(506 days)
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No
The summary describes a device for collecting and stabilizing fecal samples for microbiome analysis. While the analysis of the microbiome data might involve computational methods, the device itself, as described, does not incorporate AI or ML technology. The performance studies focus on the analytical performance of the collection and stabilization process, not on any AI/ML-driven interpretation or processing of the data.
No.
The device is intended for the non-invasive collection and stabilization of human fecal samples for subsequent assessment of the microbiome profile, not for treating any condition or disease.
Yes
The device is described as "OMNIgene. GUT Dx," with "Dx" often indicating "diagnostic." Its intended use is for "subsequent assessment of the microbiome profile by an assay validated for use with OMNIgene GUT Dx," which suggests it prepares samples for diagnostic analysis. The mention "For in vitro diagnostic use only" further confirms its role in a diagnostic context, even though the device itself is for sample collection and stabilization rather than direct diagnosis.
No
The device description clearly outlines physical components including a collection tube, tube top, pusher cap, spatula or spoon, stabilizing liquid, and a stainless-steel mixing ball. These are hardware components, not software.
Yes, this device is an IVD (In Vitro Diagnostic).
Here's why:
- Intended Use: The "Intended Use / Indications for Use" section explicitly states that the device 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." This describes a process performed in vitro (outside the body) on a biological specimen for diagnostic purposes (assessing the microbiome profile).
- Intended User / Care Setting: The "Intended User / Care Setting" section clearly states "For in vitro diagnostic use only." This is a direct declaration of its IVD status.
- Purpose: The device is designed to collect and stabilize a biological sample (fecal matter) for later analysis to provide information about the patient's microbiome, which can be used for diagnostic purposes.
The description of the device, the performance studies conducted (analytical performance, stability, neutrality, reproducibility), and the metrics evaluated (DNA yield, consistency of microbial composition) all support its classification as an IVD.
N/A
Intended Use / Indications for Use
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.
Product codes
OPO
Device Description
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.
Mentions image processing
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Mentions AI, DNN, or ML
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Input Imaging Modality
Not Found
Anatomical Site
human fecal samples
Indicated Patient Age Range
Adult Cohort 18+ years, Pediatric Cohort 3-46 months
Intended User / Care Setting
For in vitro diagnostic use only, For prescription use only
Description of the training set, sample size, data source, and annotation protocol
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Description of the test set, sample size, data source, and annotation protocol
Neutrality Study:
Sample Size: 30 total donors (initially 45, but screened down to 30)
Data Source: Human fecal samples, collected non-invasively at the donor's home or a collection site. Specimens were collected under an institutional review board (IRB) approved protocol and informed consent was obtained.
Annotation Protocol: Fecal specimens collected in OMD-200 devices with stabilization liquid ("OMD-200 baseline") were compared to fecal specimens from the same donor collected without stabilization liquid ("unstabilized control baseline"). Microbial community consistency was evaluated based on whether rarefied species-level read counts for each Microbiome Panel species in the test samples fell within the Test Sample Read Count Limit (TeSaRCol) range calculated from the unstabilized control sample. Acceptance criteria included DNA yield >= 120 ng per extraction aliquot in >= 95% of samples, and neutrality demonstrated in >= 90% of donors for each Microbiome Panel species.
Room Temperature Storage Stability Study:
Sample Size: 30 donors.
Data Source: Human fecal samples.
Annotation Protocol: Evaluated the ability of the OMD-200 device to stabilize microbial community composition during room temperature storage (20-26°C) for up to 30 days, both with and without the OM-LQR processing reagent. Acceptance criteria included DNA yield >= 120 ng per extraction aliquot in >= 95% of samples, and stability demonstrated in >= 90% of donors for each Microbiome Panel species, with read counts within the TeSaRCol range as calculated using the OMD Baseline.
Reproducibility Study:
Sample Size: 14 donors in the final dataset for both lot-to-lot and aliquot-to-aliquot reproducibility.
