Methodology and software to detect viral integration site hot-spots

BMC Bioinformatics

Table 1 Descriptions of human lentivirus (LV) and murine leukemia virus (MLV) vector integration site (VIS) data sets.

Data set Name	Study	#	Type	# VIS	Time points	Cell Type
H-LV-XALD	X-Linked ALD [8]	2	LV	2401	6-24 m	CD:34,15,3,14,16,19,56, LM
H-LV-Patient1	X-Linked ALD [8]	1	LV	1627	6-24 m	CD:34,15,3,14,16,19,56, LM
H-LV-Patient2	X-Linked ALD [8]	1	LV	774	6-20 m	CD:34,15,3,14,16,19
H-LV-acute	X-Linked ALD [8]	pre	LV	922	--	CD34
H-MLV-XCGD	CGD [9]	2	MLV	384	1-45 m	CD:3,14,15,19; PB, BM, G
H-MLV-XSCID	SCIDX1 [6, 7]	14	MLV	864	4-41 m	CD:3,13,14,19; PBL, PBMC
--	SCIDX1 [6]	5	MLV	303	9-30 m	CD:3, 13
--	SCIDX1 [7]	9	MLV	561	4-41 m	CD:3,14,19; PBL, PBMC
H-MLV-acute	GFP [20]	pre	MLV	1398	1-12 days PT	CD34

The seven data sets analyzed here originated from five LV and MLV studies. Column one indicates the data set name given in this paper, and the 'Study' column indicates the parent study where X-linked ALD (adrenoleukodystrophy), CGD (chronic granulomatous disease) and SCIDX1 (X-linked severe combined immunodeficiency) refer to human clinical trials, and GFP (green fluorescent protein) indicates a control vector study. The H-MLV-XSCID data set was derived from two different studies [6, 7] as indicated. The '#' column indicates the number of subjects analyzed; 'Type' refers to vector type, LV or MLV; '# VIS' indicates the number of unique vector integration sites; 'Time points' indicates the number of time points from which samples were obtained; and 'Cell Type' indicates the cells from which VIS were derived. LAM sequencing was used exclusively in all studies except the GFP study which used an LM/LAM combination.

ISSN: 1471-2105