Methodology and software to detect viral integration site hot-spots

BMC Bioinformatics

Table 2 Hot-spot summaries for human LV and MLV data sets using the BCP and CIS hot-spot definitions.

		# Hot-Spots		% VIS in HS		% Coverage		Size (Mb)		% Density*
Data Set	Total VIS	BCP	CIS	BCP	CIS	BCP	CIS	BCP	CIS	BCP	CIS
H-LV-acute	922	3	11	2.93	5.1	0.101	0.02	1.045	0.055	0.93	8.98
H-LV-XALD	2401	5	110	6.21	22.7	0.213	0.246	1.316	0.069	0.86	2.95
H-LV-Patient1	1627	6	56	7.74	15.86	0.251	0.119	1.291	0.066	0.96	4.69
H-LV-Patient2	774	6	12	5.56	5.81	0.17	0.018	0.874	0.047	1.04	10.07
H-MLV-acute	1398	0	15	0	3.93	0	0.017	0	0.035	0	7.29
H-MLV-XCGD	384	2	3	16.93	16.67	0.037	0.009	0.564	0.09	165.32	228.5
H-MLV-SCIDX1	864	7	22	5.9	11	0.045	0.029	0.197	0.041	4.02	13.82

Relative to the CIS method, the BCP hot-spot definition identified fewer hot-spots containing a smaller percentage of VIS for all data sets. It also gave the most consistent results across the full X-linked ALD data set, and patients 1 and 2. The % VIS in hot-spots (HS) ranged from 5.56% to 7.74% for the BCP method and 5.81% to 22.7% using the CIS hot-spot definition. The CIS definition found similar hot-spot numbers and % VIS in hot-spots for the acute infection data set and post-transplant data for patient 2. Both the BCP and CIS methods indicate differences in hot-spot patterns between the LV and MLV data sets. In particular, the CGD study data had very few hot-spots with high VIS densities. % Density was calculated as (Median # VIS per HS/# Total VIS)*100/Mb. Data set names are as in Table 1.

ISSN: 1471-2105