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510(k) Data Aggregation

    K Number
    DEN130018
    Device Name
    CYTOSCAN(R) DX
    Manufacturer
    Date Cleared
    2014-01-17

    (30 days)

    Product Code
    Regulation Number
    866.5920
    Reference & Predicate Devices
    N/A
    Predicate For
    N/A
    AI/MLSaMDIVD (In Vitro Diagnostic)TherapeuticDiagnosticis PCCP AuthorizedThirdpartyExpeditedreview
    Intended Use

    CytoScan® Dx Assay is a qualitative assay intended for the postnatal detection of copy number variations (CNV) in genomic DNA obtained from peripheral whole blood in patients referred for chromosomal testing based on clinical presentation. CytoScan® Dx Assay is intended for the detection of CNVs associated with developmental delay, intellectual disability, congenital anomalies, or dysmorphic features. Assay 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, parental evaluation, clinical genetic evaluation, and counseling, as appropriate. Interpretation of assay results is intended to be performed only by healthcare professionals, board certified in clinical cytogenetics or molecular genetics. The assay is intended to be used on the GeneChip® System 3000Dx and analyzed by Chromosome Analysis Suite Dx Software (ChAS Dx Software).

    This device is not intended to be used for standalone diagnostic purposes, preimplantation or prenatal testing or screening, population screening, or for the detection of, or screening for, acquired or somatic genetic aberrations.

    Device Description

    The CytoScan Dx consists of five reagent modules, a microarray kit, and analysis software. The five reagent modules are:

      1. MOD R L A, CytoScan® Dx Pre-PCR contains buffers, nucleotides, enzyme, and primers and adaptors for amplification;
      1. MOD T E W, CytoScan® Dx Pre-PCR contains buffer and nuclease free water for amplification;
      1. MOD F L H, CytoScan® Dx Post-PCR contains buffers, nucleotides, and enzyme for fragmentation, labeling and hybridization;
    • MOD S AH W PB, CytoScan® Dx Post-PCR contains buffers, nuclease free water, and purification beads for stain and array hold;
      1. MOD E PW CytoScan® Dx Post-PCR contains buffer for elution and purification wash.

    The CytoScan® Dx Post-PCR CytoScan® Dx Array kit, 6-pack is designed for 6 runs. The microarray contains approximately 2,696,550 functional markers, each of which is approximately 25 bases long.

    ChAS Dx Analysis Software and Browser v1.0.0 analyzes CEL file microarray data.

    AI/ML Overview

    The Affymetrix® CytoScan® Dx Assay is a qualitative assay intended for the postnatal detection of copy number variations (CNV) in genomic DNA from peripheral whole blood in patients referred for chromosomal testing based on clinical presentation. It detects CNVs associated with developmental delay, intellectual disability, congenital anomalies, or dysmorphic features.

    Here's an analysis of the acceptance criteria and supporting studies:

    1. Table of Acceptance Criteria and Reported Device Performance

    The acceptance criteria are not explicitly listed in a single table within the provided text. However, they can be inferred from the "Required Mitigations" and the detailed performance study descriptions. The reported device performance is extracted from the study results.

    Inferred Acceptance Criteria and Reported Device Performance for Affymetrix® CytoScan® Dx Assay

