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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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Oragene®•Dx is intended for use in the non-invasive collection of saliva samples for in vitro diagnostic testing of human DNA. Saliva may be collected by spitting directly into the Oragene®•Dx container or may be transferred into the Oragene® Dx container using a sponge. Saliva samples may be collected by a healthcare professional or non-healthcare professional, such as a lay user. Saliva samples collected using Oragene®•Dx are stabilized and isolated for use in downstream diagnostic testing applications. Saliva samples collected using Oragene®•Dx can be transported and/or stored long term at ambient conditions

Oragene®●Dx family of collection devices offers reliable collection, transportation and long-term ambient temperature storage of human DNA from saliva. Oragene®●Dx devices are a noninvasive alternative for collecting high quality and quantity DNA for use with prescription and over-thecounter (direct-to-consumer) diagnostic testing applications.

Oragene®●Dx devices consist of a collection tube with a funnel lid attached (containing a stabilizing liquid). Saliva is delivered directly by spitting into the collection tube or may be transferred into the Oragene®●Dx container using a sponge. Saliva collection can take place at home, in a laboratory setting, physician's office, or in the field. Untrained (naïve) or professional users can carry out saliva collection.

After saliva is collected, the stabilizing liquid is mixed with the sample. A small cap is provided to close the tube for transport and storage (funnel with lid is removed and discarded). Upon contacting saliva cells, the stabilizing liquid lyses cellular and nuclear membranes to release and stabilize nucleic acids (DNA). Samples can be immediately processed, transported or stored for future use. Samples can be shipped at ambient temperature to the laboratory for processing. Oragene® •Dx samples are stable at room temperature for up to 12 months. Device and sample integrity are preserved during typical ambient transport and storage conditions.

Oragene®●Dx saliva collection devices are suitable for use with prescription and over-the-counter (direct-to-consumer) downstream diagnostic testing applications, systems or platforms. Test or assay manufacturers must validate the use of Oragene®●Dx for their specific indications for use.

Using DNA obtained from an Oragene®●Dx sample, laboratory testing is performed on genotyping systems or platforms in a CLIA (Clinical Laboratory Improvement Amendments) certified laboratory. The resulting genetic information may be used to generate a personalized health report related to detected mutations and may be used by medical and health practitioners as an aid in patient management.

The document describes the Oragene®•Dx saliva collection device and its performance characteristics to support its intended use for in vitro diagnostic testing of human DNA.

Here's the breakdown of the acceptance criteria and supporting study information:

1. Table of Acceptance Criteria and Reported Device Performance

The acceptance criteria for the Oragene®•Dx device are largely demonstrated by referencing prior 510(k) clearances (K110701, K141410, K152556) and its compatibility with already FDA-cleared test systems. The performance characteristics focus on the stability and suitability of the collected DNA for downstream diagnostic applications.

2. Sample Size Used for the Test Set and the Data Provenance

• Test Set Sample Size: The document does not explicitly state a specific numerical sample size for the user comprehension study conducted for the K192920 submission. It mentions "Potential users enrolled in usability studies." For other performance aspects (Reproducibility, Stability, Volume Tolerance, Interfering Substances), the document largely references previous 510(k) clearances and compatibility with existing FDA-cleared test systems, implying the sample sizes from those original studies were deemed sufficient.
• Data Provenance: The document does not specify the country of origin for the data for any of the studies mentioned. The submitter is DNA Genotek Inc., located in Ottawa, Ontario, Canada.
• Retrospective/Prospective: The user comprehension study for over-the-counter use appears to be prospective, as it involved "Potential users enrolled in usability studies collected saliva samples at home." The referenced studies for stability and other analytical performance characteristics were likely prospective as well, as they involved specific testing protocols to establish performance claims.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and the Qualifications of Those Experts

• The document does not mention the use of experts to establish a "ground truth" for the test set in the traditional sense of clinical adjudication.
• For the user comprehension study, the "ground truth" was established by objective measures such as successful collection of saliva, compliance with instructions, DNA concentration, and PCR call rate, as well as subjective user comprehension surveys. This process does not typically involve expert consensus on the "truth" of a clinical condition.
• The overall "truth" for the device's function as a DNA collection device is its ability to yield high-quality DNA suitable for downstream diagnostic testing, as demonstrated by compatibility with FDA-cleared molecular diagnostic platforms.