Data Source: Fecal samples.
Annotation Protocol:
Lot-to-lot: Three different lots of OMD-200 devices, each with a different lot of stabilizing solution, were used. The same sample was collected into one device from each lot.
Aliquot-to-aliquot: Five aliquots were sequentially taken from the same collected OMD-200 sample.
Consistency in microbial community composition was assessed based on the coefficient of variation (CV) of classified read counts post-rarefaction. Acceptance criteria included DNA yield >= 120 ng (0.12 ug) per extraction aliquot in >= 95% of samples, and CV of classified read counts post-rarefaction = 90% of donors.
Whole Microbiome Analysis Studies:
Sample Size: Leveraged sequencing data from the Stability and Neutrality Study and the Reproducibility Study.
Data Source: Samples from the aforementioned studies.
Annotation Protocol: Classified read counts were rarefied to 2 million reads per sample. Read counts from test samples were compared, species-by-species, to control samples to ensure they were within the TeSaRCol range. Data analysis involved transforming counts data using center-log ratio (CLR), evaluating differences using Aitchison distance for group-wise comparisons, and ALDEx2 differential analysis for changes between individual taxa. Alpha diversity was measured by Shannon's index and number of observed taxa. PCA analysis and hierarchical cluster analysis were also performed.
Summary of Performance Studies
Stability and Neutrality Studies:
Study Type: Analytical performance study
Sample Size: For Neutrality, 30 adult and pediatric donors. For Stability, 30 adult and pediatric donors.
AUC: Not mentioned.
MRMC: Not mentioned.
Standalone Performance: Not applicable, device does not provide a result.
Key Results:
Neutrality: All species in the Microbiome Panel demonstrated neutrality in >= 90% of donors between unstabilized and OMD-200 fecal samples. 100% of specimens met the DNA yield acceptance criteria of 120 ng.
Stability: All species in the Microbiome Panel demonstrated stability in >= 90% of donors when stored at room temperature for up to 30 days, with or without OM-LQR. 100% of specimens met the DNA yield acceptance criteria of 120 ng.
Whole Microbiome Analysis (Stability): Group-wise comparison of Aitchison distance showed no difference between stability time points (P > 0.05) and that the change in microbial profile was significantly lower than donor-to-donor differences (P = 120 ng).
Neutrality Acceptance: >= 90% of donors showed neutrality per Microbiome Panel species.
Stability Study DNA yield: 100% of specimens met acceptance criteria (>= 120 ng).
Stability Acceptance: >= 90% of donors showed stability per Microbiome Panel species.
Reproducibility Study DNA yield: 100% of specimens met acceptance criteria (>= 120 ng or 0.12 ug).
Reproducibility CV:
Lot-to-lot: Min CV 0.22%, Max CV 21.95%, Mean CV 5.84%, Median CV 4.92%, Overall pass rate (CV
N/A
0
EVALUATION OF AUTOMATIC CLASS III DESIGNATION FOR OMNIgene.GUT Dx DECISION SUMMARY
A. DEN Number:
B. Purpose for Submission:
De Novo request for evaluation of automatic class III designation for the OMNIgene . GUT Dx
C. Measurands:
Storage and stability of bacterial DNA from human fecal specimens.
D. Type of Device:
Device to preserve and stabilize relative abundances of microbial nucleic acids in clinical samples
E. Applicant:
DNA Genotek Inc.
F. Proprietary and Established Names:
OMNIgene.GUT Dx
OMD-200
G. Regulatory Information:
-
- Regulation section:
21 CFR 866.2952
- Regulation section:
-
- Classification:
Class II
- Classification:
1
-
- Product code(s):
OPO
- Product code(s):
-
- Panel:
83- Microbiology
- Panel:
H. Indications for Use:
-
- Indications for use:
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.