    Acceptance Criteria CategorySpecific Performance Metric / CriterionReported Device Performance
    Reproducibility (Site-to-Site)Overall pairwise replicate agreement for CNVs (>=50% overlap, same state)79.4% for all CNVs (range 65.7-100%). 75.5% for gains, 82.4% for losses (kb-based, 50% overlap). 82.2% for all CNVs (marker-based, 50% overlap).
    Overall pairwise replicate agreement for CNVs (>=80% overlap, same state)71.9% for all CNVs (kb-based, 80% overlap).
    Reproducibility of Copy Number (0, 1, 2, 3, 4+)82.7% agreement across all CNVs (regardless of location/size/marker number).
    Median % Absolute Endpoint Deviation (Overall, excluding HR)0.03 (mean, 0.00 min, 0.00 median, 0.77 max) for both markers and kb.
    Reproducibility of LOH calls (3-4 Mb)91.9% call rate; 92.4% pairwise replicate agreement (50% overlap); 86.0% (80% overlap).
    Detection Limit (DNA Input)Reliable detection of CNV markers10 ng genomic DNA is a conservative lower limit; assay functions appropriately with input up to 500 ng.
    Detection Limit (Mosaicism)Reliable detection of mosaic segmentsReliably detects mosaicism greater than 20% (mean AUC=0.96 at 15% mosaicism, but still states >20% being reliable).
    Analytical Specificity (Interfering Substances)Array QC and assay performance to meet acceptance criteria in presence of bilirubin, triglycerides, hemoglobin.All results met sponsor's acceptance criteria; no interference observed.
    Analytical Specificity (Carryover)No significant difference in copy number state determination or array QC metrics between first and fifth runs in sequential processing.No significant difference in copy number state (Wilcoxon signed rank statistic (S) = 0.5, p-value = 1.00) or array QC metrics (p > 0.05).
    Analytical Specificity (Cross-Contamination)SNPQC ≥ 12 at approximately 20% contamination.SNPQC values ≥12 indicate absence of substantial cross-contamination.
    Accuracy (Overall CNVs vs. Sequencing)Agreement between CytoScan Dx and sequencing (>50% overlap or size, same state)78.8% agreement (all CNVs).
    Accuracy (Overall CNVs vs. Composite Method)Agreement between CytoScan Dx and composite method (>50% overlap or size, same state)88.7% agreement (all CNVs, excluding hypervariable regions).
    Accuracy (LOH Regions vs. Sequencing)PPA for LOH regions >=3 MB100.0% (159/159) for LOH regions 3 MB and greater.
    Accuracy (Syndromic LOH vs. Published)Detection of known LOH regions (e.g., from Gibson et al.)Identified all 20 (100.0%) specifically described regions (>=5 MB) by Gibson et al.
    Endpoint AccuracyEndpoint agreement (<=12 markers for losses, <=25 markers for gains) for CNVs with state agreement (excluding HR).93.4% overall (94.8% for gains, 92.4% for losses).
    Clinical Sensitivity (Sample Level)PPA between RPC (pathogenic) and CytoScan Dx (pathogenic)82.0% (105/128).
    Clinical Sensitivity (CNV Level)Analytical accuracy: percentage of RPC-identified CNVs identified by CytoScan Dx.94.0% (639/680) (analytical agreement).
    Clinical Sensitivity (Syndrome Agreement)Overall interpretation positive agreement.80.7%.
    Expected Values (Normal Population)Interpretation of CytoScan Dx Assay results for phenotypically normal individuals.3 out of 108 phenotypically normal individuals were interpreted as pathogenic.
    Minimum CNV Size DetectedSet at 25 kb and 25 markers for losses, 50 kb and 50 markers for gains.Reproducibility for gains (50-75kb) 78.8% (50% overlap); losses (25-50kb) 81.0% (50% overlap).Accuracy for gains (50-75kb) 93.5%; losses (25-50kb) 91.6% (using composite method).
    Minimum LOH Size DetectedSet at 3 Mb for LOH.Reproducibility of 3-4 Mb LOH 91.9% (call rate); accuracy with sequencing 100.0% (3-5 Mb).

    2. Sample Sizes and Data Provenance

    Reproducibility Studies (Site-to-Site and Lot-to-Lot):

    • Test Set Sample Size: 93 genomic DNA samples (48 purified from blood, 44 from cell lines from Coriell and WHO, 1 control from ATCC) for site-to-site study. 47 genomic DNA samples (including 1 control) for lot-to-lot study (12 blood gDNA, 11 cell-line gDNA, 1 cell-line control gDNA).
    • Data Provenance: The general nature of the samples (purified blood, cell lines from Coriell, WHO, ATCC) suggests a mix of sources, likely from the United States or international repositories. The site-to-site study implies data collection across three sites (details on geographic location not specified beyond "3 sites"). The lot-to-lot study was conducted at "1 investigative site - Affymetrix, Santa Clara, CA."
    • Retrospective/Prospective: These appear to be retrospective studies using pre-existing genomic DNA samples.

    Accuracy Study (Comparison to Sequencing & Composite Method):

    • Test Set Sample Size: 137 gDNA samples (48 purified from blood, 86 from Coriell Cell Repository cell lines, 3 from ATCC cell lines). 5 samples were excluded, leaving 132 evaluable samples.
    • Data Provenance: Similar to reproducibility studies, a mix of blood samples and cell lines from public repositories.
    • Retrospective/Prospective: Retrospective.

