TypeSeq2 HPV genotyping services
This technical service detects HPV types in specimens using the TypeSeq2 (TS2) assay and is provided through the Cancer Genomics Research Laboratory.
The TS2 assay is capable of individual genotyping of 46 HPV types, including all carcinogenic types (see list below). The assay amplifies targets and incorporates sequencing adapters and molecular barcodes in a single PCR reaction with three stages, generating sequence-ready, dual-barcoded Next-Generation Sequencing (NGS) libraries.
NGS is performed on an Ion S5 system, using a custom-developed analysis plugin, run within the Ion Torrent Suite software.
This service includes a report containing assay performance, based off PCR batch and internal controls, and detected HPV types (pos/neg) per sample.
Validation of the assay has been published 1 and a detailed manuscript for the assay methodology is in preparation.
Based on the Global HPV DNA Genotyping Proficiency Study testing conducted annually by the International Human Papillomavirus Reference Center (IHRC), the TS2 assay was found to be 100% proficient in 2023 & 2024 2, detecting all types with input lower than the testing threshold requirements (10 International Units [IU]/uL for HPV16 & HPV18 and 100 Genome Equivalents [GE[/uL for other HPV types) at concentrations as low as 1 IU/uL (equivalent to 7 IU input) for HPV16 and HPV18 and 10 GE/uL (equivalent to 70 GE input) for other HPV types.
The laboratory will participate in annual testing as panels are released to ensure proficient status.
Submission guidelines
Previously extracted DNA is acceptable for submission. Submitted extracted DNA will be quantitatively assessed before final acceptance. For the DNA extraction service associated with this assay, the Cancer Genomics Research Laboratory requires a minimum volume of sample based on specimen type and storage buffer (see matrix below).
All collection or prior processing details must be provided.
All samples and/or specimens submitted must be in supplied sample kits (2D barcoded Azenta tubes) in desired testing order (alternate specimen tube types may be considered upon request).
Sixty days following data delivery, residual samples and/or specimens will be discarded.
For inquiries regarding additional specimen types, storage media, or other information about the assay, please contact CGR directly at NCICGR_TS2@mail.nih.gov.
Detectable HPV types
HPV 6, 11, 13, 16, 18, 26, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 56, 58, 59, 61, 62, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 87, 89, 90, 91, 97, 114
Currently accepted validated specimen & media types
| Storage Matrix | Elution Buffer | ThinPrep PreservCyt |
|---|---|---|
| Specimen Collection Site | Any (Extracted & Purified DNA) | Cervical, Vaginal |
| Volume Required (uL) | 50 | 200 |
| Validated | Yes | Yes |
References
1. Mónica S Sierra, Carolina Coto, Carolina Porras, Rolando Herrero, Daniela Ugalde, Ashley N Sauer, Daniela Mora, Claudia P Montes, John Schussler, Amanda C Hoffman, Belynda Hicks, David Ruggieri, Bernal Cortes, Allan Hildesheim, Aimée R Kreimer, Nicolas Wentzensen, Casey Dagnall, Danping Liu. Validation of TypeSeq2, a Next-Generation–Based Sequencing Assay for the Detection of 46 Human Papillomavirus Genotypes, at the US National Cancer Institute and Costa Rica Laboratories, The Journal of Infectious Diseases, 2025;, jiaf369, https://doi.org/10.1093/infdis/jiaf369
2. Arroyo Mühr LS, Eklund C, Lagheden C, et al. Continuous global improvement of human papillomavirus (HPV) genotyping services: the 2022 and 2023 HPV LabNet international proficiency studies. J Med Virol 2024; 96:e70022.