4. Adjudication Method for the Test Set

• Not applicable in the context of this device's performance claims. The studies focus on analytical performance (DNA yield, stability, compatibility) and user comprehension/compliance, rather than diagnostic accuracy requiring adjudication of clinical findings.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, What was the Effect Size of How Much Human Readers Improve with AI vs without AI Assistance

• Not applicable. This device is a saliva collection kit, not an AI-powered diagnostic tool. Therefore, MRMC studies and AI assistance metrics are irrelevant to its evaluation.

6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done

• Not applicable. This device is a physical collection kit, not an algorithm. Its performance is inherent to the physical and chemical properties of the kit and the stabilization solution, as well as user compliance with instructions.

7. The Type of Ground Truth Used (Expert Consensus, Pathology, Outcomes Data, etc.)

• The "ground truth" for the performance of the Oragene®•Dx device is primarily based on analytical performance metrics (DNA yield, DNA concentration, purity ratios (A260/A280), microbial content, PCR call rates) and functional compatibility with established FDA-cleared molecular diagnostic test systems.
• For the Over-the-Counter use, the "ground truth" includes user compliance with instructions and successful sample collection based on objective parameters (volume, DNA quality) and user comprehension through surveys.

8. The Sample Size for the Training Set

• Not applicable. This device is a physical collection kit, not a machine learning model that requires a training set. The performance is based on established chemical and physical principles and validated through testing.

9. How the Ground Truth for the Training Set Was Established

• Not applicable, as there is no training set for this type of device.

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ORAcollect Dx is intended for use in the non-invasive collection of saliva samples. Human DNA from the saliva sample is isolated, stabilized, and suitable for use in FDA cleared molecular diagnostic applications. Saliva sample sultured using ORAcollect+Dx are stabilized and can be transported and/or stored long term at anbient can adions.

The ORAcollect-Dx family of collection devices offers reliable collection, transportation and long-term ambient temperature storage of human DNA from saliva. ORAcollect-Dx is a non-invasive alternative for collecting high quality and quantity human DNA and is suitable for use in molecular diagnostic applications.

ORAcollect-Dx consists of a collection tube containing a stabilizing liquid and a double ended cap with an integrated sponge used to collect a saliva sample. After receiving instruction from a professional, saliva collection can take place in a laboratory setting, physician's office, at home, or in the field. Untrained (naïve) or professional users can carry out saliva collection.

Using the provided instructions for use, the integrated sponge on the device to collect a saliva sample from the mouth. After saliva is collected, the cap is removed from the tube, inverted to place the sponge into the collection tube with the stabilizing liquid, and re-capped with the sponge remaining inside the tube. Upon contacting saliva cells, the stabilizing liquid lyses cellular and nuclear membranes to release and stabilize nucleic acids (DNA).

Samples can be immediately processed, transported or stored for future use. Samples can be shipped at ambient temperature to the laboratory for processing.

ORAcollect-Dx device pre-collection shelf life is 24 months at room temperature (15°C to 25°C) from the date of manufacture. Post collection, ORAcollect·Dx samples are stable at room temperature for up to 60 days. ORAcollect · Dx device and sample integrity are preserved during typical ambient transport and storage conditions.

The provided text describes the performance criteria and studies for the ORAcollect•Dx OCD-100 and ORAcollect•Dx OCD-100A saliva collection devices. The studies aim to demonstrate that the device collects high-quality human DNA suitable for FDA-cleared molecular diagnostic applications, specifically using the eSensor Warfarin Sensitivity Saliva Test.

Here's a breakdown of the requested information:

1. Table of Acceptance Criteria and Reported Device Performance

General Acceptance Criteria for DNA Endpoints (unless otherwise specified per study):

2. Sample Sizes Used for the Test Set and Data Provenance

The studies described are primarily performance evaluation studies for the device itself, rather than testing a specific clinical application on patient data. Therefore, the "test set" here refers to the samples collected specifically for these performance evaluations.