- Indications for use:
-
- Special conditions for use statement(s):
For in vitro diagnostic use only For prescription use only
- Special conditions for use statement(s):
-
- Special instrument requirements:
None
- Special instrument requirements:
I. Device Description:
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.
J. Standard/Guidance Document Referenced (if applicable):
Not applicable
K. Test Principle:
Not applicable
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L. Performance Characteristics:
1. Analytical performance:
a. Whole Genome Sequencing (WGS) Assay Validation
To assess collection device performance, a whole genome sequencing assay workflow was validated. This validation included defining a microbiome panel of bacterial species and quantitating the Limit of Blank, Limit of Detection, Lower Limit of Quantitation, Upper Limit of Quantitation, Lower Baseline Read Count Limit, Upper Baseline Read Count Limit, and Range (see definitions below) for each of these bacterial species in the microbiome panel (MP). Using these established limits and ranges for this panel, the device performance was quantitated in terms of stabilization of bacterial DNA as well as specifically the preservation of relative abundances of these specific bacterial members within fecal specimens, described as "neutrality".
Definitions of Terms:
Background DNA Mixture (BDM) - Since WGS enumerates all DNA molecules present in a library preparation, the ability to detect targets of interest is directly proportional to the abundance of the target and the presence of other non-target or 'background' DNA molecules. A mixture of non-target DNA (bacterial in origin) has been created to serve as a diluent, for the determination of LoD, LoQ and Range for targets in the Microbiome Panel.
Limit of Blank (LoB) - The highest measurement result that is likely to be observed for a blank sample.
Limit of Detection (LoD) - The Lowest amount of analyte in a sample that can be detected above the defined Limit of Blank.
Lower Limit of Quantitation (LLoQ) - The lowest amount of analyte in a sample that can be quantitatively determined with acceptable precision and trueness.
Upper Limit of Quantitation (ULOQ) - The highest amount of analyte in a sample that can be quantitatively determined with acceptable precision and trueness.
Range - Dynamic range for reliable quantification of WGS reads will be established through contrived sample sequencing and analysis. This per species range falls between the ULOQ and LoD determined in the assay validation for each species and will be applied across all sequencing studies.
Lower Baseline Read Count Limit (I-BRCL) - The minimum read count a species can have within a baseline sample (e.g. an unstabilized (fresh) sample for neutrality tests; a T0 sample for stability tests) in order for the pair of samples from a donor to be included in testing for that species. I-BRCL is a species-specific value, which will be calculated for each species during assay validation, based on the LLoO for that species.
Upper Baseline Read Count Limit (u-BRCL) - The maximum read count a species can have within a baseline sample (e.g. an unstabilized (fresh) sample for neutrality tests; a T0 sample for stability tests) in order for the pair of samples from a donor to be included in testing for that species. u-BRCL is a species-specific value, which will
3
be calculated for each species during assay validation, based on the ULOO for that species.
| Species ID | Family |
|---|---|
| (b)(4) |
The members of this panel were selected based on the following criteria:
- · High prevalence | (014) in representative donor population
- · Abundance (b)(4) in donors where species is present
- · Representative species from major bacterial families on the gut microbial community phylogenetic tree: (D)(-)
(b) Fry
- Gram-negative and Gram-positive bacteria are represented o
- (DR4) · Genomes range in GC content from
Additionally, a pathogenic species from the (54) family was included in the panel as well as three pediatric relevant species.
Lower and Upper Baseline Read Count Limits:
The purpose of the lower and upper Baseline Read Count Limits (I-BRCL and u-BRCL) was to define a read count range for baseline samples that was contained within the overall quantifiable range of the WGS assay. This was done to ensure that if the read counts of a microbiome panel species changed over time or in response to an external challenge, the change from baseline was quantifiable and did not immediately exceed the lower and upper quantification limits.
The LoQ values (LLoQ and ULoQ) were used to calculate the lower and upper Baseline Read Count Limit (I-BRCL and u-BRCL). The calculated upper and lower BRCL for each species was used in the screening of donors for OMNIgene.GUT Dx sample collections.