    Clinical Sensitivity Study:

    • Test Set Sample Size: 960 gDNA samples.
    • Data Provenance: Retrospective clinical study using samples from previously tested DD/ID (developmental delay/intellectual disability) patients referred to three clinical laboratories for routine chromosomal testing. The origin of the patients is not explicitly stated but implies clinical settings, likely within the US, given the FDA context.
    • Retrospective/Prospective: Retrospective, but samples were "collected prospectively" for the original routine testing, then retrospectively analyzed with CytoScan Dx.

    Expected Values/Reference Range Study:

    • Syndromic Samples: 149 samples representing known syndromes.
    • Normal Samples: 108 phenotypically normal subjects.
    • Data Provenance: Syndromic samples collected at 8 sites, normal samples at 1 site. No specific country mentioned.
    • Retrospective/Prospective: Retrospective.

    3. Number of Experts and Qualifications for Ground Truth

    Clinical Sensitivity Study (Establishing Clinical Interpretation Ground Truth):

    • Number of Experts: Two independent cytogeneticists for interpreting CytoScan Dx results. The historical "routine patient care (RPC)" interpretations were made by various cytogeneticists at the original clinical laboratories.
    • Qualifications: "Healthcare professionals, board certified in clinical cytogenetics or molecular genetics." This is stated in the intended use and product classification.

    Accuracy Study (Analytical Ground Truth):

    • Number of Experts: Not applicable in the same way as clinical interpretation. The ground truth was established by "validated high throughput sequencing" and a "composite analytical method" based on molecular methods. These methods themselves would have been developed and validated by experts, but the determination of CNVs from these methods is a technical analysis rather than expert consensus on clinical significance.
    • Qualifications: Not specified beyond the methods themselves being "validated."

    4. Adjudication Method

    • Clinical Sensitivity Study: For CytoScan Dx interpretations, results were provided to one of two independent cytogeneticists who then generated an overall clinical laboratory interpretation. It does not explicitly state that both cytogeneticists interpreted every case, nor does it describe a formal adjudication process if their interpretations differed. However, the study involved comparing these interpretations to historical RPC interpretations.
    • Analytical Ground Truth (e.g., Sequencing, Composite Method): Adjudication methods for the ground truth itself (sequencing results, composite method results) are not detailed, implying standard analytical pipelines were used.

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

    • A formal MRMC comparative effectiveness study where human readers interpret cases with and without AI assistance (or device assistance in this context) to measure an "effect size of how much human readers improve with AI vs without AI assistance" was not explicitly described in the provided text.
    • The clinical sensitivity study involved human cytogeneticists interpreting CytoScan Dx results and comparing them to historical RPC interpretations. This demonstrates the performance of the device in a clinical context but doesn't directly quantify the improvement of human readers with vs. without the device's assistance in real-time. The "diagnostic yield" comparison (13.8% for CytoScan Dx vs 13.3% for RPC, stratified by RPC methods) suggests comparable performance to existing complex workflows, but not necessarily an "improvement effect size" for a single reader.

    6. Standalone Performance Study (Algorithm Only)

    • The CytoScan Dx Assay includes the Chromosome Analysis Suite Dx Software (ChAS Dx Software) for analysis. The "Performance Characteristics" section describes the analytical performance (precision, accuracy, detection limits) of the device as a whole, which inherently includes the algorithm's performance in detecting CNVs.
    • However, the device's intended use specifically states: "Interpretation of assay results is intended to be performed only by healthcare professionals, board certified in clinical cytogenetics or molecular genetics. This device is not intended to be used for standalone diagnostic purposes".
    • Therefore, while the algorithm's performance is integral to the device's overall performance, a study focusing solely on the algorithm's "standalone" performance without any human-in-the-loop interpretation (e.g., direct output of diagnosis, bypassing expert review) was not presented as this falls outside its intended use as an interpretative tool for experts. The analytical accuracy studies effectively evaluate the algorithm's ability to detect CNVs compared to reference methods.

