Table 3.

Characteristics of VAFs before and after ABRA2 for FLT3 Internal Tandem Duplications (Single Clone)

Found by	Case	Sample type	Gene	Size of insertion (NGS)	∼Size of insertion (CE)	% Mismaps	% Mismaps fixed by ABRA2	VC VAF, %	Manual calculation of			CE VAF, %	Absolute difference between
									(1) Before ABRA2 VAF, %	(2) After ABRA2 VAF, %	(3) True NGS VAF, %		Before and after ABRA2 VAF (2) – (1), %	After ABRA2 VAF and true NGS VAF (3) – (2), %	Before ABRA2 VAF and true NGS VAF (3) – (1), %
BWA, VC, and CE	27	BM	FLT3	6	6	28.7	100	9.0	10.2	14.4	14.4	13.6	4.1	0	4.1
	28	PB	FLT3	15	14	63.7	100	13.9	16.3	44.9	44.9	45.2	28.6	0	28.6
	29	PB	FLT3	21	20	87.8	72.0	10.4	11.7	72.4	96.1	89.8	60.7	23.7	84.4
	30	PB	FLT3	21	19	89.1	75.6	5.7	7.7	55.2	70.5	71.0	47.5	15.3	62.8
	31	BM	FLT3	21	20	86.5	73.3	20.8	2.5	14.1	18.3	16.4	11.6	4.2	15.8
BWA and CE	32	PB	FLT3	6	7	31.0	100	ND	4.8	6.9	6.9	9.0	2.1	0	2.1
VC and CE	33	BM	FLT3	27	25	100	98.9	29.7	0	28.1	28.5	28.2	28.1	0.4	28.5
	34	BM	FLT3	30	28	100	100	27.0	0	24.6	24.6	23.6	24.6	0	24.6
	35	PB	FLT3	33	31	100	98.8	21.9	0	20.9	21.2	21.7	20.9	0.3	21.2
	36	BM	FLT3	39	37	100	98.7	14.6	0	19.2	19.5	14.7	19.2	0.3	19.5
	46	BM	FLT3	57	55	100	98.9	42.3	0	37.9	38.3	37.5	37.9	0.4	38.3
	37	BM	FLT3	63	60	100	41.2	48.0	0	15.4	37.3	35.0	15.4	21.9	37.3
CE	38	BM	FLT3	39	37	100	96.6	ND	0	9.8	10.1	9.4	9.8	0.3	10.1
	39	BM	FLT3	69	66	100	100	ND	0	33.2	33.2	30.0	33.2	0	33.2
	40	BM	FLT3	72	69	100	100	ND	0	32.0	32.0	26.5	32.0	0	32.0
	41	PB	FLT3	84	82	100	99.2	ND	0	15.1	15.3	12.4	15.1	0.2	15.3
	42	BM	FLT3	87	84	100	99.0	ND	0	12.1	12.2	9.3	12.1	0.1	12.2

VC VAF % calculated by the VC before the use of ABRA2; (1), (2), and (3): manually calculated from visualizing reads in Integrative Genomics Viewer.

ABRA2, Assembly-Based ReAligner; BM, bone marrow; BWA, Burrows-Wheeler Aligner; CE, capillary electrophoresis; FLT3, fms-related receptor tyrosine kinase 3; ND, not detected; NGS, next-generation sequencing; PB, peripheral blood; VAF, variant allele frequency; VC, variant caller.