Vaginal health tests (like ours) are becoming more common — and more accessible — thanks to advances in lab testing and growing interest in personal health. These tests can give you an in-depth look at the makeup of your microbiome, reporting on things like bacterial balance, yeast infections, bacterial vaginosis (BV), sexually transmitted infections (STIs), ulcers, and more.
But all tests are not created equally — so how do they work and which one is best for you?
Most of the at-home vaginal tests on the market use one of two technologies to analyze your sample: PCR testing (polymerase chain reaction) or NGS (next generation sequencing.) Both are powerful tools, and there are pros and cons to each.
At MyPathAdvantage, we utilize real-time PCR in order to achieve the most accurate and sensitive results — doing everything we can to prevent false negatives and false positives.
PCR vs. NGS: What’s the Difference in Vaginal Health Tests
Let’s break it down.
PCR: A Targeted Approach
PCR is like using a high-powered magnifying class to search for specific organisms. It looks for known bacteria by making millions of copies or amplifying specific sequences of DNA.
This involves a series of cycles that include denaturation (breaking apart DNA), annealing (re-binding the DNA strands to probes and primers) and extension (amplification) resulting in millions of copies of the target DNA which is then easier to detect.
PCR is highly specific, avoiding false positive results, and sensitive, avoiding false negative results. But it only looks for specific bacteria.
Real-Time PCR (RT-PCR) is a type of PCR that can quantify the amount of DNA, as it is being read, so you can get an idea of the amount of bacteria in your sample. This is also a faster, highly sensitive method of PCR making false negatives even less likely.
Both PCR (Polymerase Chain Reaction) and Next-Generation Sequencing (NGS) are powerful tools in molecular biology, each with strengths and weaknesses. So, which would be better for analyzing the vaginal microbiome? Consider the following, before you answer this question:
- Pros:
- High Sensitivity: PCR excels at detecting specific target organisms or genes, even at low abundance.
- Target Specificity: By amplifying only the desired DNA sequence, PCR offers precise and accurate results.
- Rapid Turnaround Time: PCR is fast, making it suitable for time-critical applications (such as healthcare!)
- A Valued Clinical Test: A PCR test is the same medical test we make available to our medical clients. Your doctor would likely use a PCR test in diagnosing you, though they may choose one that is even more limited in what it looks for. This is not a marketing tool or gimmick; this is a literal medical test available to our clients
- Cons
- A PCR test only finds what it is looking for. The good news, in the case of MyPathAdvantage, is that we are looking for a list of clinically significant organisms, put together by key opinion leaders in test design and women’s health.
NGS: A Broad-Spectrum Approach to Vaginal Health Tests
Next-generation sequencing (NGS), is like doing a full scan of the entire neighborhood. It will identify all of the DNA in the sample but that includes organisms that aren’t important to diagnosing any issues.
This technology rapidly sequences and identifies entire genomes (an organism’s DNA) or specific DNA regions of interest. It involves fragmenting DNA, attaching adapters, and sequencing millions of DNA fragments at the same time.
NGS can detect novel sequences and variations that may not be known beforehand. That can be helpful in research or when you’re studying an unknown environment. But when it comes to an at-home vaginal infection test, it can mean getting results that are confusing or hard to interpret.
- Pros
- A Wide Range of Detection: NGS can detect a wide range of organisms, including unexpected ones. This can be both good, and frustrating. A list of detected organisms, with the interpretation of ‘uncertain clinical significance’ can leave both the doctor and the patient scratching their heads.
- Holistic Analysis: NGS provides a comprehensive view of the microbial community, enabling the study of complex ecological interactions. Although NGS is used in many areas, it is more commonly used in research settings.
- Cons:
- Cost: NGS can be expensive, requiring significant investment in equipment and reagents.
- Interpretation Challenges and Data Analysis: NGS generates massive amounts of data and can detect a wide range of microorganisms, necessitating advanced bioinformatics skills and computational resources and making interpretation complex.
- Lower Sensitivity: While NGS can detect a wide range of organisms, it may not be as good at preventing false-negatives as PCR for specific targets, especially at low quantities. This is especially a concern in vaginal health tests.
- Turnaround Time: NGS can be time-consuming, especially for complex analyses. The entire process, including sample preparation, sequencing, and data analysis, can still take several days. This may not be suitable for time-critical clinical decisions.
Choosing the Right Tool
As a pathologist, the choice between PCR and NGS depends on the specific research question, the desired level of sensitivity and specificity, and available resources.
While NGS offers significant potential, its widespread adoption in clinical settings is limited. It is an excellent tool for studying unknown environments, which can then be further studied. For example, NGS identifies bacteria in new environments (such as soil and water) which can then be examined further.
But for those looking for an at-home vaginal health test, an NGS test may not make sense, especially given the likelihood for false negatives. The vaginal microbiome isn’t an unknown environment. We are actually quite familiar with the organisms you could find in it. So it’s more suited to real-time PCR which provides for more accuracy.
The organisms detected by the MyPathAdvantage test kit are well-described in the medical literature, with evidence-based treatments. With NGS, you not only get a lot of information that may not be useful, but you are also facing lower accuracy.
