Genotyping by Luminex - Mucosal Types

Genotyping by an in-house Luminex assay for mucosal Human Papillomaviruses.

Genital, anal, oropharyngeal specimens, and biopsies. Other specimen types may be accepted upon request. No genital warts. The minimum volume required is 1/4 of the collected sample, or 1.0 mL. For fixed tissue, please submit 5 scrolls or entire block. Please see patient criteria below for submission of mucosal lesions.

Cervical cytobrushes in ThinPrep PreserCyt or Surepath solutions.  Swabs for genital, anal and oro-pharyngeal specimens in transport medium. Swabs for condyloma acuminatum or other visible lesions in transport medium.  Fresh biopsy or fixed tissue of any lesion.

Place swabs in transport medium and provide entire collected specimen, or no less than 1.0 mL of specimen. Specimens collected by cytobrush and swab may be stored and shipped refrigerated (4°C) to NML within 48h of specimen collection or must be stored and shipped frozen. Fresh biopsies must be always stored frozen and shipped on dry ice. Fixed tissue may be stored and shipped at room temperature.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

This service is offered for reference and confirmation only when HPV genotyping is required to confirm a diagnosis of cancer or oropharyngeal lesions. This test is unsuitable for HPV cervical cancer screening. Samples for routine cervical cancer screening, ASCUS triage, or genital wart differential diagnosis are not accepted, unless part of a pre-arranged collaborative study. Please describe the anatomical site, the type of lesion, the type of specimen and the reason for testing. This information is necessary to assess if requests are within our mandate. This test does not detect HPV types that cause common warts and other cutaneous skin lesions.

Completed “Sexually Transmitted and Opportunistic Infections” requisition form including sender lab name, address and telephone number, patient identifier, date of birth or age, sex, specimen reference #, anatomical site, type of specimen, type of lesion, date collected, test requested, reason for testing, and any other relevant clinical information.

N/A

The in-house assay consists of a nested PCR followed by genotyping using Luminex technology (1). The precise HPV type(s) are reported. Presence of additional types other than the ones tested for cannot be excluded. The detection limit is between 10 and 100 copies for most mucosal HPV types. This assay targets L1 DNA for the following HPV types with varying degrees of risk for carcinomas (2): 6, 11, 13, 16, 18, 26, 30, 31, 32, 33, 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, 85, 86, 87, 89, 90, 91, and 97. Please note that when testing formalin-fixed specimens, the presence of HPV may not be detected due to the decreased sensitivity of the assay. Specimens that test negative using the in-house Luminex assay will be re-tested using a validated commercial assay that targets E6/E7 HPV DNA, to account for potential L1 disruption due to HPV integration events. Specimens from confirmed invasive cancers, that have tested negative by both assays, will be further analysed using next-generation sequencing (NGS) (3,4).

14 calendar days. This turnaround time does not apply to specimens processed for NGS. Please contact lab to inquire about turnaround times.

1. Zubach, V., Smart, G., Ratnam, S., Severini, A. 2011. Novel microsphere-based method for the detection and typing of 46 mucosal human papillomavirus types. J. Clin Microbiol. 50(2): 460-4.
2. Arroyo, L S., Lagheden, C., Eklund, C., Dillner, J. 2009. Chapter 2 – Human Papillomavirus Types. Human Papillomavirus e-Laboratory Manual (1st Edition). 5.
3. Arroyo ühr, L S., Lagheden, C., Eklund, C., Lei, J., Nordqvist-Kleppe, S., Sparén, P., Sundström, K., Dillner, J. 2020. Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers. J. Gen Virol. 101:265-270.
4. Takara Bio USA, Inc. SMART-Seq® Total RNA Library Prep with ZapR® Depletion User Manual. Takarabio.com