    7. Type of Ground Truth Used

    • Analytical Performance Studies (Reproducibility, Accuracy, Detection Limits):

      • Sequencing: For overall CNV accuracy and LOH accuracy. This is a high-resolution molecular method.
      • Validated High-Throughput Method: Also used for CNV accuracy.
      • Composite Analytical Method: Combining results from various molecular methods (e.g., sequencing, qPCR) was used when sequencing alone didn't confirm CNVs. This aims to provide a more robust ground truth.
      • Published LOH Regions: For LOH accuracy, comparison to a published table from Gibson et al., derived from HapMap sample genotypes, which can be considered highly curated and expert-validated data.
      • Known Chromosomal Aberrations: For detection limit and matrix comparison studies, cell lines with "known chromosomal aberrations" were used.
    • Clinical Sensitivity Study:

      • Clinical Interpretation by Board-Certified Cytogeneticists: This formed the ground truth for potential diagnostic yield and sample/syndrome agreement. The comparison was against "routine patient care (RPC)" interpretations, which themselves were based on various methods (karyotype, FISH, microarray, etc.) and interpreted by cytogeneticists.

    8. Sample Size for the Training Set

    • The provided document describes validation studies, not product development or machine learning model training. It does not specify a separate "training set" for the algorithms within the ChAS Dx software.
    • The signal intensity of the patient sample is compared to a "reference DNA, which is based on an average of over 400 samples." This "reference DNA" could be considered analogous to a training or calibration dataset used to establish baseline copy number profiles, but it's not described as a "training set" in the context of supervised machine learning.

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

    • As mentioned above, there is no explicit "training set" described for a machine learning algorithm. The "reference DNA, which is based on an average of over 400 samples" is key for baseline comparison.
    • The method for establishing the ground truth for these 400+ reference samples is not detailed in the provided text. It is implied these are normal, healthy samples used to establish a baseline for copy number variations.
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    K Number
    K103112
    Manufacturer
    Date Cleared
    2011-05-04

    (195 days)

    Product Code
    Regulation Number
    862.2570
    Reference & Predicate Devices
    Predicate For
    N/A
    AI/MLSaMDIVD (In Vitro Diagnostic)TherapeuticDiagnosticis PCCP AuthorizedThirdpartyExpeditedreview
    Intended Use

    Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system.

    Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

    Device Description

    The Affymetrix® Gene Profiling Reagents were designed for in vitro diagnostic use as an accessory to the GeneChip® MicroArray Instrumentation System. Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system. Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

    The Affymetrix Gene Profiling Reagents consist of three kits.

    Kit 1 is the RNA Control Kit consisting of Poly-A Control and Dilution Buffer. These reagents are designed to provide exogenous positive controls to monitor the entire target labeling process. The Poly-A Control and Dilution Buffer are provided with the kit to prepare the appropriate serial dilutions. After the appropriate dilution of the Poly-A Control, they are added to the total RNA and then amplified and labeled together. Examining the hybridization intensities of these controls on the array helps to monitor the amplification and labeling processes.

    Kit 2 is comprised of the Transcript Synthesis and Labeling Kits A and B and includes enzyme mixes, labeling reagent, reaction buffers and purification reagents for the preparation of the labeled cRNA target. Kit 2 is optimized specifically for producing amplified and biotinylated cRNA targets to hybridize to arrays for expression analysis.

    Kit 3 is comprised of Transcript Detection Kits A, B and C and includes all of the reagents to perform fragmentation of the labeled cRNA target, prepare the hybridization cocktail (including Oligo B2 and hybridization controls) and process the arrays in the Affymetrix Fluidics Station 450. The arrays are then ready to be scanned by the Affymetrix GeneChip Scanner.

    AI/ML Overview

    Here's an analysis of the acceptance criteria and the study that proves the device meets them, based on the provided text:

    Device: Affymetrix® Gene Profiling Reagents (K103112)
    Intended Use: Preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system. Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.


