(765 days)
The Eonis™ SCID-SMA kit is intended for the semi-quantitative determination of TREC (T-cell receptor excision circle) as an aid in screening newborns for Severe Combined Immunodeficiency (SCID) and for the semi-quantitative determination of KREC (Kappa-deleting recombination excision circle) as an aid in screening newborns for X-linked agammaglobulinemia (XLA). The test is intended for DNA from blood specimens dried on a filter paper and for use on the QuantStudio™ Dx Real-Time PCR instrument.
This test is not intended for screening of SCID-like Syndromes, such as DiGeorge Syndrome, or Omenn Syndrome. lt is also not intended to screen for less acute SCID syndromes such as leaky-SCID or variant SCID. The test is not indicated for screening B-cell deficiency disorders other than XLA, such as atypical XLA, or for screening of XLA carriers.
This test is not intended for use as a diagnostic test and a positive screening result should be followed by confirmatory testing.
The Eonis SCID-SMA kit is a multiplex real-time PCR-based assay. It uses target sequence-specific primers and TaqMan™ probes to amplify and detect three targets: TREC, and RPP30, in the DNA extracted from newborn dried blood spot (DBS) using Eonis DNA Extraction kit in a single PCR reaction.
Each Eonis SCID-SMA kit contains reagents for up to 384 reactions (for 3241-001U) or 1152 reactions (for 3242-001U) including kit controls.
The document describes the Eonis SCID-SMA kit, a real-time PCR-based assay for newborn screening of Severe Combined Immunodeficiency (SCID) and X-linked agammaglobulinemia (XLA). The study provided demonstrates the device's analytical and screening performance to support its substantial equivalency to a predicate device.
Here's a breakdown of the requested information:
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state "acceptance criteria" as a separate table. However, it presents Sensitivity and Specificity for both TREC and KREC analytes, which serve as key performance metrics. These values are compared to the predicate device.
Reported Device Performance of Eonis SCID-SMA Kit:
| Analyte | Metric | Percent | Confidence Limits |
|---|---|---|---|
| TREC | Sensitivity | 100 % | 80.5 % - NA |
| False-negative rate | 0 % | NA - 19.5 % | |
| Specificity | 99.7 % | 99.4 % - 99.9 % | |
| False-positive rate | 0.3 % | 0.1 % - 0.6 % | |
| KREC | Sensitivity | 100 % | 54.1 % - NA |
| False-negative rate | 0 % | NA - 45.9 % | |
| Specificity | 99.7 % | 99.4 % - 99.9 % | |
| False-positive rate | 0.3 % | 0.1 % - 0.6 % |
Comparison to Predicate Device (PerkinElmer EnLite Neonatal TREC Kit) for TREC:
| Analyte | Metric | Percent | Confidence Limits |
|---|---|---|---|
| TREC | Sensitivity | 100 % | 79.4 % - NA |
| False-negative rate | 0 % | NA - 20.6 % | |
| Specificity | 99.7 % | 99.4 % - 99.8 % | |
| False-positive rate | 0.3 % | 0.2 % - 0.6 % |
The reported performance clearly aims to meet or exceed the performance of the predicate device, demonstrating 100% sensitivity and high specificity for both analytes.
2. Sample Size Used for the Test Set and Data Provenance
- Sample Size for Screening Performance Study (Test Set):
- Total DBS specimens: 3090
- Confirmed SCID positive: 17
- Confirmed XLA positive: 6
- Normal newborn screening specimens: 3018 (retrospective archived)
- Data Provenance: Retrospective archived dried blood spot specimens.
- Country of Origin: US and Denmark.
- Study conducted in Denmark.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts
- Number of Experts: Not explicitly stated as a specific number. The document mentions "clinical experts" were used.
- Qualifications of Experts: The document states "clinical experts" retrospectively reviewed the clinical status of routine subjects to confirm they were from unaffected individuals. Further specific qualifications (e.g., specific medical specialty, years of experience) are not provided in this document.
4. Adjudication Method for the Test Set
- Adjudication Method: The document describes a retesting protocol for initial "screen positive" results.
- "The specimens having TREC and KREC levels below the cut-off values in the initial round of testing were re-tested in duplicate."
- "The final results (presumptive positive, invalid result) were classified after the second round of testing."
- This implies a form of internal re-adjudication based on duplicate retesting for samples near the cut-off. There is no mention of external expert adjudication for discordant results or a specific "X+Y" type of adjudication.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was done
- MRMC Study: No, a Multi-Reader Multi-Case (MRMC) comparative effectiveness study was not done. This device is an in-vitro diagnostic (IVD) kit for semi-quantitative determination of biomarkers, not an AI assisting human readers of medical images. Therefore, the concept of human readers improving with AI assistance is not applicable to this type of device.
