Methodology and software to detect viral integration site hot-spots

BMC Bioinformatics

Table 3 BCP hot-spots for the LV acute infection, full X-linked ALD, and patient 1 and 2 data sets.

Data set	# VIS	Chr	Location (Mb)	# VIS (%)	Size (Mb)	% Density
H-LV-acute	922	Chr 11	65.020-65.721	12 (1.30%)	0.7	1.86
H-LV-acute	922	Chr 16	0.425-1.929	7 (0.76%)	1.5	0.51
H-LV-acute	922	Chr 17	77.185-78.117	8 (0.87%)	0.93	0.93
Median	-	-	-	8 (0.87%)	0.93	0.93
H-LV-XALD	2401	Chr 6	31.967-33.000	35 (1.46%)	1.03	1.41
H-LV-XALD	2401	Chr 11	64.005-66.969	61 (2.54%)	2.96	0.86
H-LV-XALD	2401	Chr 12	6.085-6.993	16 (0.67%)	0.91	0.73
H-LV-XALD	2401	Chr 17	2.000-2.522	17 (0.71%)	0.52	1.36
H-LV-XALD	2401	Chr 17	73.098-74.252	20 (0.83%)	1.15	0.72
Median	-	-	-	20 (0.83%)	1.03	0.86
H-Patient1	1627	Chr 6	31.967-33.000	25 (1.54%)	1.03	1.49
H-Patient1	1627	Chr 11	64.019-66.969	47 (2.89%)	2.95	0.98
H-Patient1	1627	Chr 12	6.085-6.993	14 (0.86%)	0.91	0.95
H-Patient1	1627	Chr 17	73.098-74.252	15 (0.92%)	1.15	0.8
H-Patient1	1627	Chr 17	77.093-77.863	13 (0.8%)	0.77	1.04
H-Patient1	1627	Chr 19	53.882-54.813	12 (0.74%)	0.93	0.79
Median	-	-	-	14.5 (0.89%)	0.98	0.965
H-Patient2	774	Chr 1	2.038-2.954	6 (0.78%)	0.92	0.85
H-Patient2	774	Chr 3	47.057-47.926	6 (0.78%)	0.87	0.89
H-Patient2	774	Chr 6	31.867-32.976	11 (1.42%)	1.11	1.28
H-Patient2	774	Chr 16	0.592-1.838	7 (0.9%)	1.25	0.73
H-Patient2	774	Chr 17	2.000-2.452	7 (0.9%)	0.45	2
H-Patient2	774	Chr 17	76.215-76.864	6 (0.78%)	0.65	1.19
Median	-	-	-	6.5 (0.84%)	0.89	1.04

Five hot-spots were identified by the BCP method for the post infection X-linked ALD data set, ranging in size from 0.52-2.96 Mb with a median density of 0.86% total VIS/Mb. When the ALD study patients were analyzed separately, six hot-spots were observed for each patient with similar sizes and densities. Patient 1 had four hot-spots that overlapped with the full X-linked ALD data set on chromosomes (Chr) 6, 11, 12 and 17; as well as two additional hot-spots on Chr 17 and 19. Patient 2 had two hot-spots that overlapped with the full data set on Chr 6 and 17, as well as four additional hot-spots on Chr 1, 3, 16 and 17. In comparison, the acute infection data with three hot-spots had one overlap with the full ALD data set on Chr 11, a unique hot-spot on Chr 16, and a hot-spot on Chr 17 that overlapped with Patient 1's Chr 17 hot-spot. % Density was calculated as (# VIS per HS/# Total VIS)*100/Mb. Data set names are as in Table 1.

ISSN: 1471-2105