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. Author manuscript; available in PMC: 2023 Dec 2.
Published in final edited form as: Cancer Res. 2023 Jun 2;83(11):1768–1781. doi: 10.1158/0008-5472.CAN-22-3030

Figure 4. Structure of the SNU-1245 integration locus and HPV expression.

Figure 4.

A. A diagram of a region of chromosome 1q24.2 is shown divided into six segments (a-f). Above the diagram are copy number values normalized to segments a and f. B. A contig supported by multiple long reads obtained from ONT WGS, CRISPR targeted sequencing, and adaptive sampling is shown. The two human regions are rearranged, consistent with integration at 209,411,668 bp and looping back to 209,359,637 bp. Human coordinates are above the contig and HPV18 coordinates are below. The total HPV contig is 16.6 kb. The blue bars represent junctions confirmed by PCR and Sanger sequencing. C. Plots of full-length direct cDNA sequencing are shown, displaying an abundant expression of the E6/E7 gene regions with frequent splicing of E6 and deficient expression of the E1/E2 gene region. D. The estimated level of HPV proteins is shown based on content and abundance of transcripts in Supplementary Table S9 and Supplementary Figure S5, assuming transcripts produce equal amounts of protein.