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The Progenika A1AT genotyping kit is a qualitative, polymerase chain reaction (PCR) and hybridization-based in vitro diagnostic test to be used with the Luminent (with xPONENT software) for the simultaneous detection and identification of 14 allelic variants and their associated alleles found in the Alpha-1 antitrypsin (AIAT) codifying gene SERPINA1. The test is intended for use with genomic DNA extracted from human whole blood samples collected as dry blood spots (DBS) or in K2-EDTA or from human saliva samples collected as buccal swabs using ORAcollect Dx OCD-100. The A1AT allelic variant genotypes and associated allele results, when used in conjunction with clinical findings and other laboratory tests, are intended as an aid in the diagnosis of individuals with A1AT deficiency (A1ATD). The kit is indicated for prescription use only.

Alpha 1 antitrypsin (A1AT) Genotyping Test utilizes Luminex xMAP technology. Genomic DNA is extracted from DBS, from human EDTA anticoagulated whole blood or from human saliva samples collected as buccal swabs using ORAcollect-Dx OCD-100. Extracted DNA is amplified and biotinylated by multiplex PCR and PCR products are denatured and hybridized to oligonucleotide probes coupled to color-coded beads. Hybridized DNA is labeled with a fluorescent conjugate and the resulting signal is detected with a Luminex® 200 system. Raw data obtained is processed with the A1AT Genotyping Test ANALYSIS SOFTWARE in order to obtain the final report. The A1AT Genotyping Test ANALYSIS SOFTWARE algorithm converts the allelic variant genotypes into associated alleles, based on the current literature.

The A1AT Genotyping Test Kit is composed of 4 reagent components (A1AT PCR Master Mix, A1AT Beads Master Mix, SAPE, SAPE Dilution Buffer) required to perform all the abovementioned processing steps. The A1AT Genotyping Test ANALYSIS SOFTWARE, instructions for use and other necessary files are uploaded on a Grifols website. Two kit configurations are available: for 48 or 192 tests (different amounts of the same reagent components are provided in each case).

The provided document describes the A1AT Genotyping Test. This 510(k) submission (K211115) is for a modified version of a previously cleared device (K192858), primarily involving a software update. Therefore, much of the performance data refers back to the original submissions (K192858 and K171868).

Here's a breakdown of the acceptance criteria and study information based on the provided text:

1. Table of Acceptance Criteria and Reported Device Performance

2. Sample Sizes and Data Provenance

• Test Set Sample Size:
  • LoD: 20 replicates of nine DNA dilutions for a "Sample Panel" (total of 180 tests per lot, across two lots used).
  • Precision (Lot-to-Lot): Five DNA samples ("Sample Panel") tested in triplicate, with three different reagent lots, by two operators, on six non-consecutive days, alternating between two Luminex instruments (5 samples * 3 replicates * 3 lots * 2 operators * 6 days = 540 tests, plus additional factors for instruments).
  • Accuracy: For the predicate device, 147 samples were used. The document refers to K171868 and K192858 for specific method comparison data for the modified device, so the exact number for the modified device's accuracy testing isn't explicitly stated but would be similar to or larger than the predicate's 147.
• Data Provenance: Not explicitly stated as "country of origin for data" or "retrospective/prospective." However, the applicant is Progenika Biopharma S.A. based in Spain, suggesting the studies likely occurred in Spain or affiliated regions. The nature of the studies (analytical performance) implies laboratory-based testing, which can be seen as a form of controlled prospective data collection for the device's technical performance.

3. Number of Experts and Qualifications for Ground Truth (Test Set)

• The document does not mention the use of experts to establish ground truth for the test set for the analytical performance studies described (LoD, Precision). These studies focus on the device's ability to consistently and accurately detect specific genetic variants based on known DNA samples.
• For Accuracy (Method Comparison), the ground truth was established by Bi-directional Sanger sequencing. This is considered a gold standard in genetic sequencing, not typically requiring "experts" to interpret the sequence output, but rather highly skilled laboratory personnel and bioinformaticians.

4. Adjudication Method (Test Set)

• Not applicable as the ground truth for analytical performance studies is typically objective (e.g., known DNA concentrations, Sanger sequencing results). The results are compared directly to these objective standards.

5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study

• No, an MRMC comparative effectiveness study was not done. This device is an in vitro diagnostic (IVD) genetic test, which generates objective results (detection of allelic variants). The performance evaluation focuses on the analytical accuracy and precision of the device itself, rather than human interpretation of complex images or clinical scenarios that would necessitate an MRMC study.

6. Standalone Performance Study (Algorithm Only)

• Yes, a standalone performance study was done. The entire "Performance Data" section (H) describes the analytical studies to determine the device's capabilities (LoD, precision, stability, accuracy). These are evaluations of the algorithm and the assay itself, demonstrating its standalone performance from DNA input to reported genotype. The device includes "A1AT Genotyping Test ANALYSIS SOFTWARE" which processes raw data to obtain the final report, indicating its role as a standalone algorithm in the diagnostic process once the PCR and hybridization steps are completed.

