Detection of recurrent rearrangement breakpoints from copy number data

BMC Bioinformatics

Table 2 Predicted Recurrent Breakpoints in 227 GBM Samples and 107 Blood Samples.

Breakpoint Type	Rearrangement Type(s)	# Predicted	# in DGV	# in Blood	# Novel
Recurrent Probes in Tumor	Highly Conserved Breakpoints	538	343	13	189
Recurrent Genes in Tumor	Gene Truncations	92	69	23	23
Pairs of Recurrent Probe in Blood*	Germline Structural Variants	88	53	N/A	35
Pairs of Recurrent Genes in Tumor w/Fusion Gene Config. **	Intrachromosomal Fusion Genes	75	45	5	7
	Interchromosomal Fusion Genes	396	316	53	26

Columns are described in Table 1, except for '# in Blood' which indicates the number of predictions that also appear in the blood samples and are ignored as somatic predictions.
* FDR is increased to < 0.1 for blood samples.
** Novel pairs of recurrent gene breakpoints consistent with the fusion gene configuration.

ISSN: 1471-2105