(296 days)
The xTAG® CYP2D6 Kit v3 is a device used to simultaneously detect and identify a panel of nucleotide variants found within the highly polymorphic CYP2D6 gene located on chromosome 22 from genomic DNA extracted from EDTA and citrate anticoagulated whole blood samples. This kit can also identify gene rearrangements associated with the deletion (*5) and duplication genotypes. The xTAG® CYP2D6 Kit v3 is a qualitative genotyping assay which can be used as an aid to clinicians in determining therapeutics that are metabolized by the CYP2D6 gene product. This kit is not indicated for stand-alone diagnostic purposes. This test is not intended to be used to predict drug response or nonresponse.
The xTAG CYP2D6 Kit v3 includes the following components:
- xTAG® 2D6 v3 PCR Primer Mix A
- xTAG® 2D6 v3 PCR Primer Mix B
- xTAG® 2D6 v3 ASPE Primer Mix
- xTAG® 2D6 v3 Bead Mix
- xTAG® 10x Buffer
- xTAG® Shrimp Alkaline Phosphatase
- xTAG® Exonuclease I
- xTAG® Streptavidin, R-Phycoerythrin Conjugate
- Platinum TI Exo(-) DNA Polymerase
- Platinum® Tfl Reaction Buffer, 5x
- Tfi 50mM MgCl3
- xTAG® Hot Start Taq (Long Acting)
- xTAG® 10x Tag Buffer (Long Acting)
- xTAG® Data Analysis Software (TDAS) CYP2D6
The provided document describes the xTAG® CYP2D6 Kit v3, a qualitative genotyping assay for detecting nucleotide variants and gene rearrangements in the CYP2D6 gene. The performance characteristics focus on accuracy, reproducibility, detection limit, analytical specificity, and matrix comparison, using bidirectional DNA sequencing as the comparator.
1. Table of acceptance criteria and the reported device performance
| Performance Characteristic | Acceptance Criteria (Implicit) | Reported Device Performance |
|---|---|---|
| Accuracy | High agreement with gold standard (bidirectional sequencing) for all alleles, including rare ones. | Overall Accuracy: 98.47% across all mutant and wild-type alleles (first test). 99.56% after re-testing of initial discrepant samples. |
| Accuracy for Rare Alleles | 100% accurate genotyping call rate for samples containing rare alleles. | Genotype Call Rate: 100% for plasmid clone-genomic DNA blends of rare alleles (n=20). |
| Reproducibility | 100% reproducible results after allowable re-runs. | Overall Reproducibility: 100% after allowable re-runs (due to operator error). No incorrect calls. |
| Detection Limit | Established minimum and maximum DNA concentrations for reliable detection. | Established Range: 2 ng/µL (Limit of Detection) to 300 ng/µL. |
| Input DNA Concentration | Established recommended input DNA concentration. | Recommended Concentration: 10 ng/µL. |
| Analytical Specificity / Interfering Substances | No interference from elevated levels of common biological substances. | No interference observed from Hemoglobin (500 mg/dL), Bilirubin (20 mg/dL), Albumin (3000 mg/dL), and Triglycerides (2000 mg/dL). |
| Matrix Comparison (EDTA vs. Citrate) | Identical genotyping calls across different anticoagulant types for the same samples. | No differences observed in final genotyping calls between EDTA and citrate anticoagulated samples. No "No Calls." |
2. Sample size used for the test set and the data provenance
- Sample Size for Accuracy Study (Test Set): 459 clinical samples.
- Data Provenance: The majority of samples were "left-over, anonymized, banked extracted DNA from EDTA or citrate anticoagulated whole-blood specimens." For rare alleles, the sample set was supplemented with "blended" samples where linearized plasmid DNA was quantitatively added to genomic DNA to mimic heterozygous samples. The country of origin is not explicitly stated, but the applicant is based in Toronto, Canada. Given the nature of banked specimens, it implies retrospective data.
3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts
The ground truth was established by bidirectional DNA sequencing, which is a laboratory method, not human expert interpretation in this context. Therefore, the concept of "number of experts" and their "qualifications" for ground truth establishment does not directly apply here. The sequencing results themselves are considered the gold standard.
4. Adjudication method (e.g. 2+1, 3+1, none) for the test set
There is no mention of an adjudication method used in this report. The comparison is directly between the device's results and the bidirectional DNA sequencing results. Discrepancies were "re-tested," but a formal adjudication process involving multiple readers/reviewers is not described.
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
No, a multi-reader, multi-case (MRMC) comparative effectiveness study was not done. This device is a qualitative genotyping assay, not an AI-assisted diagnostic tool that would involve human readers interpreting images or results with and without AI. The output is a qualitative genetic call.
6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done
Yes, the accuracy and reproducibility studies represent the standalone algorithm performance (referred to as "device performance"). The xTAG® CYP2D6 Kit v3, with its associated Data Analysis Software (TDAS), performs the genotyping and provides qualitative calls. While human operators are involved in the laboratory procedures, the final "call" or genotype determination is made by the system, as evidenced by the method comparison against sequencing. The intended use also states, "This kit is not indicated for stand-alone diagnostic purposes," referring to clinical diagnosis, not the algorithmic performance itself.
7. The type of ground truth used (expert consensus, pathology, outcomes data, etc.)
The type of ground truth used was bidirectional DNA sequencing. This is a molecular biology technique considered highly accurate for determining DNA sequences and identifying genetic variants, serving as the gold standard for genetic genotyping in this context.
8. The sample size for the training set
The document does not explicitly state a sample size for a training set. Given the nature of a laboratory assay, it's likely that internal validation and optimization were performed during development, but these are not reported as distinct "training sets" in the context of machine learning, which is where that term is most commonly applied. The "Performance Characteristics" section details validation studies (accuracy, reproducibility, etc.) which act as a test of the final product.
9. How the ground truth for the training set was established
Since a distinct training set is not explicitly mentioned or characterized, the method for establishing its ground truth is not provided. If internal developmental samples were used for optimization, it is highly probable that similar gold standard methods, such as DNA sequencing, would have been employed.
§ 862.3360 Drug metabolizing enzyme genotyping system.
(a)
Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA) extracted from clinical samples to identify the presence or absence of human genotypic markers encoding a drug metabolizing enzyme. This device is used as an aid in determining treatment choice and individualizing treatment dose for therapeutics that are metabolized primarily by the specific enzyme about which the system provides genotypic information.(b)
Classification. Class II (special controls). The special control is FDA's guidance document entitled “Class II Special Controls Guidance Document: Drug Metabolizing Enzyme Genotyping Test System.” See § 862.1(d) for the availability of this guidance document.