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

From: Methodology and software to detect viral integration site hot-spots

   # 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
  1. 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.