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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Jun 26, 2025

RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma
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HPV genotyping in clinical samples using long-read single-molecule real-time sequencing.

Christophe Pasquier1, Stéphanie Raymond1, Romain Carcenac1

  • 1Department of Virology, Toulouse University Hospital, Toulousel, France.

Journal of Medical Virology
|May 10, 2024
PubMed
Summary

PacBio SMRT sequencing offers accurate human papillomavirus (HPV) genotyping using the E6/E7 region. This method is effective for detecting multiple HPV infections and is a valuable tool for cervical cancer screening.

Keywords:
HPVSMRT sequencinggenotypingpapillomavirus

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Area of Science:

  • Molecular Biology
  • Virology
  • Genetics

Background:

  • Human papillomavirus (HPV) genotyping is crucial for cervical cancer screening, often combined with high-risk (HR) HPV detection.
  • Existing methods like L1 sequencing and APTIMA HPV genotyping have limitations in comprehensive HPV profiling.

Purpose of the Study:

  • To develop and evaluate a novel HPV genotyping method utilizing PacBio single molecule real-time (SMRT) sequencing of the E6/E7 region.
  • To assess the performance of this new method against established techniques (MY09-11 L1 sequencing and APTIMA HPV genotyping).

Main Methods:

  • PacBio SMRT sequencing was employed to analyze approximately 800 bp sequences in the E6/E7 region of HPV.
  • The performance of PacBio E6/E7 SMRT genotyping was compared with MY09-11 L1 sequencing and the APTIMA HPV genotyping assay.

Main Results:

  • PacBio E6/E7 SMRT sequencing demonstrated 100% concordance with MY09-11 L1 sequencing and 90.8% concordance with APTIMA HPV genotyping.
  • The sensitivity of PacBio E6/E7 SMRT was comparable to L1 sequencing and lower than HR-HPV tests, as expected.
  • PacBio SMRT sequencing offers unbiased genotyping, capable of detecting multiple HPV infections and intra-genotype variations (haplotypes).

Conclusions:

  • PacBio E6/E7 SMRT sequencing is a robust and accurate method for both high-risk (HR) and low-risk (LR) HPV genotyping in clinical samples.
  • This technique is particularly useful as a follow-up genotyping assay after a positive HPV test in cervical cancer screening protocols.
  • The ability to detect multiple infections and haplotypes makes PacBio SMRT sequencing a valuable advancement in HPV diagnostics.