6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) was done
- Standalone Performance: Yes, the entire performance data regarding sensitivity, specificity, reproducibility, precision, limit of detection, and linearity are based on the standalone performance of the Eonis SCID-SMA kit (the algorithm of the kit combined with the instrument) on dried blood spot samples. This device operates as an automated assay, therefore, its performance is inherently "standalone" in terms of its analytic and clinical validity.
7. The Type of Ground Truth Used
- Ground Truth Type:
- Confirmatory testing: For SCID and XLA positive cases, "Confirmatory test results were used as the comparator." This implies clinical diagnosis or gold standard laboratory tests.
- Clinical expert retrospective review: For normal newborn screening specimens, "The clinical status of the routine subjects was determined through a retrospective review by clinical experts to confirm the routine subject cohort samples were from unaffected individuals." This indicates clinical outcomes or medical records adjudicated by experts.
8. The Sample Size for the Training Set
- Training Set Sample Size: The document does not explicitly state the sample size of a separate "training set" for the assay. The study described is a clinical validation (test set). For assay development (which would include "training" for establishing parameters like cut-offs), the document mentions:
- Cut-off values were established using "an independent dataset." The size of this independent dataset is not specified.
- Reproducibility and precision studies used panels of dried blood spots at different TREC/KREC levels, but these are for analytical validation rather than establishing classification criteria.
9. How the Ground Truth for the Training Set Was Established
- Training Set Ground Truth Establishment: As no specific "training set" is detailed, the method for establishing ground truth for any data used during the assay's development or cut-off determination (the "independent dataset" mentioned for cut-off study) is not explicitly described. However, it's reasonable to infer that similar methods to the test set ground truth (confirmatory testing for affected individuals and clinical review for unaffected individuals) would have been applied during the development phase.
§ 866.5930 Newborn screening test for severe combined immunodeficiency disorder (SCID).
(a)
Identification. A newborn screening test for SCID is a prescription device intended to measure T-cell receptor excision circle (TREC) DNA obtained from dried blood spot specimens on filter paper using a polymerase chain reaction based test as an aid in screening newborns for SCID. Presumptive positive results must be followed up by diagnostic confirmatory testing. This test is not intended for use as a diagnostic test, or for screening of SCID-like syndromes, such as DiGeorge syndrome or Omenn syndrome. It is also not intended to screen for less acute SCID syndromes, such as leaky SCID or variant SCID.(b)
Classification. Class II (special controls). The special controls for this device are:(1) Premarket notification submissions must include the following information:
(i) The intended use must indicate:
(A) The test is not intended for diagnostic use, or for screening of SCID-like syndromes, such as DiGeorge syndrome or Omenn syndrome; and
(B) The test is not intended to screen for less acute SCID syndromes, such as leaky SCID or variant SCID.
(ii) A detailed description of all components in the test that includes:
(A) A detailed description of the test components, all required reagents, instrumentation and equipment, including illustrations or photographs of nonstandard equipment or methods;
(B) Detailed documentation of the device software including, but not limited to, standalone software applications and hardware-based devices that incorporate software;
(C) Specifications for the filter paper, which must be appropriately labeled for in vitro diagnostic use, to be used in specimen collection and how it will be used in specimen collection validation. These specifications must include: descriptive characteristics of the filter paper, instructions on how a lab should choose the appropriate filter paper, chemical properties of the filter paper, interference concerns associated with the chemicals in the filter paper, absorption properties of the filter paper, punch size, absorption capacity, testing for homogeneity of punches, diameter of the circle for the dried blood spot aliquot, absorption time, physical composition, and number and size of punches to be tested;
(D) Methodology and protocols for detection of T-cell receptor excision circles and methods for determination of results. The cutoff must be selected before conducting clinical and analytical studies;
(E) A description of the result outputs along with sample reports. Sample reports must include the scale used in reporting of results (
e.g., TREC copies/µL) and the range of values that will be reported out; and(F) A description of appropriate internal and external controls that are recommended or provided. The description must identify those control elements that are incorporated into the testing procedure.
