A new synthetic control methodology promises to enhance metatranscriptomic diagnostics by overcoming significant challenges posed by traditional patient-derived control materials.
Researchers have developed a method that generates synthetic positive controls (SPCs) for high-throughput diagnostics, which could lead to a revolution in molecular diagnostics in various medical applications.
Metatranscriptomics (MT) has emerged as a pivotal method for analyzing all transcripts from organisms within a sample, significantly enhancing diagnostic capabilities for chronic and infectious diseases. However, one major hurdle in the implementation of MT diagnostics has been the acquisition of appropriate control materials. Typically, these materials are derived from patient samples, posing logistical challenges and variability in test results.
The team led by Viome Life Sciences has now addressed this challenge by introducing synthetic controls (SCs), which can produce over 100,000 samples from a single amplification cycle—thereby ensuring laboratories can operate at high throughput without needing constant patient-derived specimens.
In their recent publication, the authors of the article highlighted their method for generating SPCs, which duplicate the nucleic acid signatures essential for accurate disease testing. They validated these SPCs by implementing them within a clinical environment. The SPCs demonstrated reliability with an average oral cancer risk score of 0.996 and a low coefficient of variation in their performances, indicating consistent results across multiple tests.
“This development not only facilitates the logistics of obtaining control material but also enhances the reproducibility and accuracy of MT-based assays,” said the authors of the article.
The methodology utilized for developing these SPCs involved two saliva samples from patients diagnosed with oral squamous cell carcinoma (OSCC). From these samples, the researchers purified total nucleic acids, removed human and microbial ribosomal RNAs, and proceeded with a series of PCR amplifications and in vitro transcription to yield the final SPCs.
The researchers noted that while the initial amplification (denoted as F0) could produce sufficient templates for extensive testing, additional rounds of amplification led to a marginal decrease in the strength of the positive signals, indicating that their maximum efficiency is achieved after the first amplification step. However, SPCs maintained a significant contrast in OC risk scores when compared to samples from the general population, consistently producing results that underline their diagnostic reliability.
With the successful validation of SPCs in clinical laboratories, this synthetic control approach shows the potential to streamline the adoption of metatranscriptomics into broader healthcare applications. “By utilizing synthetic controls, we remove much of the variability associated with patient-derived materials, which can fluctuate with time and disease progression,” emphasized the authors of the article.
As the field of molecular diagnostics continues to evolve, the introduction of SCs for MT analysis may pave the way for increased utilization of these automated processes, effectively making advanced diagnostics affordable and accessible.
This groundbreaking work, documented in the article published by Viome Life Sciences, positions SCs as a crucial advancement for the implementation of metatranscriptomic diagnostics in various fields of medicine, showcasing a future where diagnostic testing becomes more standardized and precise.
