(364 days)
The clonoSEO Assay is an in vitro diagnostic that uses multiplex polymerase chain reaction (PCR) and next-generation sequencing (NGS) to identify and quantify rearranged IgH (VDJ), IgH (DJ), IgK, and IgL receptor gene sequences, as well as translocated BCL1/IgH (J) and BCL2/IgH (J) sequences in DNA extracted from bone marrow from patients with B-Cell acute lymphoblastic leukemia (ALL) or multiple myeloma (MM).
The clonoSEQ Assay measures minimal residual disease (MRD) to monitor changes in burden of disease during and after treatment. The test is indicated for use by qualified healthcare professionals in accordance with professional guidelines for clinical decisionmaking and in conjunction with other clinicopathological features.
The clonoSEQ Assay is a single-site assay performed at Adaptive Biotechnologies Corporation.
A description of required equipment, software, reagents, vendors, and storage conditions were provided, and are described in the product labeling. Adaptive Biotechnologies assumes responsibility for the device.
Here's an analysis of the acceptance criteria and the study that proves the clonoSEQ® Assay meets those criteria, based on the provided text:
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria are derived from the "Special Controls" section (S(b) Design verification and validation must include...) and from the performance study results. The reported device performance aligns with specific metrics and ranges demonstrated in the various analytical and clinical studies.
| Acceptance Criteria Category | Specific Acceptance Criteria (from S.(b).1.iv) | Reported Device Performance (from L. Performance Characteristics) |
|---|---|---|
| Device Precision (Repeatability & Reproducibility) | Data using clinical samples covering the range of MRD frequencies and DNA inputs. Report SD/CV with 95% CI. Evaluate all sources of variability (site, operator, day, run, lot, instrument). | Precision of MRD Frequency: |
- MM: %CV ranged from 29.6% to 70.0% (Tables 1).
- ALL: %CV ranged from 25.9% to 76.9% (Table 2).
Precision of Malignant Cells Detected: - %CV ranged from 72% at 2.14 cells to 21% at 612.56 cells (Table 3).
- Minimal contribution from Operator, Instrument Sets, Reagent Lots, Day, Run (0-3%).
- All studies included assessment of instrument sets, operator, processing day, processing run, and reagent lot. |
| Device Linearity | Data generated from samples covering the device measuring range using a dilution panel created from clinical samples. | Linearity using Cell Lines (Table 5): - ALL: Linear range 0% to 100% (200ng), 3x10-5 to 30% (2µg), 0% to 10% (20µg). Average slopes close to 1 (0.95-1.01).
- MM: Linear range 0% to 100% (200ng), 9.8x10-6 to 30% (2µg), 0% to 10% (20µg). Average slopes close to 1 (0.98-1.03).
Linearity using Clinical Specimens (Table 6): - Linear range across several orders of magnitude for each condition (e.g., ALL 500ng: 2.8x10-5 to 8x10-3). Average slopes close to 1 (0.948-0.985).
- Maximum deviation from linearity less than 5%. |
| Device Accuracy (Quantitative Measurement) | Comparison to flow cytometry across the measuring interval or to the predicate method. | Accuracy in Cell Mixtures Comparing to mpFC (Figure 6): Similar quantitative accuracy when comparing clonoSEQ with mpFC at frequencies above 1x10-4.
Quantitation Bias on Clinical Specimens (Figure 8): Quantitative accuracy within ±25% across all tested diseased cell inputs. Modest upward bias at lower MRD and downward bias at higher MRD frequencies. |
| Device Analytical Sensitivity (LoB, LoD, LoQ) | Data using a dilution panel created from clinical samples. | Limit of Blank (LoB): Zero (based on 95th percentile of MRD frequencies in healthy bone marrow samples at 500 ng and 20 µg gDNA input).
Limit of Detection (LoD): 1.903 malignant cells (95% CI; 1.75 - 2.07) across DNA input levels (Table 7).
Limit of Quantitation (LoQ): 2.390 malignant cells (95% CI; 1.90 - 9.14) across DNA input levels (Table 7). |
| Analytical Specificity (Interference, Cross-Contamination) | Data including interference and cross-contamination, and index cross-contamination. | Interfering Substances (Tables 8 & 9): 5 endogenous and 3 exogenous substances tested. All conditions passed pre-specified MRD frequency equivalence margin of ±30%, concluding no substantial influence.
Cross-Contamination/Sample Carryover: - Automated DNA extraction: 0 of 44 BMA/BMMC false calibrations for run-to-run; 1 of 44 BMA for well-to-well (minor, unimpactful).
- gDNA contamination: No run-to-run (0 of 36); 8 of 712 well-to-well (likely vendor issue, unimpactful as
§ 866.6100 DNA-based test to measure minimal residual disease in hematological malignancies.
