Comparison of in vivo and ex vivo lentiviral vector integration sites to the integration sites from control infections of Jurkat cells—analysis of proximity to genomic features. (a) Chromosomal distribution of integration sites in the ex vivo sample, the patient-derived sample, and the control infections of Jurkat cells. Random integration would correspond to the line at one. Favored integration is indicated by the bars above the line, disfavored by the bars below. Only every other chromosome is numbered. The right-most chromosome is Y. (b) Frequency of integration in RefGenes. (c) Frequency of integration in Giemsa dark and light bands. The Giemsa dark regions (left side) are higher in gene density. (d) Integration frequency in gene rich regions (scored over 8-Mb intervals surrounding integration sites). (e) Integration frequency in regions of differing transcriptional intensity (scored over 8-Mb intervals surrounding integration sites). The transcriptional intensity measure is similar to the gene density measure, but only genes scored as active using Affymetrix microarrays are counted. (f) Integration frequency in regions of differing CpG island density (scored over 8-Mb intervals surrounding integration sites). (g) Frequency of integration near proto-oncogene 5′-ends. Random integration would have bar heights of one on the y-axis.