7. Type of Ground Truth Used

• For LoD and Precision: Known DNA samples with established genotypes/concentrations were used.
• For Accuracy (Method Comparison): Bi-directional Sanger sequencing was used as the comparator (a gold standard laboratory method) to establish the ground truth for the samples tested.

8. Sample Size for the Training Set

• The document does not explicitly state the sample size used for the training set. This is a 510(k) submission for a device with a software update (v1.0.8.16 from v1.0.6.1). The software's algorithm for converting allelic variant genotypes into associated alleles is based on current literature. It's possible that the "training" for such an algorithm is not based on a 'training set' in the machine learning sense, but rather on established scientific knowledge and rules coded into the software. If any machine learning components were present, their training data is not disclosed here.

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

• Given that the document refers to the algorithm converting genotypes into alleles "based on the current literature," the ground truth for the "training" (or more accurately, the ruleset development) of the algorithm would be derived from published scientific literature and established genetic associations between allelic variants and their corresponding alleles for the SERPINA1 gene. There is no indication of a specific "training set" of patient samples with prospectively established ground truth for algorithm development in this context.

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The Progenika A1AT genotyping kit is a quantitative, polymerase chain reaction (PCR) and hybridization-based in vitro diagnostic test to be used with the Luminex 200 instrument (with xPONENT software) for the simultaneous detection and identification of 14 allelic variants and their associated alleles found in the Alpha-1 antitrypsin (A1AT) codifying gene SERPINA1. The test intended for use with genomic DNA extracted from human whole blood samples collected as dry blood spot (DBS) or in K2-EDTA or from human saliva samples collected as buccal swabs using ORAcollect Dx model OCD-100. The A1AT allelic variant genotypes and associated allele results, when used in conjunction with clinical findings and other laboratory tests, are intended as an aid in the diagnosis of individuals with A1AT deficiency (A1ATD). The kit is indicated for prescription use only.

Alpha 1 antitrypsin (A1AT) Genotyping Test utilizes Luminex xMAP technology. Genomic DNA is extracted from DBS or from human EDTA anticoagulated whole blood or from human saliva samples collected as buccal swabs using ORAcollect-Dx model OCD-100. Extracted DNA is amplified and biotinylated by multiplex PCR and PCR products are denatured and hybridized to oligonucleotide probes coupled to color-coded beads. Hybridized DNA is labeled with a fluorescent conjugate and the resulting signal is detected with a Luminex® 200 system. Raw data obtained is processed with the A1AT Genotyping Test ANALYSIS SOFTWARE in order to obtain the final report. The A1AT Genotyping Test ANALYSIS SOFTWARE algorithm converts the allelic variant genotypes into associated alleles, based on the current literature.

The A1AT Genotyping Test Kit is composed of 4 reagent components (A1AT PCR Master Mix, A1AT Beads Master Mix, SAPE, SAPE Dilution Buffer) required to perform all the above mentioned processing steps, and a CD containing the A1AT Genotyping Test ANALYSIS SOFTWARE and other necessary files. Two kit configurations are available: for 48 or for 192 tests (different amounts of the same reagent components are provided in each case).

Here’s a summary of the acceptance criteria and study details for the A1AT Genotyping Test, as extracted from the provided FDA 510(k) submission.

1. Table of Acceptance Criteria and Reported Device Performance

The submission does not explicitly list "acceptance criteria" in a separate section with specific numerical thresholds for each performance metric. Instead, the study aims to demonstrate "100% concordance" with bi-directional Sanger sequencing for accuracy. The "Performance specifications" section outlines the areas tested, and the "Comparison Data" section reports the accuracy.

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

• Sample Size for Accuracy Test Set: 147 DNA samples.
  • 140 archived left-over clinical genomic DNA samples obtained from human saliva (buccal swabs using ORAcollect Dx model OCD-100).
  • 3 genomic DNA samples extracted from cell lines.
  • 4 synthetic DNA samples.
• Data Provenance: The 140 clinical samples were "archived left-over clinical genomic DNA samples," suggesting a retrospective collection of samples from clinical practice. The country of origin for the clinical samples is not specified in the provided text.

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

Not applicable. The ground truth was established by bi-directional Sanger sequencing, which is a laboratory method, not human expert interpretation.

4. Adjudication Method for the Test Set

Not applicable, as the ground truth was based on a laboratory method (bi-directional Sanger sequencing) rather than expert review requiring adjudication.

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 genotyping test, not an image-based AI-assisted diagnostic tool for human readers. It provides direct genetic results.

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

A standalone performance study was done for the device, where its results were compared directly against bi-directional Sanger sequencing (the ground truth). The A1AT Genotyping Test ANALYSIS SOFTWARE algorithm processes raw data to obtain the final report, effectively representing the "algorithm only" performance against the comparator.

7. The Type of Ground Truth Used

The ground truth used for the accuracy study was bi-directional Sanger sequencing.

