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HPV-KITE: sequence analysis software for rapid HPV genotype detection.

Marek Nowicki1,2, Magdalena Mroczek1,3, Dhananjay Mukhedkar4,5

  • 1Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Tyniecka 15/17, PL-02-630 Warsaw, Poland.

Briefings in Bioinformatics
|April 10, 2025
PubMed
Summary

A new algorithm, HPV-KITE, rapidly and accurately detects human papillomaviruses (HPVs) from sequencing data. This k-mer based method offers a sensitive and scalable solution for HPV genotyping, improving cancer diagnostics.

Keywords:
DNAHPVJavaNGSPCJRNATverskyhigh-performancesequence analysis

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Human papillomaviruses (HPVs) are a diverse viral family, with high-risk types linked to significant cancers like cervical cancer.
  • Accurate HPV genotyping is crucial for diagnosis and management, but challenging with deep sequencing due to numerous similar genotypes and sample complexity.
  • Existing diagnostic methods, including PCR and sequencing, face limitations in speed, accuracy, and scalability for comprehensive HPV detection.

Purpose of the Study:

  • To introduce HPV-KITE (HPV K-mer Index Tversky Estimator), a novel algorithm for rapid and sensitive HPV detection.
  • To leverage k-mer analysis and Tversky indexing for improved HPV genotyping from metagenomic and transcriptomic data.
  • To provide a scalable and accurate alternative to current HPV detection methods for next-generation sequencing.

Main Methods:

  • Developed HPV-KITE, a novel algorithm utilizing k-mer data analysis and Tversky indexing.
  • Applied HPV-KITE to three HPV infection-related datasets (1430 samples) for assessment.
  • Benchmarked HPV-KITE against standard HPV sequencing analysis algorithms, including mapping and k-mer classification methods.

Main Results:

  • HPV-KITE demonstrated rapid processing times through parallelization and shingling.
  • Scalability analysis confirmed optimal performance with multiple nodes.
  • The algorithm achieved high accuracy and speed in detecting HPV genotypes across diverse datasets, outperforming standard methods.

Conclusions:

  • HPV-KITE offers a fast, accurate, and user-friendly method for HPV genotype detection from next-generation sequencing data.
  • The algorithm is highly scalable and adaptable for detecting other microorganisms beyond HPV.
  • HPV-KITE represents a significant advancement in viral diagnostics, particularly for HPV-related disease research and clinical applications.