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OMNIgene. GUT Dx is intended for the non-invasive collection of human fecal samples and the stabilization of DNA from the bacterial community for subsequent assessment of the microbiome profile by an assay validated for use with OMNIgene GUT Dx.

The OMNIgene . GUT Dx device consists of a collection tube with a tube top and pusher cap with a screw seal, along with a spatula or spoon for transferring fecal specimen into the collection tube. The tube contains 2 mL of the stabilizing liquid and a stainless-steel mixing ball. These components are intended to stabilize bacterial DNA in human fecal specimens. notably to preserve the relative abundances of bacterial organisms, for potential downstream analysis of the fecal microbiome. The collection device is designed for storage of fecal specimens at room temperature (20-26°C/68-79°F) for up to 30 days.

Here's a breakdown of the acceptance criteria and the studies conducted to prove the OMNIgene.GUT Dx device meets these criteria, based on the provided text:

Acceptance Criteria and Reported Device Performance

The device's performance was evaluated through several analytical studies focusing on DNA yield, microbial community neutrality (preservation of relative abundances), and stability at room temperature, as well as reproducibility.

Table of Acceptance Criteria and Reported Device Performance

Study Details

1. Sample Sizes and Data Provenance

• Test Set Sample Sizes:
  • Neutrality Study: 30 total donors (Adult Cohort: minimum 30 donors, Pediatric Cohort: minimum 30 donors initially, but final dataset included 30 total after screening; tables indicate "45" collected, "30" in final dataset for adults and 30 total for pediatrics with specific sub-cohort counts).
  • Room Temperature Storage Stability Study: 30 total donors (same 30 OMD-200 baseline samples from Neutrality Study, plus additional samples for different time points/conditions).
  • Reproducibility Study (Lot-to-lot & Aliquot-to-aliquot): 14 donors in the final dataset (adult cohort, screened).
• Data Provenance:
  • Human fecal specimens collected from adult and pediatric donors.
  • Specimens were collected under an Institutional Review Board (IRB) approved protocol and informed consent was obtained.
  • Retrospective/Prospective: Primarily prospective or collected for the purpose of these studies (e.g., "Fecal collection occurred at either the donor's home or a collection site").
  • Country of Origin: Not explicitly stated, but implies a US-based study given the FDA regulatory context and IRB mention.

2. Number of Experts and Qualifications for Ground Truth

• Number of Experts: Not applicable. These studies are analytical performance assessments of a collection device, not diagnostic interpretation by human experts. The "ground truth" is derived from the WGS assay results of unstabilized (fresh) fecal samples and the established quantification limits for bacterial species.
• Qualifications: N/A

3. Adjudication Method for the Test Set

• Adjudication Method: Not applicable. This is an analytical performance study, not one requiring adjudication by human readers/experts for a diagnostic outcome. The primary measurements are DNA yield and relative read counts of specific bacterial species.

4. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study

• MRMC Study: No. This type of study is not relevant for evaluating the performance of a sample collection and stabilization device. MRMC studies are typically used for evaluating the effectiveness of diagnostic imaging tools or AI algorithms that assist human interpretation.

5. Standalone Performance (Algorithm Only)

• Standalone Performance: Not applicable in the traditional sense of an "algorithm." The device itself is a collection and stabilization tool. Its "performance" is assessed by its ability to preserve the biological sample's integrity for downstream analysis. The "algorithms" used are bioinformatics analyses (WGS, CLR transformation, Aitchison distance, ALDEx2, Shannon's index, PCA) to quantify changes in the microbial community, not algorithms that provide a diagnostic output on their own.

6. Type of Ground Truth Used

• Ground Truth:
  • Analytical Ground Truth: Unstabilized (fresh) fecal samples collected from the same donors, processed immediately, serving as the "baseline" or "in vivo state" for comparison of microbial community composition.
  • Quantitative Ground Truth: Established Limit of Blank (LoB), Limit of Detection (LoD), Lower Limit of Quantitation (LLoQ), Upper Limit of Quantitation (ULoQ), and corresponding Baseline Read Count Limits (BRCLs) and Test Sample Read Count Limits (TeSaRCol) for a defined Microbiome Panel of bacterial species. These limits provide quantitative thresholds for acceptable performance.

7. Sample Size for the Training Set

• Training Set Sample Size:
  • The document implies that the WGS Assay Validation section (L.1.a) describes the process of establishing the LoQ values and BRCLs for the Microbiome Panel species. This can be considered analogous to a "training" or "assay establishment" phase.
  • The specific sample size for that validation is not explicitly stated in terms of number of donors or samples for each bacterial species to define these limits. However, it mentions using "contrived sample sequencing and analysis" and calculations based on the LoQ values.

8. How the Ground Truth for the Training Set was Established

• Ground Truth for Training/Assay Validation:
  • The "ground truth" for defining the WGS assay limits (LoB, LoD, LLoQ, ULoQ) and subsequently the BRCLs and TeSaRCols was established through analytical validation methods. This involved:
    • Defining a Microbiome Panel (MP) of bacterial species based on criteria like prevalence, abundance, phylogenetic representation, and GC content, plus specific pathogenic/pediatric species.
    • Using "Background DNA Mixture (BDM)" as a diluent for determining LoD, LoQ, and Range.
    • Establishing these limits through quantitative experimental procedures (e.g., "contrived sample sequencing and analysis") to determine the lowest and highest amounts of analyte that can be determined with acceptable precision and trueness.
    • The BRCLs were calculated based on these LLoQ and ULoQ values for each species, ensuring that baseline samples fell within the quantifiable range of the WGS assay.

In summary, the device's performance was rigorously evaluated through analytical studies using well-defined quantitative acceptance criteria related to DNA preservation, microbial community neutrality, and stability, with comparisons made against immediate processing of unstabilized samples from the same donors to establish "ground truth" for its performance claims.

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