Skip to main content

Table 1 Barnacle predictions in AML datasets A08823 and A08878

From: Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

  Type Gene(s) Exon(s)1 Read support2 Pred. in Val.3 Relative Coverage4
1 fusion PML/RARA e3/e3 192 A08823 WGS 27.8%/40.0%
2 fusion RARA/PML e2/e4 276 A08823 WGS 33.1%/33.2%
3 fusion TMEM14B/TMEM14C 3′-utr/3′-utr 110 A08823 Failed MI 18.8%/9.8%
4 PTD MLL e3-e6 80 A08878 WGS 28.2%
5 PTD SEC62 e3-e7 40 / 69 both No WGS, RT-PCR 5.0%/8.2%5
6 ITD ACADVL e1 236 A08823 WGS 27.7%
7 ITD ACIN1 e6 259 / 655 both WGS 61.9%/80.4%5
8 ITD AKAP2 e2 61 A08878 WGS 33.6%
9 ITD DNHD1 e21 76 A08878 WGS 99.1%
10 ITD FLT36 e14 268 A08823 WGS 21.8%
11 ITD FLT36 e14 950 A08878 WGS 19.6%
12 ITD FOXP1 3′-utr 64 A08878 WGS 19.6%
13 ITD HSPBP1 e3 56 A08878 WGS 17.8%
14 ITD KIAA1211 e8 44 A08823 WGS 51.3%
15 ITD MRPS34 e1,i1 52 A08823 WGS 40.5%
16 ITD PIEZO1 e32 620 A08878 WGS 57.0%
17 ITD SND1 e1 370 A08823 WGS 9.3%
18 ITD SSPO e74 35 A08878 WGS 40.3%
  1. 1 Exon numbers are from hg19 UCSC gene annotations.
  2. 2 For the two chimeras predicted in both datasets, read support is presented as A08823 support / A08878 support.
  3. 3 Validation. WGS: validated via whole-genome shotgun sequencing. RT-PCR: validated via RT-PCR. Failed MI: failed manual inspection.
  4. 4 Relative coverage is presented as the local coverage attributable to the chimera, as a percent of the total local coverage (see Stage 5). For fusions, relative coverage with each parental gene is ordered as in Gene(s) column.
  5. 5 Relative coverage is presented as A08823 relative coverage / A08878 relative coverage.
  6. 6 The FLT3 duplications predicted in A08823 and A08878 have different sequences.