(a)
Identification. A DNA-based test to measure minimal residual disease in hematological malignancies is a prescription in vitro diagnostic device that identifies and quantifies specific nucleic acid sequences within human tissues to estimate the percentage of cells that harbor the specific sequence(s). The test is intended to be used as an aid to measure minimal residual disease to assess the change in burden of disease during monitoring of treatment. The test is indicated for use by qualified healthcare professionals in accordance with professional guidelines for clinical decision-making, in conjunction with other clinicopathological features.(b)
Classification. Class II (special controls). The special controls for this device are:(1) Design verification and validation must include:
(i) A detailed description of the device, including:
(A) A detailed description of all test components, reagents, instrumentation, and software, including software applications and any hardware-based devices that incorporate software.
(B) A detailed description of all genomic regions that are detected and quantified by the assay.
(C) A detailed description of the methodology and protocols for each step of the test, including description of the quality metrics, thresholds, and filters at each step of the test that are implemented for final result reporting and a description of the metrics for run-failures, specimen-failures, and invalids, as appropriate.
(D) Detailed specifications and procedures for sample collection, processing, and storage.
(E) A description of the internal and external controls that are recommended or provided. The description must identify those control elements that are incorporated into the testing procedure. If appropriate, this description must include a description of the controls and control procedures used during the sequencing and data analysis.
(ii) Identification of risk mitigation elements used by the device, including a detailed description of all additional procedures, methods, and practices incorporated into the instructions for use that mitigate risks associated with use of the device.
(iii) As part of the risk management activities, an appropriate end user device training program must be offered as an effort to mitigate the risk of failure from user error, as appropriate.
(iv) Description of analytical and clinical studies, including:
(A) Device performance data that demonstrates the ability to measure minimal residual disease in the claimed specimen type(s) from patients that are representative of the intended use population. Data can be obtained via:
(
1 ) A method comparison study comparing the device to a predicate device with clinical data for the specified hematological neoplastic indication using the specified specimen type(s); or(
2 ) A clinical study demonstrating clinical validity using well characterized clinical specimens from patients with known clinical outcomes using a study design deemed acceptable by FDA.(B) Device precision (repeatability and reproducibility) data using clinical samples covering the range of minimal residual disease frequencies reported by the test and covering the stated range of DNA inputs that are indicated as allowable for use with the test. Results shall be reported as the standard deviation and/or percentage coefficient of variation with the 95 percent confidence interval for each level tested. The study must evaluate all sources of variability, including, as appropriate, between-site and between operator (minimum of three sites of which two must be external with a minimum of two operators per site), between-day (minimum of 3 days), between-run, within-run, between-lot (minimum of three lots), between instrument (minimum of three instruments), and total variation.
(C) Device linearity data generated from samples covering the device measuring range using a dilution panel created from clinical samples.
(D) Device accuracy by comparison to flow cytometry across the measuring interval or to the predicate method across the measuring interval.
(E) Device analytic sensitivity data, including limit of blank, limit of detection, and limit of quantitation, using a dilution panel created from clinical samples.
(F) Analytical specificity data, including interference and cross-contamination, and index cross-contamination, as appropriate.
(G) Validation of pre-analytical methods, including DNA extraction methods and cell enrichment methods, as appropriate.
(H) Device stability data, including real-time stability of reagents under various storage times and temperatures.
(I) Specimen and prepared sample stability data established for each specimen matrix in the anticoagulant combinations and storage/use conditions that will be indicated, including specimen transport, as appropriate.
(2) The intended use for the labeling required under § 809.10(a)(4) of this chapter and for the labeling required under § 809.10(b)(5)(ii) of this chapter, as applicable, must include:
(i) The clinical hematopoietic malignancy for which the assay was designed and validated (
e.g., multiple myeloma or B-cell acute lymphoblastic leukemia);(ii) Specimen type (
e.g., bone marrow);(iii) The specific DNA regions that are being identified and quantified (
e.g., rearranged IgH (VDJ), IgH (DJ), IgK, and IgL receptor gene sequences); and(iv) A statement that the results are indicated to be interpreted by qualified healthcare professionals in accordance with professional guidelines for clinical decision-making in conjunction with other clinicopathological features.
(3) The labeling required under § 809.10(b) of this chapter must include information that demonstrates the performance characteristics of the test, including a detailed summary of the performance studies conducted and their results, as described in paragraphs (b)(1)(iv)(A) through (I) of this section.
(4) The device output, including any test report, must include the estimated minimal residual disease (MRD) frequency and an appropriate range of the uncertainty of that frequency based on the amount of DNA that was evaluated by the test and the number of specific nucleic acid sequences that were detected (
e.g., “MRD = 1.2 × 10−5 [Range = 0.8 × 10−6 to 2.0 × 10−5 ]”).