Supplementary Figures S1-S6 and Tables S1-S5 from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

Figure S1.1. Circos plots of human genomes. Figure S1.2. Circos plots of HPV genomes. Figure S1.3. PacBio HiFi read length distributions. Figure S1.4. Oxford Nanopore (ONT) read length distributions. Figure S2.1. Detection of circularized mitochondrial DNA by LR-seq reads. Figure S2.2. Detection of HPV concatemers by LR-seq reads. Figure S2.3. ONT reads show structural rearrangements in HPV concatemers. Figure S3.1. Absence of sequence variants at breakpoints. Figure S3.2. AmpliconArchitect predicts inaccurate HPV ecDNA structures. Figure S4.1. Evolution of structural variants at Chr. 22 of Tumor 2. Figure S4.2. Evidence of heterocateny in Tumor 5 and Tumor 3. Figure S5.1. HPV integration into icDNA in GUMC-395, HeLa, and HTEC. Figure S5.2. HPV integrants at Chr. 17 and Chr. X of VU147. Figure S5.3. Metaphase FISH identifies HPV-containing ecDNAs in cell lines. Figure S5.4. Circle-seq analysis of HeLa, GUMC-395, VU147, and HTEC cells. Figure S6. Transcription levels of HPV genes. Table S1.1. Depths of autosomal and mitochondrial genome sequencing coverage from WGS and LR-seq. Table S1.2. Depths of autosomal and HPV genome sequencing coverage from WGS and LR-seq. Table S2.1. Breakpoints and normal segment junctions in Tumor 4. Table S2.2. Definition of genomic segments flanking HPV integrants in Tumor 4. Table S3.1. Breakpoints and normal segment junctions in Tumor 2. Table S3.2. Definition of genomic segments flanking HPV integrants in Tumor 2. Table S3.3. Breakpoints and normal segment junctions in Tumor 5. Table S3.4. Definition of genomic segments flanking HPV integrants in Tumor 5. Table S3.5. Breakpoints and normal segment junctions in Tumor 3. Table S3.6. Definition of genomic segments flanking HPV integrants in Tumor 3. Table S4.1. Breakpoints and normal segment junctions in GUMC-395 cells. Table S4.2. Definition of genomic segments flanking HPV integrants in GUMC-395 cells. Table S5.1. Breakpoints and normal segment junctions in HeLa cells. Table S5.2. Definition of genomic segments flanking HPV integrants in HeLa cells. Table S5.3. Breakpoints and normal segment junctions in VU147 cells. Table S5.4. Definition of genomic segments flanking HPV integrants in VU147 cells. Table S5.5. Breakpoints and normal segment junctions in HTEC cells. Table S5.6. Definition of genomic segments flanking HPV integrants in HTEC cells.