Towards accurate characterization of clonal heterogeneity based on structural variation

BMC Bioinformatics

Table 1 Novel sub-clonal somatic structural variants detected by BreakDown

SAMPLE	CHR1	POS1	CHR2	POS2	TYPE	Size(bp)	GENE	EST_VAF
PD4120	10	117351105	10	117352856	Deletion	1751	ATRNL1	0.12
PD4120	5	86223184	5	86225988	Deletion	2804		0.38
PD4120	14	51889637	14	51896099	Deletion	6462		0.39
PD4120	22	19372768	22	21122617	Translocation	N/A	HIRA, PI4KA	0.055
PD4115	1	10151402	1	10152851	Deletion	1449	UBE4B	0.296
PD4115	9	108351356	9	108352767	Deletion	1411	FKTN	0.285
PD4115	9	140773612	9	140777195	Deletion	3583	CACNA1B	0.400
PD4115	X	73061886	X	73067477	Deletion	5591	XIST	0.394
PD4088	10	60908547	10	60920370	Inversion	11823		0.594

Listed are the novel somatic structural variants in the breast cancer sample PD4120, PD4115 and PD4088 along with BreakDown estimated VAFs (column 9). Also shown (column 8) are the genes overlapping with either deletion loci or translocation breakpoints.

ISSN: 1471-2105