8. The Sample Size for the Training Set

The document does not explicitly mention a "training set" for the device itself in the context of an AI/ML algorithm. This device is a PCR and hybridization-based assay with associated analysis software. The performance data presented refers to the evaluation of this assay. If the "ANALYSIS SOFTWARE" incorporates machine learning, the training set details are not provided. However, given the nature of the device (genotyping test), it is unlikely to involve a dynamic machine learning model in the typical sense that would require a separate, distinct training set in the context of this submission. The software's algorithm converts allelic variants into associated alleles based on existing literature.

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

Not applicable, as a distinct training set (in the context of AI/ML) and its ground truth establishment are not discussed in the provided text. The "analysis software algorithm" is described as converting genotypes into alleles "based on the current literature," implying established scientific knowledge rather than a learned model from a specific training dataset.

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The Progenika A1AT genotyping kit is a qualitative, polymerase chain reaction (PCR) and hybridization-based in vitro diagnostic test to be used with the Luminex 200TM instrument (with xPONENT® software) for the simultaneous detection and identification of 14 allelic variants and their associated alleles found in the Alpha-1 antitypsin (A1AT) codifying gene SERPINA1. The test is intended for use with genomic DNA extracted from human whole blood samples collected as dry blood spots (DBS) or in K2-EDTA. The A1AT allelic variant genotypes and associated allele results, when used in conjunction with clinical findings and other laboratory tests, are intended as an aid in the diagnosis of individuals with A1AT deficiency (A1ATD).

The kit is indicated for prescription use only.

Alpha 1 antitrypsin (A1AT) Genotyping Test utilizes Luminex xMAP technology. Genomic DNA is extracted from DBS or from human K2-EDTA anticoaqulated whole blood. Extracted DNA is amplified and biotinylated by multiplex PCR and PCR products are denatured and hybridized to oligonucleotide probes coupled to color-coded beads. Hybridized DNA is labeled with a fluorescent conjugate and the resulting signal is detected with a Luminex® 200 system. Raw data obtained is processed with the A1AT Genotyping Test ANALYSIS SOFTWARE in order to obtain the final report. The A1AT Genotyping Test ANALYSIS SOFTWARE algorithm converts the allelic variant genotypes into associated alleles, based on the current literature.

The A1AT Genotyping Test Kit is composed of 4 reagent components (A1AT PCR Master Mix, A1AT Beads Master Mix, SAPE, SAPE Dilution Buffer) required to perform all the above mentioned processing steps, and a CD containing the A1AT Genotyping Test ANALYSIS SOFTWARE and other necessary files. Two kit configurations are available: for 48 or for 192 tests (different amounts of the same reagent components are provided in each case).

Here's a breakdown of the acceptance criteria and study information for the A1AT Genotyping Test, based on the provided text:

1. Table of Acceptance Criteria and Reported Device Performance

The FDA summary does not explicitly list "acceptance criteria" but rather presents the results of various performance studies. The reported performance implies the acceptance criteria were met for each category.

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

The "test set" for the primary method comparison study consisted of 116 DNA samples.

• Data Provenance:
  • Clinical Samples: 66 samples, type not specified (retrospective/prospective, country of origin not specified).
  • Genomic DNAs from Cell Lines: 46 samples, type not specified.
  • Synthetic DNA Samples: 4 samples, type not specified.

For the External Reproducibility study, 17 samples were used (5 collected in DBS, 11 archived genomic DNA samples, and 1 synthetic sample). These were tested at external sites in the USA (LifeShare Blood Center and Progenika Inc.) and Italy (University of Pavia). This suggests a mix of prospective and retrospective data, depending on the nature of the archived samples.

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

The ground truth for the test set in the Method Comparison study was established by bi-directional Sanger sequencing. This is a laboratory-based method of genetic sequencing and does not involve human experts in the interpretation of the results to establish ground truth in the same way clinical image or pathology interpretation would. Therefore, the concept of "number of experts" or their "qualifications" is not directly applicable in this context.

4. Adjudication Method for the Test Set

Not applicable. The ground truth was established by bi-directional Sanger sequencing, which is an objective laboratory method, not subject to adjudication by multiple human readers.

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, an MRMC comparative effectiveness study was not done. This device is a diagnostic test for genetic variants, not an AI-assisted interpretation tool for human readers. Its performance is evaluated fundamentally as a standalone test against an established gold standard (Sanger sequencing).

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

Yes, a standalone performance study was done. The entire performance data presented (analytical and method comparison) reflects the performance of the A1AT Genotyping Test system (including the assay and its associated software) as a standalone diagnostic tool. The A1AT Genotyping Test ANALYSIS SOFTWARE algorithm converts the allelic variant genotypes into associated alleles.

7. The Type of Ground Truth Used

The primary ground truth used for the method comparison study was bi-directional Sanger sequencing, a molecular biology technique considered a gold standard for genetic sequence verification.

8. The Sample Size for the Training Set

The document does not specify a training set size. As a diagnostic test that relies on PCR and hybridization, it is unlikely to have a "training set" in the machine learning sense. The device's underlying chemistry and software algorithm are likely developed and validated using a different process than data-driven AI models.

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

Not applicable, as a "training set" in the context of machine learning for an AI algorithm is not explicitly mentioned or implied for this device. The development of the assay and its software would involve standard molecular biology and software engineering validation processes.

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