 DUP | 2.01 | O | 34 | O | 43 | X | 2 | O | 62 | |
NA06805 | 80.13 | GALC | NM_000153 | EX11–17 DEL | 17.73 | O | 44 | O | 8 | O | 1 | O | 86 | |
NA12217 | 269.08 | CYP21A2 | NM_000500 | 30 KB DEL | 1.14 | X | 1 | X | 7 | X | 3 | X | 11 | |
NA22208 | 199.64 | PCCA | NM_000282 | EX13–20 DEL | 146.38 | O | 3 | O | 17 | O | 2 | O | 15 | |
IMD_PCR | NA01741 | Pool 1: 408.0, Pool 2: 556.0, Pool 3: 271.0 | GALT | NM_000155 | Entire gene DEL | 4.01 | O | 10 | O | 9 | X | 0 | O | 1 |
NA12217 | Pool 1: 192.0, Pool 2: 117.0, Pool 3: 99.0 | CYP21A2 | NM_000500 | 30 KB DEL | 1.14 | X | 37 | X | 22 | X | 8 | X | 71 | |
GM14603 | Pool 1: 215.0, Pool 2: 141.0, Pool 3: 90.0 | GAA | NM_000152 | EX18 DEL | 0.16 | O | 25 | X | 32 | O | 6 | O | 40 | |
NA14734 | Pool 1: 359.0, Pool 2: 275.0, Pool 3: 335.0 | CYP21A2 | NM_000500 | 30 KB DEL, Entire gene DEL | 3.35 | O | 9 | O | 12 | O | 4 | X | 12 | |
NA22208 | Pool 1: 235.0, Pool 2: 99.0, Pool 3: 158.0 | PCCA | NM_000282 | EX13–20 DEL | 146.38 | O | 27 | X | 13 | O | 4 | O | 12 | |
GM24007 | Pool 1: 37.0, Pool 2: 20.0, Pool 3: 16.0 | OTC | NM_000531 | Entire gene DEL | 68.97 | X | 1 | X | 23 | X | 0 | X | 0 | |