4
The per-panel species defined Limits and Ranges are summarized below.
Summary of Final Limits and Range for the WGS assay and the upper and lower limits for Baseline samples (BRCLs)
Test Sample Read Count Limits (TeSaRCol):
The above defined WGS assay limits are designed to define the read count range in which a Microbiome Panel species can be tested with confidence. The OMNIgene GUT Dx analytical testing used these limits in the context of the Test Sample Read Count Limit (TeSaRCol) method (Figure 1).
Image /page/4/Picture/4 description: The image is a gray rectangle with a red border. The text '(b)(4)' is in the upper center of the rectangle. The text is in red and is small in size.
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5
Image /page/5/Figure/0 description: The image shows a gray rectangle with the text "Test Sample" on the left side. There is also the text "(b)(4)" at the top of the rectangle. On the right side of the rectangle, there is a legend that says "Limit" with "Max" and "Min" listed below.
-
b. Stability and Neutrality Studies
This section describes two studies evaluating device performance in terms of: -
- Microbiome Relative Abundance Preservation ("Neutrality")
-
- Room Temperature Storage Stability
These studies were conducted in two population cohorts, which followed identical study designs:
6
- Adult Cohort 30 minimum donors, ages 18+ years .
- · Pediatric Cohort 30 minimum donors, ages 3-46 months
Fecal collection occurred at either the donor's home or a collection site following provided user instructions. For the pediatric cohort, the actual collection was performed by a parent/guardian. Specimens were collected under an institutional review board (IRB) approved protocol and informed consent was obtained prior to collection. Collection was performed using a container (not the candidate device) without the stabilization liquid to a fill-to line to acquire bulk specimen, which was sent to the processing lab on ice within 24 hours of collection (adult cohort) or 48 hours of collection (pediatric cohort).
Donor Screening and Inclusion:
A sample from each donor was screened to ensure that each donor met set inclusion criteria for these studies. For adult donors to be included, screened fecal specimens had to contain a minimum of 10 species from the Microbiome Panel ( ( (6)(4) within Baseline Read Count Limits determined during the WGS assay validation study. Additionally, each adult relevant species of the Microbiome Panel ( on () (b)(4) ) had to be represented in the screened sample within BRCLs by a minimum of (0) donors. The clinically relevant species in the Microbiome Panel ( DKA) was evaluated as it appeared and had no criteria for minimum number of donors.
For pediatric donors to be included, due to inherent low prevalence and lack of species diversity in the youngest pediatric donors, each pediatric sub-cohort had different inclusion criteria. which increased with age to reflect the change to an adultlike microbial diversity. Specifically, the screened sample from the pediatric donor must have the minimum number of species (listed below) from the Microbiome Panel within their BRCLs as determined during assay validation:
- 3-14 months: Minimum of 2 species total, with a minimum of 1 species from . (0)(4) specifically
- · 15-30 months: Minimum of 6 species total, no restrictions on which species
- · 31-46 months: Minimum of 8 species total, no restrictions on which species
Each pediatric relevant species of the Microbiome Panel ( @10) must be represented in the screened sample within BRCLs by a minimum of 10 donors.
| (0)(4) | |
|---|---|
7
(b)(4)
Control samples included 1 positive specimen control (PSC)
(b)(4)
(b)(4)
One (1) negative specimen control (NSC) sample was included (b)(4)
(b)(4)
One (1) no template control (NTC) was included
(b)(4)
(b)(4)
(b)(4)
(b)(4)
Normalized libraries were pooled
together
(b)(4)
loaded onto the cartridge and the sequencing run is started. Sequencing
8
was done on the Illumina NextSeq 550 [
(0)(4)
(0)147 Note that each step (extraction,
quantification, library prep, sequencing) was individually validated using the same principles as described above for the whole genome sequencing assay.
