Glossary · Laboratory techniques
PCR and qPCR
In one sentence
PCR (polymerase chain reaction) is a technique that copies a chosen stretch of DNA millions of times so it can be detected. qPCR, or real-time PCR, tracks amplification cycle by cycle, allowing the target to be quantified.
Also known as: PCR · qPCR · polymerase chain reaction · real-time PCR · quantitative PCR · RT-PCR
What is PCR?
The polymerase chain reaction was developed in the 1980s by Kary Mullis, who shared the 1993 Nobel Prize in Chemistry for it. It amplifies a pre-selected fragment of DNA exponentially, bounded by two primers designed for that sequence. Starting from a handful of copies, 30-40 cycles yield enough to detect.
Each cycle has three steps: denaturation (separating the strands), primer annealing and extension by a heat-stable DNA polymerase. When the target is RNA, as with many viruses, it is first copied into DNA by reverse transcriptase; this is RT-PCR. Note the abbreviation: RT stands for reverse transcription, not real time.
How it is measured: real-time PCR
In conventional PCR the product is visualised at the end. In qPCR (real-time PCR) a fluorescent probe or dye lets the instrument follow amplification as it happens. The key output is the Ct (cycle threshold): the cycle at which fluorescence crosses a threshold. A sample rich in target reaches it early and gives a low Ct; a sample with little target gives a high Ct.
To make results reliable and comparable, the MIQE guidelines (Bustin et al., Clinical Chemistry, 2009), updated as MIQE 2.0 in 2025, set out the minimum information on controls, efficiency and data analysis. Ct cut-offs are not universal and vary between assays.
Strengths and limitations
- Sensitive and fast: detects tiny amounts of a specific organism within hours.
- Targeted: it only finds what it is designed to look for; a PCR panel will miss a pathogen not on the list.
- No viability information: it amplifies DNA or RNA from live and dead organisms alike.
- Amplification bias: in community profiling, such as 16S rRNA gene sequencing, the preceding PCR step can favour some sequences over others.
For sexually transmitted infections, the 2021 CDC STI treatment guidelines recommend nucleic acid amplification tests, including PCR, for chlamydia and gonorrhoea.
Example
A sexual health clinic runs a multiplex PCR on a self-taken vaginal swab for Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. The report is positive for gonorrhoea and negative for the others. Because PCR gives no susceptibility data, the clinician also sends a culture before treatment to check antimicrobial resistance, then manages partner notification.
PCR at Xenogene
Xenogene’s STI test, AMC ETS (SeXitest), is not a targeted PCR: it uses Nanopore NGS to identify the microorganisms present in the sample (first-void urine, urethral or vaginal swab, or blood/serum), with results in 15 working days. It is a clinical metagenomics approach that does not rely on a closed list of targets, and it complements rather than replaces PCR when the clinician needs a rapid answer on specific pathogens.
PCR appears elsewhere in the catalogue: the vaginal microbiota test describes a targeted amplification step before sequencing, and the liquid biopsy test lists qPCR and ddPCR for quality control and validation. By contrast, the blood metagenomics test (AMC in Blood) avoids PCR amplification to reduce bias.
Frequently asked questions
What is the difference between PCR and qPCR?
Conventional PCR shows whether the target was amplified at the end of the run, for instance on a gel. qPCR measures fluorescence during every cycle, so it can estimate how much target was present at the start and gives a Ct value.
What does a Ct value mean?
It is the cycle at which the fluorescent signal crosses a set threshold. A lower Ct means more target genetic material in the sample. There is no universal cut-off: it depends on the assay and the laboratory and should be read in clinical context.
Does a positive PCR mean an active infection?
Not always. PCR detects nucleic acid, which may come from live or dead organisms or from colonisation without disease. A positive result is therefore weighed against symptoms, sample type and, where available, the Ct value.
Related terms
- NGS (next-generation sequencing)
NGS (next-generation sequencing) is a family of technologies that read millions of DNA or RNA fragments in parallel in a single run, making it possible to study whole genomes, targeted genes or entire microbial communities at scale.
- 16S rRNA gene sequencing
16S rRNA gene sequencing amplifies and reads a marker gene found in all bacteria and archaea to show which groups are present in a sample and in what proportions. It is inexpensive but usually resolves to genus level and does not measure function directly.
- Sexually transmitted infection (STI)
A sexually transmitted infection (STI) is an infection caused by bacteria, viruses or parasites that spreads mainly through vaginal, anal or oral sex. Many cause no symptoms, so testing is often the only way to find them.
- Clinical metagenomics
Clinical metagenomics (mNGS) is the untargeted sequencing of the genetic material in a patient sample to detect bacteria, viruses, fungi or parasites without choosing the pathogen in advance. It complements culture and susceptibility testing rather than replacing them.
- Blood culture
A blood culture incubates a blood sample in bottles of nutrient broth to find out whether live bacteria or fungi are circulating in the bloodstream. If anything grows, it is identified and tested against antibiotics to guide treatment.
Educational content for healthcare professionals and the general public. It does not replace assessment by a healthcare professional: ordering and interpreting any test is the responsibility of the requesting clinician.
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