Targeted next generation sequencing panel for HPV genotyping in cervical cancer

Area of Science:

• Oncology
• Virology
• Genetics

Background:

• Cervical cancer is primarily caused by persistent high-risk human papillomavirus (HPV) infections.
• HPV integration into the host genome is a critical step in cervical carcinogenesis.
• Accurate and early detection of HPV genotypes and integration is crucial for cervical cancer prevention and management.

Purpose of the Study:

• To develop a sensitive targeted amplicon-based next-generation sequencing (NGS) method for detecting high-risk HPV genotypes.
• To investigate the utility of NGS for HPV genotyping in cervical lesions and detecting HPV integration.
• To evaluate the cost-effectiveness and clinical applicability of the developed NGS assay.

Main Methods:

• Development of a custom targeted NGS panel to detect 25 high-risk and 2 low-risk HPV genotypes.
• Analysis of cervical biopsies (CIN3+, CIN2), plasma samples, and cell lines.
• Validation of NGS results against established methods like SPF10-PCR-DEIA-LiPA25 and digital droplet PCR (ddPCR).

Main Results:

• The NGS assay demonstrated high concordance (K=0.92) with the SPF10-PCR-DEIA-LiPA25 assay for HPV genotyping.
• NGS identified a predominant HPV type in samples, unlike other methods that detected multiple types.
• The assay successfully detected HPV-16 integration in the SiHa cell line and showed agreement with ddPCR for plasma samples.

Conclusions:

• Targeted NGS is a sensitive and precise method for detecting and genotyping HPV in FFPE biopsies and plasma samples.
• This NGS approach facilitates early diagnosis and prognosis of cervical cancer, potentially improving patient survival.
• The developed HPV NGS panel offers a cost-effective solution for HPV detection and genotyping, with a list price of approximately €75 per sample.