Genotyping by Sequencing - Cutaneous Types

Next generation sequencing (NGS) for genotyping of cutaneous HPV types.

Skin lesions, swabs or biopsies. No common or plantar warts. For swab specimens, 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 cutaneous lesions.

Swabs for 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. Specimens collected by swab may be stored and shipped refrigerated (4°C) to NML within 48h of sample collection or must be stored and shipped frozen. Fresh biopsies must be stored frozen at all times 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 skin cancer lesions, recurring or severe lesions of unclear origin, or suspected epidermodysplasia verruciformis. Common or plantar warts for differential diagnosis are not accepted.  Please describe the anatomical site, the type of lesion, the type of specimen and the reason for testing.   Contact the laboratory to determine if requests are acceptable and within our mandate. 

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 skin malignancies, date collected, test requested, reason for testing and any other relevant clinical information.

Special request. Not for routine diagnostic testing of common or plantar skin warts.  Contact the laboratory prior to sending specimens. 

NGS of clinical specimens is performed using a non-targeted (unbiased) approach (1,2). In this method, total nucleic acids are processed and RNA is reverse transcribed to cDNA (without DNase treatment), so both cDNA and residual DNA may be sequenced. Sequencing reads are filtered to remove human sequences, and the remaining (non-human) reads are aligned to HPV reference genome databases to detect and genotype HPV. Clinical specimens and fixed tissues with >250 pg of RNA can be processed using this method. This test is qualitative (not quantitative); if HPV is detected, the precise HPV type is reported. Please note that when testing formalin-fixed specimens, HPV may not be detected due to decreased assay sensitivity.

Testing is performed, in whole or in part, using a lab-developed test which has not been fully validated/verified.

This test (HPV genotyping of cutaneous specimens) is performed on special request. Please inquire with the laboratory for turnaround time.

1. Arroyo Mühr, L S., Hultin, E., Dillner, J. 2021. Transcription of human papillomaviruses in non melanoma skin cancers of the immunosuppressed. Int. J. Cancer. 149(6):1341-1347.
2. Takara Bio USA, Inc. SMART-Seq® Total RNA Library Prep with ZapR® Depletion User Manual. Takarabio.com