    1. Table of Acceptance Criteria and Reported Device Performance

    Performance CharacteristicAcceptance CriteriaReported Device Performance
    Precision/ReproducibilityMedian probeset signal %CV from detected probesets < 20% (between lots and between days within a lot).Met for all combinations. - Between days (MAQC A): One-Cycle: 7.97%; Gene Profiling (1000ng): 7.17%; Gene Profiling (100ng): 7.03% - Between days (MAQC B): One-Cycle: 7.68%; Gene Profiling (1000ng): 7.24%; Gene Profiling (100ng): 9.33% - Between lots (MAQC A): One-Cycle: 8.70%; Gene Profiling (1000ng): 9.54%; Gene Profiling (100ng): 8.74% - Between lots (MAQC B): One-Cycle: 9.52%; Gene Profiling (1000ng): 9.93%; Gene Profiling (100ng): 11.72%
    RepeatabilityMedian probeset signal %CV from detected probesets < 10% for replicates.Met for all conditions, internal and external sites. Examples from internal testing (MAQC A, 100ng): 5.31%, 5.81%, 5.41%, 4.24%, 4.04%. External sites also met the criteria.
    Input Total RNAReagents perform as expected with 100 ng and 1000 ng of input total RNA, and produced sufficient cRNA for hybridization (≥ 20 µg or ≥ 15 µg for Pathchip).Testing demonstrated reagents performed as expected with 100 ng and 1000 ng. When tested with 200 ng (clinical study amount), sufficient cRNA was produced (≥ 15 µg).
    cRNA YieldInternal: ≥ 90% of samples yield ≥ 20 µg cRNA and cRNA concentration ≥ 0.625 µg/µL. External: ≥ 96% of samples yield > 20 µg cRNA and cRNA concentration ≥ 0.625 µg/µL.Internal: 100% (30/30) of samples yielded ≥ 20 µg cRNA and concentration ≥ 0.625 µg/µL. External: 100% (32/32) of samples at both sites achieved yields of ≥ 20 µg cRNA and concentration ≥ 0.625 µg/µL.
    Performance of Controls1. .CEL files generated by successful automatic gridding for all samples with Oligo B2. 2. 3' AFFX-r2-Bs probe sets for lys, phe, dap present, with signal intensities and r-squared values ≥ 0.900 for correlation of signal intensities with relative ratio. 3. 3' AFFX-r2 probeset for bioB called present. 4. Hybridization controls (bioB, bioC, bioD, cre) followed expected relative concentration (bioB < bioC < bioD < cre).All criteria met. Internal study: 100% (80/80) of samples passed. External study: 100% (64/64) of samples passed. Clinical studies: 100% (135/135 from 3 sites, and 32/32 from 1 site) passed.
    Clinical Method Comparison1. Specimen processing specifications met. 2. Overall success rate for generating Tissue of Origin Test - Frozen results > 90%. 3. Observed percent correct when using Gene Profiling Reagents no different from expected percent correct when using One-Cycle Reagent Kit (α = 0.05).1. Not explicitly stated "met," but implied by successful study completion. 2. Not explicitly reported as a percentage, but implied by the overall conclusions. 3. The observed percent correct with Gene Profiling Reagents was "no different" (α = 0.05) from the One-Cycle Kit (95% bootstrap confidence limits: [-5.9%, 3.4%]). Acceptance criteria achieved.

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

    • Precision/Reproducibility:

      • Sample Size: MAQC A and B total RNAs were used. Specific numbers: 3 lots of Gene Profiling Reagents and 3 lots of Pathwork® Expression 3'-Amplification One-Cycle Target Reagents were each tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate. For internal consistency, one lot of each reagent was tested with 100 ng/1000 ng MAQC A/B total RNAs in quadruplicate, repeated on three different days.
      • Data Provenance: Not explicitly stated (e.g., country of origin). The use of "MAQC A and B total RNAs" suggests standardized reference materials. This was an analytical, non-clinical study.
    • Repeatability:

      • Sample Size: Same as Precision/Reproducibility for internal testing. Additionally, two external sites tested 8 replicates each using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples.
      • Data Provenance: Internal Affymetrix testing, and two external sites. Analytical, non-clinical.
    • cRNA Yield:

      • Sample Size: Internal: 100 ng of total RNA from ten commercially available human tissues (run in triplicate). External: Eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples at two external sites.
      • Data Provenance: Internal Affymetrix testing, and two external sites. Analytical, non-clinical.
    • Performance of Controls:

      • Sample Size: Internal: Three lots of Gene Profiling Reagents tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate. External: Eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples at two external sites. Clinical studies: 45 total RNA samples tested at each of 3 clinical sites (total 135 samples) and 16 total RNA samples from 16 frozen tissues (tested twice, so 32 data points) at one site.
      • Data Provenance: Internal Affymetrix testing, two external sites, and multiple prospective clinical sites.
    • Clinical Method Comparison (Tissue of Origin Study):

