HPV Nucleic Acid Detection Oligomers
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Solution Overview
Problem
There is a need for efficient and sensitive detection methods to identify human papillomavirus (HPV) in biological specimens, particularly for high-risk HPV types associated with cervical cancer, as well as for determining the efficacy of HPV vaccinations, as current methods may not provide adequate diagnostic and prognostic information.
Innovation Solution
The development of oligonucleotide sequences and methods for amplifying and detecting HPV33 and HPV31 nucleic acids using specific oligonucleotides that target the E6/E7 region, allowing for sensitive and specific detection through amplification and hybridization techniques, including transcription-mediated amplification (TMA), with the use of labeled probes for real-time detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If molecular screening for HPV nucleic acid is performed, then diagnostic sensitivity is improved, but detection complexity increases
Solution Approach 1:
The detection system is segmented into distinct functional modules: sample preparation module, nucleic acid extraction module, amplification module (TMA or PCR), and detection module (hybridization with labeled probes). Each module performs a specific function, allowing the complex detection process to be managed through standardized, interchangeable components that can be operated independently.
Solution Approach 2:
Labeled oligonucleotide probes serve as intermediaries between the amplified HPV nucleic acid target and the detection system. These probes hybridize specifically to the target sequence and carry detectable labels (fluorescent, chemiluminescent, or radioactive), translating the molecular recognition event into a measurable signal without requiring direct interaction between the target and the detection instrument.
2Measurement precision
If specific oligonucleotides targeting E6/E7 region are used, then detection specificity is improved, but assay development difficulty increases
Solution Approach 1:
The assay utilizes specific parameter changes in the oligonucleotide probes, including their sequence composition (designed to match conserved regions of HPV E6/E7 genes), length (optimized for hybridization stability), and chemical modifications (such as locked nucleic acids or fluorescent labels). These parameter optimizations enable high specificity while providing a standardized framework that simplifies assay development and transfer between laboratories.
3Measurement precision
If amplification techniques are used, then detection sensitivity is improved, but detection time is increased
Solution Approach 1:
The nucleic acid amplification employs periodic thermal cycling (in PCR) or isothermal periodic reactions (in TMA) where denaturation, annealing, and extension steps are repeated cyclically. This periodic action allows exponential amplification of the target sequence over multiple cycles, achieving high sensitivity. The use of efficient polymerases and optimized cycle parameters minimizes the time required, typically completing amplification within 1-2 hours.
Data Source
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AI summary
There is disclosed an oligomer combination for detecting a human papillomavirus (HPV) target nucleic acid in a sample suspected of containing HPV type 31 (HPV31) or HPV type 33 (HPV33) and at least one of HPV types 52 and 58, said oligomer combination comprising: (i) first and second amplification oligomers for specifically amplifying an HPV33 nucleic acid target region, wherein the first HPV33 amplification oligomer comprises a first target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:66 and that includes at least the sequence of SEQ ID NO:67, SEQ ID NO:68, or SEQ ID NO:69; and the second HPV33 amplification oligomer comprises a second target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:70 and that includes at least the sequence of SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73; and (ii) first and second amplification oligomers for specifically amplifying an HPV31 nucleic acid target region, wherein the first HPV31 amplification oligomer comprises a first target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:74 and that includes at least the sequence of SEQ ID NO:75, SEQ ID NO:76, or SEQ ID NO:77; and the second HPV31 amplification oligomer comprises a second target-hybridizing sequence that is from about 15 to about 30 contiguous nucleotides contained in the sequence of SEQ ID NO:78 and that includes at least the sequence of SEQ ID NO:79, SEQ ID NO:80, or SEQ ID NO:81.