Skip to main content

Table 3 Comparison of various algorithms on the 188× coverage breast cancer genome

From: THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

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%)
  1. 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.
  2. 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.
  3. c For ASCAT we use virtual SNP array data as input. ASCAT performs its own segmentation; we list only the large aberrations.
  4. 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.