Table 1. Number of reads for the different virus types (established HPV types, known and novel putative HPV types and non-HPV viruses) detected in pool D (142 multiple displacement amplified skin swab samples) by at least one of the platforms. *SCC = squamous cell carcinoma, AK = actinic keratosis. **The data from GSFLX and PGM platforms are previously published13.
| Disease | SCC* and AK* | |||
|---|---|---|---|---|
| Number of patients | 82 SCCs and 60 AKs | |||
| Sample type | Swab samples from the top of lesions | |||
| Pre-sequencing treatment | Whole genome amplification | |||
| Sequencing platform | GSFLX** | PGM 300 bp** | PGM 400 bp** | MiSeq |
| HPV8 | 189 | 1360 | 429 | 56896 |
| HPV12 | 1 | 8 | 4 | 381 |
| HPV20 | 2 | 1 | 0 | 149 |
| HPV22 | 0 | 0 | 0 | 1 |
| HPV24 | 0 | 0 | 0 | 2 |
| HPV28 | 0 | 0 | 0 | 15 |
| HPV36 | 0 | 0 | 0 | 45 |
| HPV38 | 0 | 1 | 0 | 2 |
| HPV45 | 0 | 1 | 0 | 0 |
| HPV59 | 0 | 1 | 0 | 0 |
| HPV76 | 0 | 0 | 0 | 18 |
| HPV93 | 0 | 0 | 0 | 2 |
| HPV104 | 7 | 32 | 28 | 1168 |
| HPV105 | 0 | 1 | 0 | 370 |
| HPV107 | 0 | 0 | 1 | 83 |
| HPV109 | 0 | 0 | 0 | 5 |
| HPV110 | 0 | 0 | 0 | 4 |
| HPV124 | 0 | 5 | 0 | 48 |
| HPV125 | 0 | 0 | 0 | 4 |
| HPV128 | 0 | 0 | 0 | 2 |
| HPV134 | 0 | 0 | 0 | 6 |
| HPV155 (SE42) | 156 | 1199 | 255 | 33668 |
| HPV161 | 0 | 0 | 0 | 4 |
| FA73 | 0 | 0 | 1 | 0 |
| HPV 915 F 06 007 FD1 | 1 | 3 | 0 | 94 |
| SE46 | 22 | 132 | 44 | 4881 |
| SE355 | 0 | 0 | 0 | 369 |
| SE356 | 0 | 0 | 0 | 42 |
| SE357 | 0 | 0 | 0 | 6 |
| Torque teno virus | 1 | 1 | 1 | 22 |
| Human polyomavirus 6 | 0 | 0 | 1 | 205 |
| Merkel cell polyomavirus | 1 | 2 | 1 | 36 |
| Human endogenous retrovirus | 0 | 3 | 0 | 7 |
| Total reads | 121752 | 912218 | 381017 | 23699142 |
| Total viral reads | 380 | 2750 | 765 | 98535 |
| Total HPV reads | 378 | 2744 | 762 | 98265 |
| Total established HPV types | 5 | 10 | 5 | 21 |
| Total known putative HPV types | 2 | 2 | 2 | 2 |
| Total novel putative HPV types | 0 | 0 | 0 | 3 |