Our Tests

Why is studying RNA more powerful than DNA?

In the context of chronic diseases, RNA sequencing has major advantages over DNA sequencing, for both humans and our microbial symbionts. RNA (gene expression) is an extremely useful resource for studying health and disease, as gene expression is constantly changing throughout the course of a disease. DNA on the other hand, does not incur change and has been shown only to have a weak contribution to chronic diseases. For example, just think of a chronic disease such as IBD that goes through remission-relapse phases. The DNA will remain the same regardless of which disease phase you are in; however, the RNA will change to reflect the different disease phases. Very importantly, these changes in gene expression can be modulated, either via nutrition or microbiome functions.

What are the main features & advantages of Viome Life Sciences' tests?

  • They identify and quantify all microorganisms, including RNA viruses (human, plant, and phages). No other taxonomic classification method is all-inclusive.

  • All metatranscriptomic tests identify and quantify only the living microorganisms, because RNA from dead microorganisms quickly degrades. In contrast, microbial DNA remains in the sample long after a microorganism dies and can cause false positive calls.

  • They quantify the expression of all genes present in the sample, human and/or microbial.

  • Laboratory methods are automated, minimizing or eliminating batch effects. Our tests are performed in a CLIA-licensed lab, and most of them are clinically validated. This means that:

    • All lab technicians have a B.S. in laboratory sciences

    • All lab technicians are trained and competency tested

    • Every step of every method follows SOPs that are validated and approved by the Lab Director

    • All reagents and every lot must pass strict quality control standards

    • Every instrument must have documented satisfactory performance

    • Labs are environmentally-controlled and monitored

    • Every sample and every batch of 96 samples have quality control acceptance criteria that must pass. These include positive and negative process controls, etc.

  • All tests, except for serum/plasma analysis, utilize at-home sample collection. Even our whole blood transcriptome test requires just 50 microliters of finger prick blood.

  • All samples can be shipped at ambient temperature globally. No refrigeration, freezing, or rapid and expensive shipping are needed.

  • Metatranscriptomic data are relevant to chronic diseases and actionable. That means we can develop better diagnostic tests and implement nutritional/lifestyle strategies that can modulate human gene expression and prevent/cure chronic illness.

Gut Microbiome Test

Our gut microbiome test is a metatranscriptomic (RNA sequencing) stool test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and a pre-paid return mailer

  • Can be collected anywhere and shipped at ambient temperature

  • Isolates total RNA from stool (DNA is degraded)

  • Physically removes microbial rRNAs from total RNA

  • All remaining RNAs are sequenced using full-length transcripts and a directional library preparation method

  • Produces quantitative strain-, species-, and genus-level taxonomic classification data (average number of species per stool sample is 338)

  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential. The GI test measures the actual microbial functions. A typical gut microbiome has >1 million genes, but only 50,000 are expressed at a level of 1 part per million or above.

  • A peer-reviewed article on this test is available for reference

GI test data provided by VLS to the grantee:

  • List of genera and their relative activity

  • List of species and their relative activity

  • List of strains and their relative activity

  • List of KOs and their relative activity

Human Gene Expression Test

Human Gene Expression (HGE) test is a transcriptomic (RNA sequencing) blood test that provides comprehensive analysis of human gene expression patterns.

  • Includes a collection kit with instructions, all necessary components, and a pre-paid return mailer

  • Requires 50 microliters of blood from a finger prick

  • Can be collected anywhere and shipped at ambient temperature

  • Isolates total RNA from blood (DNA is degraded)

  • Physically selects polyadenylated (protein-coding) RNAs

  • Sequences the remaining (polyadenylated) RNAs using a full-length transcript, directional method

  • Produces quantitative gene expression data for human genes (average is ~14,000 per sample)

  • A pre-print of our article describing this test is available for reference

HGE test data provided by VLS to the grantee:

  • List of human genes and their gene expression level (can be counts per million or transcripts per million)

Saliva Test

Our saliva test is a metatranscriptomic (RNA sequencing) saliva test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and pre-paid return mailer

  • Can be collected anywhere and shipped at ambient temperature

  • Isolates total RNA from saliva (DNA is degraded)

  • Physically removes microbial and human rRNAs from total RNA

  • Sequences all remaining RNAs using a full-length transcript, directional method

  • Produces quantitative strain-, species-, and genus-level taxonomic classification data

  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential.

Data provided by VLS to the grantee:

  • List of genera and their relative activity

  • List of species and their relative activity

  • List of strains and their relative activity

  • List of KOs and their relative activity

Vaginal Test

Our Vaginal test is a metatranscriptomic (RNA sequencing) vaginal test that identifies and quantifies all living microorganisms in the sample down to 1 part per million. This includes RNA viruses (human, plant, and phages).

  • Includes a collection kit with instructions, all necessary components, and pre-paid return mailer

  • Can be collected anywhere and shipped at ambient temperature

  • Isolates total RNA from vaginal samples (DNA is degraded)

  • Physically removes microbial and human rRNAs from total RNA

  • Sequences all remaining RNAs using a full-length transcript, directional method

  • Produces quantitative strain-, species-, and genus-level taxonomic classification data

  • Produces quantitative microbial gene expression data that are clustered into KEGG orthologies (KOs). This is very different from metagenomic functional outputs, which can only tell you about the functional potential. The GI test measures the actual microbial functions.

Data provided by VLS to the grantee:

  • List of genera and their relative activity

  • List of species and their relative activity

  • List of strains and their relative activity

Plasma Test

Our Plasma test is a metatranscriptomic (RNA sequencing) plasma or serum test that identifies and quantifies all living microorganisms in the sample, including RNA viruses (human, plant, and phages). It can also identify cell-free RNAs.

  • Samples must be collected by a phlebotomist, requiring a venous blood draw and centrifugation

  • The phlebotomist must be trained to:

    • Use the VLS' skin prep kit for the removal of skin contaminants

    • Properly generate and transfer plasma/serum into VLS' sample preservation kit

    • Properly package the sample and ship at ambient temperature in a timely fashion

  • Includes all instructions, necessary components, and a pre-paid return mailer

  • Isolates total RNA from plasma or serum (DNA is degraded)

  • Physically removes microbial and human rRNAs from total RNA

  • Sequences all remaining RNAs using a full-length transcript, directional method

  • Produces quantitative strain-, species-, and genus-level taxonomic classification data

  • Produces quantitative microbial gene expression data clustered into KEGG orthologies (KOs). This is different from metagenomic functional outputs, which only indicate functional potential, whereas this test measures actual microbial functions

Data provided by VLS to the grantee:

  • List of genera and their relative activity

  • List of species and their relative activity

  • List of strains and their relative activity

  • List of KOs and their relative activity

  • List of human genes and their gene expression level (can be counts per million or transcripts per million)

FAQS

References

Hatch, A., et al. A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health, Int. J. Gen. Volume 2019 |Article ID 1718741

Toma, R., et al. A clinically validated human capillary blood transcriptome test for global systems biology studies, BioTechniques 2020, Vol. 69, No. 4

Banavar, G., et al. The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer, Genomic Medicine, 2020, accepted for publication.

Leek, J., Scharpf, R., Bravo, H., Simcha, D., Langmead, B., Johnson, W., Geman, D., Baggerly, K., Irizarry, R. (2010). Tackling the widespread and critical impact of batch effects in high-throughput data Nature Reviews Genetics 11(10), 733-739. https://dx.doi.org/10.1038/nrg2825