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Table 3 The identified HPV-HPV junction positions and sequence reads in the tumors containing the deleted HPV populations

From: Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas

Tumor

HPV-HPV junction positions in HPV16 genome

Deleted length (nt)

Deleted viral genes

Identified HPV-HPV junction sequence

683

501 --- 6984

6447

E1a, E2, E4, E5, L2, L1, URRa

AGTATAGTGGTGGAAGTGGGGGGGGTGTGCAAACCGTTTT

601

6204 --- 3689

5391

L2a, E6, E7, URR, E1, E2, E4, E5

TTCCTTTAGGACGCAAATTTTTACTACAAGCAGGATTGAA

711

1865 --- 7037

5172

E1a, E2, E4, E5, L2, L1, URRa

GACGTGGTCCAGATTAAGTTTACTAAACTACAATAATTCA

568

6680 --- 6924

244

URRa

TAAACTTGTACGTTTCCTGCAGTTCATACATGAACTGTGT

515

1221 --- 7062

5841

E1a, E2, E4, E5, L2, L1, URRa

TTGTAAAGGATTGTGCAACACTAAGGGCGTAACCGAAATCGGT

532

1091 --- 6897

5806

E1a, E2, E4, E5, L2, L1, URRa

TCACAGATGGTACAATGGGCTTCTAAGGCCAACTAAATGT

676

5852 ---6002

150

L1a

TACATATAAAAATACTAACTGGAATTTTGGTCTACAACCT

624

6967 --- 1493

2452

URRa, E6, E7, E1a

TAAATGTCACCCTAGTTCATACATGAACTGTGTAAAGGTT

  1. aindicates that only partial deletion was found in that viral gene