(b)(4)
WGS Bioinformatics Analysis Procedure:
9
Microbiome Relative Abundance Preservation ("Neutrality"):
The objective of this "Neutrality" study was to validate the ability of the OMD-200 device to not interfere with the microbial community composition at the point of collection such that it maintains an unbiased representation of the in vivo state, i.e. preserves the relative abundances of bacterial organisms in the specimen. This study compared fecal specimens collected in OMD-200 devices containing the stabilization liquid ("OMD-200 baseline") to fecal specimens from the same donor collected without the stabilization liquid contained within the OMNIgene GUT Dx device ("unstabilized control baseline").
15141
While this study initially included 45 donors, only 30 total donors were included in the final dataset after screening donors for specified inclusion criteria identified in the
10
donor screening section above. Importantly, the OMD-200 baseline specimen data from this study were also used for the room temperature storage stability study described below.
| Number of Donors | 45 | |
|---|---|---|
| Control Specimens | ||
| without | ||
| Stabilization | ||
| Liquid | # specimens collected per donor | 1 |
| # of DNA extractions per specimen | 1 | |
| Total # extracted control specimens | 45 | |
| Total # of control specimens in final dataset | 30 | |
| OMD-200 | ||
| Collected | ||
| Specimens | # specimens collected per donor | 1 |
| # of DNA extractions per specimen (OMD Baseline) | 1 | |
| Total # extracted OMD-200 specimens | 45 | |
| Total # extracted OMD-200 specimens in final dataset | 30 | |
| Total # of Extracted Samples | 90 | |
| Total # of Samples for Final Data Set | 60 |
Number of Donor Specimens and Extracted Samples in Neutrality Study
Representation of Microbiome Panel species in the adult cohort of the neutrality
Image /page/10/Picture/4 description: This image shows a table with two columns. The first column is labeled "Species ID" and the second column is labeled "Total Number of Donors". The table appears to be empty, with no data present in either column. The table is part of a study.
Representation of Microbiome Panel species in the pediatric cohort of the neutrality study
Total Number of Donors Species ID
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| Species ID | Total Number of Donors |
|---|---|
| Pediatric Sub cohort representation in the neutrality study | |||||
|---|---|---|---|---|---|
| -- | -- | -- | ------------------------------------------------------------- | -- | -- |
| Pediatric Sub-Cohort | # Donors | Representation |
|---|---|---|
| 3-14 months | 10 | 33.3% |
| 15-30 months | 12 | 40.0% |
| 31-46 months | 8 | 26.7% |
Microbial community consistency between control and test samples was evaluated based on whether rarefied species-level read counts for each Microbiome Panel species in the test samples fell within TeSaRCol range calculated from the unstabilized control sample:
Image /page/11/Picture/4 description: The image is a gray rectangle with a red border. In the top center of the rectangle is the text "(b)(4)". The text is also red.
Neutrality Acceptance Criteria:
The acceptance criteria for this study included a total DNA yield ≥ 120 ng 0 (b)(4) per extraction aliquot in ≥ 95% of samples. Additionally, microbial community neutrality is demonstrated as follows:
- Per donor, each Microbiome Panel species in the stored sample has read . counts within the TeSaRCol range as calculated above using the unstabilized Control Baseline
- Neutrality per Microbiome Panel species will be demonstrated in ≥ 90% of . donors that were successfully screened to contain that species
Neutrality Results: For the neutrality study, microbial DNA They
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(6)(5) The results of this study showed that all species examined as part of the Microbiome Panel demonstrated neutrality in ≥ 90% of donors between unstabilized and OMD-200 fecal samples. Furthermore, for both the adult and pediatric cohorts evaluated, 100% of specimens met the DNA yield acceptance criteria of 120 ng ( (0)(4)
Colley
Statistical summary of OMD-200 device DNA yields (ug) for neutrality samples of both cohorts
| Adult Cohort | Pediatric Cohort | ||
|---|---|---|---|
| (b)(4) | (b)(4) | (b)(4) | |
| Mean ± SD | $11.98 \pm 4.37$ | $9.69 \pm 5.65$ | |
| 95% CI of Mean | 10.35, 13.62 | 7.58, 11.81 | |
| Median | 11.45 | 8.51 | |
| Min, Max | 5.10, 26.47 | 2.41, 27.81 | |
| % ≥ | 100% | 100% |
Room Temperature Storage Stability:
The objectives of this stability study were to validate the ability of the OMD-200 device to stabilize the microbial community composition during room temperature storage and to validate that the addition of the OM-LQR processing reagent does not impact the ability of the OMD-200 device to stabilize samples during room temperature storage (20℃ - 26℃).
