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Saliva Test IDs Early Oral Cancer Signature

Detect cancer scrabble

(Marco Verch, Flickr)

16 Dec. 2021. An analysis is shown to identify characteristic patterns found in microbial communities in saliva indicating early stages of oral and throat cancer. A team from Viome Life Sciences in Bellevue, Washington and Queensland University in Brisbane, Australia report their findings in the 8 Dec. issue of the journal NPJ Genomic Medicine.

Viome Life Sciences is a five year-old enterprise designing diagnostics and therapies from biomarkers, or molecular indicators in the body. The company’s technology, licensed from Los Alamos National Lab, analyzes messenger RNA, or mRNA, a nucleic acid based on the genetic code from DNA, with instructions for cells to produce the amino acids in proteins for cellular functions. Viome says it has access to more than a quarter-million samples with mRNA that it maps to human gene and biological pathways. The company’s mRNA collections are also mapped to the human microbiome, communities of microbes in the body.

Viome says its technology, called ViOS, associates its mRNA-derived data with human health information, from its customers or clinical studies, analyzed further with machine-learning algorithms to identify more precise biomarkers and signatures for various diseases. These indicators, says the company, are then validated independently in clinical studies.

The Viome-Queensland team is seeking a reliable non-invasive test for oral cancer, a type of head and neck cancer, which now requires a surgical tissue biopsy for conclusive results. The researchers cite data showing oral cancer has an overall five-year survival rate of 40 percent, which has remained stagnant for about 40 years. The authors note that if caught in its early stages, oral cancer has a five-year survival rate of 84 percent, but only about three in 10 patients (29%) are diagnosed with oral cancer in its early stages.

Access to company systems and databases at no cost

The researchers led by Viome’s chief technology officer Guru Banavar and Chamindie Punyadeera, professor of clinical chemistry at Queensland University (now at Griffith University), devised a process to identify microbial signatures for oral cancer in human saliva samples. The team applied Viome’s mRNA and microbial analytics to 433 saliva samples from 242 individuals considered at high risk for oral cancer, such as a history of tobacco use. The researchers also collected 71 saliva samples from oral cancer patients, and 171 samples from the general population. Data from the samples helped train Viome’s machine-learning algorithms for analyzing their microbial composition, but different samples were used to independently validate the algorithms.

From the saliva samples, the researchers found 1,587 microbial species connected to more than 4,900 common genetic functions across the species, according to a standard genetic database. The team’s analysis yielded a microbial signature of 101 microbial species with 247 active genetic functions for predicting oral cancer. Using that signature, the researchers say their diagnostic test for oral cancer shows a true-positive sensitivity of 83 percent overall and 92 percent for early-stage disease. Likewise, the test shows a true-negative specificity of 97 percent.

“Oral cancer is a life threatening disease that is highly prevalent in some parts of the world, but without early diagnostics that can enable treatment and save lives,” says Punyadeera in a company statement released through Cision. “The Viome platform has enabled us to quickly extract a strong signal from this sample set.”

Viome Life Sciences says it now offers access to its ViOS technology for independent researchers through the company’s grants program. The program offers in-kind access to the Viome systems and databases at no cost to design new diagnostics and therapies.

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