      • Sample Size:
        • Part 1 (Tissue Study): 16 frozen tissues (representing 15 tumor types), each tested twice with Gene Profiling Reagents and twice with One-Cycle Reagent Kit (total 32 reactions per reagent type, 64 total).
        • Part 2 (Total RNA Study): 45 total RNA samples processed using Gene Profiling Reagents (45 reactions per site at 3 sites, total 135 reactions). For comparison, 39 of these samples had prior One-Cycle Kit results available from two sites, and 6 additional samples had prior One-Cycle Kit results from one site.
        • Combined Analysis: 16 tissues from Part 1, and 45 total RNA samples from Part 2.
      • Data Provenance: Prospective clinical studies conducted at 1 external site (Part 1) and 3 clinical sites (Part 2). Tissue sources and resulting .CEL files were blinded to the analysis labs (Pathwork Diagnostics). Not specified if the data was from the US or international.

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

    • Not applicable directly for these studies. The ground truth for the clinical comparison was the available diagnosis of each tissue specimen (implied from clinical pathology, but not explicitly stated how many experts or their qualifications). The study design blinded the testing sites and the analysis center to this diagnosis, suggesting it was established independently.
    • For the analytical studies (precision, repeatability, yield, controls), the "ground truth" is based on the inherent properties of the RNA samples (MAQC A/B, commercially available human tissues) and the expected performance of the control spike-ins, not expert interpretation.

    4. Adjudication Method for the Test Set

    • Not applicable. The clinical study compared the performance of the Gene Profiling Reagents to a predicate (One-Cycle Reagent Kit) in generating results for the Pathwork® Tissue of Origin-Frozen Test. The "truth" in this context was the existing diagnosis of the tissue, and the comparison was on the output "percent correct" of the assay, not on expert consensus readings of an image or signal. The study notes that the sites and Pathwork Diagnostics were blinded to the available diagnosis.

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

    • No, an MRMC study was not done. This device is a reagent kit for gene profiling, not an imaging or diagnostic algorithm requiring human interpretation. The clinical study was a method comparison to evaluate if the new reagents performed equivalently to predicate reagents within an existing diagnostic assay (Pathwork® Tissue of Origin-Frozen Test), which involves an algorithm for analysis, not direct human reading of raw data. Therefore, an effect size of human readers improving with AI vs. without AI assistance is not relevant here.

    6. Standalone (i.e. algorithm only without human-in-the-loop performance) Study

    • Yes, a standalone study was done in essence. The analytical performance studies (Precision, Repeatability, cRNA Yield, Performance of Controls) are all measuring the performance of the reagents and their output without human interpretation of the final diagnostic result.
    • The clinical method comparison study evaluates the reagents' contribution to the Pathwork® Tissue of Origin-Frozen algorithm's performance. The algorithm itself (from Pathwork Diagnostics) provides the interpretation, and it was "blinded to the available diagnosis for each specimen." The comparison was between the output of the Pathwork algorithm when using RNA prepared with Affymetrix Gene Profiling Reagents versus when using RNA prepared with the One-Cycle Reagent Kit. The "observed percent correct" was comparing the algorithm's output to the known diagnosis. This represents the performance of the system (reagents + instrumentation + algorithm) in a standalone fashion compared to known ground truth.

    7. Type of Ground Truth Used

    • Analytical Studies: Chemical/biological properties of standardized RNA samples (MAQC A and B, commercially available human tissues), and expected signals from internal controls (spike-ins).
    • Clinical Method Comparison Study: "Available diagnosis of each tissue specimen." This would typically be established by pathology (histopathology, immunohistochemistry) to confirm the tissue of origin and tumor type, but the specific method or number of pathologists is not detailed. It represents an established clinical diagnosis.

    8. Sample Size for the Training Set

    • Not explicitly stated in the provided text. The document describes a premarket notification for a reagent kit, not a machine learning algorithm that typically requires a training set. The reagents are used to prepare samples for an existing FDA-cleared microarray assay (Pathwork® Tissue of Origin-Frozen Test, K080896) and instrumentation (Affymetrix GeneChip® MicroArray Instrumentation System, K080995), which presumably had their own training and validation data (if applicable, for the Pathwork algorithm). The current submission focuses on demonstrating that the new Gene Profiling Reagents perform equivalently to the reagents used in the predicate device for this assay.