• Reproducibility/Precision:
  • Sample-to-sample, Lot-to-Lot, day-to-day and operator-to-operator: 10 donors, each collecting 9 saliva samples (total 90 samples). Data provenance is not explicitly stated (e.g., country of origin, retrospective/prospective), but the study design suggests prospective collection for the purpose of the evaluation.
  • Multi-centre reproducibility: 30 donors, each collecting multiple saliva samples from 3 sites. Data provenance is not explicitly stated, but the study design suggests prospective collection.
• Post-collection Sample Stability: 30 donors provided samples (total 120 DNA samples analyzed, subset of 10 donors tested on eSensor assay). Data provenance is not explicitly stated, but likely prospective.
• User Study (Sampling Variability):
  • Effect of incorrect collection methods: 10 donors, multiple samples each.
  • Effect of collection from incorrect site: 10 donors, multiple samples each.
    Data provenance not explicitly stated, likely prospective.
• Dry Mouth Study: 13 donors. Data provenance not explicitly stated, likely prospective and with specific selection criteria for dry mouth.
• Human Factors: Naive donors (number not specified, but multiple donors implied). Data provenance not explicitly stated, likely prospective.
• Interfering Substances (Endogenous): Donors provided 4 ORAcollect•Dx samples each (number of donors not specified). Data provenance not explicitly stated, likely prospective.
• Interfering Substances (Exogenous): Donors provided 3 samples each for 5 test groups (number of donors not specified, but implied multiple). Data provenance not explicitly stated, likely prospective.
• Matrix Comparison (OCD-100A vs OCD-100): 45 donors, 1 sample each using OCD-100A format and samples collected by the same donors using OCD-100 format. Data provenance not explicitly stated, likely prospective.
• Method Comparison (Overall Analytical Performance): "100% of samples" (total number not specified, but refers to overall performance data generated across various studies).

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts

The ground truth for genotyping in these studies was established by bidirectional sequencing. This is an objective laboratory method and does not typically involve human "experts" in the same way, for example, a radiologist would establish ground truth for image interpretation. Therefore, the concepts of "number of experts" and "qualifications of experts" are not directly applicable in this context. The "expert judgment" lies in the robust establishment and validation of the bidirectional sequencing method itself.

4. Adjudication Method for the Test Set

Not applicable. The ground truth (bidirectional sequencing) is an objective laboratory result. Discrepancies would typically lead to re-sequencing or investigation of laboratory error, rather than adjudication between human experts. "First-pass" and "final-pass" results are mentioned for the eSensor Warfarin Sensitivity Saliva Test, indicating that initial results might be re-evaluated or re-tested if they don't meet criteria, but this is an evaluation of the device performance against the objective ground truth, not an adjudication of human interpretation.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance

Not applicable. This device is a saliva collection kit, not an AI-powered diagnostic tool for human interpretation. The studies evaluate the device's ability to collect and preserve DNA for subsequent molecular diagnostics, not its impact on human reader performance.

6. If a Standalone (i.e. algorithm only without human-in-the loop performance) was done

This refers to the performance of the ORAcollect•Dx device itself, which is a standalone collection device. The performance evaluation includes the collection, stabilization, and suitability of the DNA for use in a downstream molecular diagnostic application (the eSensor Warfarin Sensitivity Saliva Test). The device's performance is assessed "algorithm only" in the sense that its output (DNA) is objectively measured and then fed into another diagnostic algorithm (the eSensor test).

7. The Type of Ground Truth Used

The primary ground truth used for validating the accuracy of genotyping results from DNA collected by ORAcollect•Dx (when tested with the eSensor Warfarin Sensitivity Saliva Test) was bidirectional sequencing.

For other endpoints:

• DNA concentration, total DNA yield, A260/A280 ratio were measured using standard laboratory equipment and protocols, with established acceptance criteria.
• Microbial content was assessed against baseline measurements.
• Human Factors study involved task observation and post-collection surveys.

8. The Sample Size for the Training Set

The document does not explicitly mention a "training set" in the context of machine learning or algorithm development for this device. The studies described are performance validation studies. The device itself (ORAcollect•Dx) is a physical collection kit, not an algorithm that requires a training set. The downstream eSensor Warfarin Sensitivity Saliva Test would have its own training and validation sets as part of its development, but those are not detailed here.

9. How the Ground Truth for the Training Set Was Established

Not applicable, as a "training set" in the context of an algorithm is not described for this device. If the downstream eSensor Warfarin Sensitivity Saliva Test had a training set, its ground truth would likely have been established by methods such as bidirectional sequencing, pathology confirmation, or other clinical gold standards relevant to warfarin sensitivity genotyping.

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