Number of Donor Specimens and Extracted Samples in Room Temperature Stability Study
| Stability Study | ||
|---|---|---|
| Number of Donors | ||
| RT Storage | ||
| With OM-LQR | # specimens collected per donor |
of DNA extractions per specimen
Total # extracted specimens | (b)(4) |
| RT Storage
Without OM-LQR | # specimens collected per donor
of DNA extractions per specimen
Total # extracted specimens | |
| Total # of Extracted Samples | | |
| Total # of Samples for Final Data Set | | |
*30 samples are the shared OMD Baseline samples extracted as part of neutrality testing.
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Representation of Microbiome Panel species in the adult cohort of room temperature stability study
| Species ID | Total Number of Donors |
|---|---|
| 2274 | |
Pediatric Sub cohort representation in the room temperature storage study
| Pediatric Sub-Cohort | # Donors | Representation |
|---|---|---|
| 3-14 months | 8 | 26.7% |
| 15-30 months | 17 | 56.7% |
| 31-46 months | 5 | 16.7% |
Representation of Microbiome Panel species in the pediatric cohort of room temperature storage stability study
Image /page/13/Picture/5 description: This image shows a table with two columns, "Species ID" and "Total Number of Donors". The table contains one row with the value "(DK-1)" in the "Species ID" column. The "Total Number of Donors" column is empty.
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Image /page/14/Figure/0 description: The image is a gray rectangle with a thin red border. In the center of the rectangle, there is the text "(b)(4)" in a small, light-colored font. The background is a uniform gray color, and the red border is a simple, thin line that outlines the entire rectangle.
Room Temperature Storage Stability Acceptance Criteria:
The acceptance criteria for this study included a total DNA yield ≥ 120 ng ( per extraction aliquot in ≥ 95% of samples. Additionally, microbial community stability is demonstrated as follows:
- . Per donor, each Microbiome Panel species in the stored sample has read counts within the TeSaRCol range as calculated using the OMD Baseline
- Stability per Microbiome Panel species will be demonstrated in ≥ 90% of . donors that were screened to contain that species
Room Temperature Storage Stability Results:
For both the adult and pediatric cohorts evaluated, 100% of specimens met the DNA yield acceptance criteria of 120 ng ( b | Furthermore, all species examined as part of the Microbiome Panel demonstrated stability in ≥ 90% of donors when stored at room temperature for up to 30 days either with or without the addition of OM-LQR (auxiliary liquefaction reagent).
Statistical summary of DNA yields (ug) for room temperature stability samples of both cohorts.
Image /page/14/Figure/8 description: The image shows a table with two columns. The first column is labeled "Adult Cohort" and the second column is labeled "Pediatric Cohort". The table appears to be empty, with no data present in either column.
Reproducibility Study C.
The primary objectives of this study were to evaluate: 1) performance reproducibility of the OMD-200 collection device across multiple device lots when used to collect from the same fecal sample, and 2) microbiome profile reproducibility across multiple aliquots of the same OMD-200 collected fecal sample. (0)(4) 10/4)
15
Three different lots of OMD-200 devices, each containing a different lot of stabilizing solution, were used. The same sample was collected into one device from each lot to evaluate the reproducibility between device lots. To evaluate the reproducibility between aliquots, five aliquots were sequentially taken from the same collected OMD-200 sample. This study included 14 donors in the final dataset. These 14 were selected after screening for the inclusion criteria ========================================================================================================================== (0)(4)
15/4
section of the adult cohort.
