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

BMC Genomics

Table 1 Barnacle predictions in AML datasets A08823 and A08878

	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 Exon numbers are from hg19 UCSC gene annotations.
² For the two chimeras predicted in both datasets, read support is presented as A08823 support / A08878 support.
³ Validation. WGS: validated via whole-genome shotgun sequencing. RT-PCR: validated via RT-PCR. Failed MI: failed manual inspection.
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 Relative coverage is presented as A08823 relative coverage / A08878 relative coverage.
⁶ The FLT3 duplications predicted in A08823 and A08878 have different sequences.

ISSN: 1471-2164