(iii) Information that demonstrates the performance characteristics of the test, including:
(A) Data that demonstrates the clinical validity of the device, using well characterized prospectively or retrospectively obtained clinical specimens representative of the intended use population. A minimum of 10 to 15 confirmed positive specimens must be obtained from more than 1 site, including relevant annotation, and, at 1 year or beyond, a SCID diagnosis by flow cytometry or clinically meaningful information regarding the status of the subject must be obtained. Additional specimens should have been obtained that are characterized by other disorders that can be found by screening specimens that have low or absent TREC (
e.g., other T-cell lymphopenic disorders) to supplement the range of results. The clinical validation study must have a pre-specified clinical decision point (i.e., cutoff to distinguish positive and negative results). Results must be summarized in tabular format comparing interpretation of results to the reference method. Point estimates together with two-sided 95 percent confidence intervals must be provided for the positive percent agreement, negative percent agreement, and overall percent agreement. Data must include the retest rate, the false positive rate before retest, the final false positive rate, and the false negative rate;(B) Device reproducibility data generated, using a minimum of three sites of which at least two must be external sites, with two operators at each site. Each site must conduct a minimum of five runs per operator over five nonconsecutive days evaluating a minimum of six different relevant TREC concentrations that span and are well distributed over the measuring range and include the clinical cutoff. Specimens must include cord blood and cord blood diluted with ABO matched adult blood specimens. Identical specimens from the same sample panel must be tested at each site. Each specimen must be run in triplicate and include controls run in triplicate. Results must be reported as the standard deviation and percentage coefficient of variation for each level tested. Results must also be displayed as a dichotomous variable around the cutoff. Total variation must be partitioned into the sum of within-lab and between-lab variations with pre-specified acceptance criteria and 95 percent confidence intervals for all data. Pre-specified acceptance criteria must be provided and followed;
(C) Device precision data using clinical samples to evaluate the within-lot, between-lot, within-run, between run, and total variation. A range of TREC levels of the specimen must include samples within the measuring range, samples above and below the measuring range, as well as with samples very near above and below the cutoff value. At least three replicates of each specimen must be tested with controls and calibrator(s) according to the device instructions for use. The precision study must use well characterized samples using different lots, instruments, and operators. Results must be summarized in tabular format. Pre-specified acceptance criteria must be provided and followed;
(D) Linearity of the test must be demonstrated using a dilution panel from clinical samples. The range of dilution samples must include samples within the measuring range, samples above and below the measuring range, as well as with samples very near above and below the cutoff value. Results of the regression analysis must be summarized in tabular format and fitted into a linear regression model with the individual measurement results against the dilution factors. Pre-specified acceptance criteria must be provided and followed;
(E) Device analytic sensitivity data, including limit of blank, limit of detection, and limit of quantification;
(F) Device specificity data, including interference, carryover, cross-contamination, and in silico analysis of potential off-target genomic sequences;
(G) Device stability data, including real-time stability of samples under various storage times, temperatures, and freeze-thaw conditions. A separate shipping stability study must be performed;
(H) Lot-to-lot reproducibility study of each filter paper that will be validated with the test. The lot-to-lot study must include a minimum of three lots of each blood spot card that will be validated with the test and be conducted over five nonconsecutive days. The sample panel must consist of specimens with a range of TREC levels and include samples within the measuring range, samples above and below the measuring range, and samples very near above and below the cutoff value. Multiple punches must be obtained from each card for demonstration of homogeneity of the analyte across the dried blood spot. Comparability of the test performance for each filter paper must be demonstrated. Stability and storage of TREC DNA on each blood spot card must be demonstrated. Results of the lot-to-lot study must be summarized providing the mean, standard deviation, and percentage coefficient of variation in a tabular format. Data must be calculated for within-run, between-run, within-lot, and between-lot. Data demonstrating the concordance between results across different filter papers must be provided. Study acceptance criteria must be provided and followed; and
(I) If applicable, a thermocycler reproducibility study must be performed using thermocyclers from three independent thermocyler manufacturers. The sample panel must consist of specimens with a range of TREC levels and must include samples within the measuring range, samples above and below the measuring range, and samples very near above and below the cutoff value. The study must be done using three filter paper lots and conducted over five nonconsecutive days. Results of the thermocycler reproducibility study must be summarized providing the mean, standard deviation, and percentage coefficient of variance in a tabular format. Data must be calculated for the within-run, between-run, within-lot, between-lot, and between thermocycler manufacturer study results. Study acceptance criteria must be provided and followed.
(iv) Identification of risk mitigation elements used by your device, including a description of all additional procedures, methods, and practices incorporated into the directions for use that mitigate risks associated with testing.
(2) Your § 809.10 compliant labeling must include:
(i) A warning statement that reads “This test is not intended for diagnostic use, preimplantation or prenatal testing, or for screening of SCID-like syndromes, such as DiGeorge syndrome or Omenn syndrome. It is also not intended to screen for less acute SCID syndromes, such as leaky SCID or variant SCID.”;
(ii) A warning statement that reads “Test results are intended to be used in conjunction with other clinical and diagnostic findings, consistent with professional standards of practice, including confirmation by alternative methods and clinical evaluation, as appropriate.”;
(iii) A description of the performance studies listed in paragraph (b)(1)(iii) and a summary of the results; and
(iv) A description of the filter paper specifications required for the test.