Number of Donor Specimens and Extracted Samples in the Lot-to-lot Reproducibility Study
| Total Number of Donors | 14 |
|---|---|
| Number of specimens collected per donor | 3 |
| Number of specimens collected per lot | 14 |
| Number of DNA extractions per specimen | 1 |
| Total # of Extracted Samples for Final Data Set | 42 |
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Number of Donor Specimens and Extracted Samples in the Aliquot-to-aliquot Reproducibility Study
| Total Number of Donors | 14 |
|---|---|
| Number of specimens collected per donor | 1 |
| Number of DNA extractions per specimen | 5* |
| Total # of Extracted Samples | 56 |
| Total # of Samples for Final Data Set | 70* |
- One extraction was performed during the Lot-to-lot Reproducibility Study
Reproducibility Study Procedures:
| From a single specimen, each donor collected (b)(4) aliquots into (b)(4) OMD-200
devices, representing (b)(4) unique device lots. Specimens were received and
| processed by lab personnel. |
|---|
| (b)(4) |
| (b)(4) |
| (b)(4) All |
aliquots from one donor were extracted by a single operator. DNA was extracted, quantified, sequenced, and analyzed. Consistency in microbial community composition across samples was assessed based on the coefficient of variation (CV) of classified read counts post-rarefaction.
Representation of Microbiome Panel species in the donor cohort
Image /page/16/Picture/7 description: The image shows a table with two column headers: "Species ID" and "Number of donors". The table itself is empty, with no data populated beneath the headers. The image is a close-up of the table headers, with a gray background filling the rest of the frame. The table is outlined in a light green color.
Reproducibility Acceptance Criteria:
The acceptance criteria for this study included a total DNA yield ≥ 120 ng (0.12 ug) per extraction aliquot in ≥ 95% of samples. Additionally, microbial community composition consistency is shown as follows:
- CV of classified read counts post-rarefaction 1), and statistically significant (Benjamini-Hochberg adjusted P-value 0.05), and that the change in microbial profile was significantly lower than observed donorto-donor differences (P 0.1). This indicates that the differences between these conditions did not exceed the inferred sample variability within the group.
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A: Adult Cohort
CHECK
B: Pediatric Cohort
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Image /page/23/Figure/0 description: The image is a gray rectangle with a red border. The text '(b)(4)' is located at the top center of the rectangle. The text is small and in black font.
Neutrality (Whole Microbiome) Results:
Group wise comparison of the Aitchison distance using the Kruskal-Wallis H test and a two-group t-test showed that the change in microbial profile was significantly lower between OMD-200 collected fecal samples at baseline (OMDB) and unstabilized control fecal samples at baseline (CB) than that observed for donor-to-donor differences at baseline (P 0.1) (shown below for both adult and pediatric cohorts). This indicated that the differences between these conditions did not exceed the inferred sample variability within the group.
(b)(4)
A: Adult Cohort
B: Pediatric Cohort
PCA analysis (both adult and pediatric cohorts) and hierarchical cluster analysis of the data showed intra-donor clustering, regardless of collection and storage condition.
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Reproducibility (Whole Microbiome) Study:
Reproducibility (Whole Microbiome) Results:
Group wise comparison of the Aitchison distance using the Kruskal-Wallis H test and a two-group t-test showed that, as expected, the difference between the same fecal sample collected into | OMD-200 collection devices (lot-to-lot) was significantly lower than the difference between stability time points (30 days). Furthermore, the difference between (1) aliquots extracted from a single OMD-200 collected fecal sample (aliquot-to-aliquot) also showed smaller changes in Aitchison distance compared to the stability time points (30 days) (Figure below).
Significant change (P