Table 3.
Comparison of various algorithms on the 188× coverage breast cancer genome
| Sample PD4120a | |||
|---|---|---|---|
| Algorithm | % normal admixture | Clonal (% tumor purity)a | Subclonal (%)a |
| THetA, n = 2 | 34.3% | Del: 1p, 4q, 13, 16q, 22q | - |
| (segmentation) | +1: 1q | ||
| (65.7%) | |||
| THetA, n = 2 (chromosome arms) | 38.3% | Del: 1p, 4q, 13, 16q, 22q | - |
| +1: 1q | |||
| (61.7%) | |||
| CNAnormb (chromosome arms) |
32.8% | Del: 1p, 4q, 13, 16q, 22q | - |
| +1: 1q | |||
| (67.2%) | |||
| ASCATc | 34% | Del: 1p, 4q, 13, 16q, 22q | - |
| (virtual SNP array) | +1: 1q, 17q, 18, 19, 20 | ||
| (66.0%) | |||
| ABSOLUTEd (segmentation) | 35% | (65.0%) | - |
| THetA | 28.0% | Del: 1p, 4q, 16q, 22q12.2- | Del: 13, 22q11.2-12.1 |
| n = 3 | 13.3 | +1: 1q | |
| (72.0%) | (61.9%) | ||
| Del: 8, 11, 12, 14, 15 | |||
| (10.1%) | |||
|
Del: 2, 7, 4p, 6, 9, 18, 21 |
|||
| Nik-Zainal et al. (2012) | 30% | Del: 4q | Del: 13, t(1;22) |
| [25] | +1: 1q | (47.6%) | |
| (70.0%) | Tetraploid with: | ||
| Del(-2): 2, 7 | |||
| Del(-1): 6, 8, 9, 11, 12, | |||
| 14, 15, 18, 21 | |||
| (9.8%) | |||
a Entries in bold are differences between THetA and [25]. Entries in italics were not input to the n = 3 THetA analysis but were inferred using THetA's output.
b When CNAnorm was run using BIC-Seq intervals the normal admixture was estimated at 6.7%, therefore we report results from CNAnorm using chromosome arms. CNAnorm does not return integer copy numbers - and thus we report aberrations where the returned copy number was within 0.15 of the nearest integer, other aberrations were considered inconclusive.
c For ASCAT we use virtual SNP array data as input. ASCAT performs its own segmentation; we list only the large aberrations.
d We report here the maximum likelihood solution returned by ABSOLUTE when considering only karyotypes. When considering only somatic copy number aberrations or a combination, ABSOLUTE infers a tetraploid solution. For this sample, ABSOLUTE returns copy numbers for only a subset of the input intervals, so we do not report specific copy number aberrations predicted.