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

    • Not applicable as no training set for the Gene Profiling Reagents themselves is described. If the Pathwork® Tissue of Origin-Frozen Test's algorithm involved a training set, the ground truth for that would have been established during its own development and clearance process (K080896), but this information is not provided in the current document.
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    K Number
    K080995
    Manufacturer
    Date Cleared
    2008-07-30

    (114 days)

    Product Code
    Regulation Number
    862.2570
    Reference & Predicate Devices
    N/A
    Predicate For
    N/A
    AI/MLSaMDIVD (In Vitro Diagnostic)TherapeuticDiagnosticis PCCP AuthorizedThirdpartyExpeditedreview
    Intended Use

    The Affymetrix GeneChip® Microarray Instrumentation System consisting of GeneChip® 3000Dx scanner with autoloader, FS450Dx fluidics station and GCOSDx software is intended to measure fluorescence signals of labeled DNA and RNA target hybridized to GeneChip® arrays.

    Device Description

    Affymetrix GeneChip® Microarray Instrumentation System consisting of GeneChip® 3000Dx scanner with autoloader, FS450Dx fluidics station and GCOSDx software.

    AI/ML Overview

    I am sorry, but the provided text does not contain the detailed information necessary to answer your request about acceptance criteria and the study proving device performance. The document is a 510(k) clearance letter from the FDA for a medical device ("Affymetrix Genechip Microarray Instrumentation System"), indicating that the device has been deemed substantially equivalent to a predicate device.

    While it mentions the device name, regulation number, and product code, it does not include:

    • A table of acceptance criteria and reported device performance.
    • Details about sample sizes, data provenance, or ground truth establishment for an AI model.
    • Information on expert reviews, adjudication methods, or MRMC studies.
    • Any discussion of standalone algorithm performance.

    The document is purely a regulatory clearance notice and does not contain the technical study data you are asking for.

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    K Number
    DEN040012
    Manufacturer
    Date Cleared
    2004-12-23

    (50 days)

    Product Code
    Regulation Number
    862.2570
    Reference & Predicate Devices
    N/A
    Predicate For
    N/A
    AI/MLSaMDIVD (In Vitro Diagnostic)TherapeuticDiagnosticis PCCP AuthorizedThirdpartyExpeditedreview
    Intended Use

    The Affymetrix GeneChip® Microarray Instrumentation System consisting of GeneChip® 3000Dx scanner with autoloader, FS450Dx fluidics station and GCOSDx software is intended to measure fluorescence signals of labeled DNA target hybridized to GeneChip® arrays.

    Device Description

    The Affymetrix GeneChip Microarray Instrumentation System is designed to work with microarrays based on Affymetrix GeneChip ® technology. The system includes the FS450Dx Fluidics Station, GCS3000Dx Scanner, and GCOSDx Software. The FS450Dx performs hybridization, washing, and staining. The GCS3000Dx Scanner is a wide-field, epifluorescent, confocal, scanning laser microscope which scans the chip after staining. The GCOSDx Software provides the interface between the user and instrument systems, controls the instruments, and processes arrays and data collection.

    AI/ML Overview

    The provided document describes the Affymetrix GeneChip Microarray Instrumentation System, which includes the FS450Dx Fluidics Station, GCS3000Dx Scanner, and GCOSDx Software. This system is intended to measure fluorescence signals of labeled DNA target hybridized to GeneChip® arrays, to be used with separately cleared GeneChip microarray assays.

    The submission is for a new device with no predicate, and the performance characteristics described focus on the analytical performance for reproducibility, as accuracy, linearity, carryover, and interfering substances are to be assessed during the clearance of individual assays run on the system.

    Here's an analysis of the provided information based on your request:

    1. Table of Acceptance Criteria and Reported Device Performance

    Given that this is an instrumentation system intended for use with various assays, the acceptance criteria are largely focused on the consistency and reproducibility of the hardware components. The document explicitly mentions targets for uniformity CVs.

    Acceptance CriteriaReported Device Performance
    Scanner Uniformity (Global): CV for global uniformity < 10% (for the array used to assess scanner performance alone)Scanner Uniformity (Global): The between-scan %CV range for all bright features was 4.2-5.2% for scanner 1, 3.2-4.0% for scanner 2, and 0.3-1.9% for scanner 3. For between-scanner, the %CV ranges for all bright features across the scanners were 4.4-10.9% across different time points. This suggests the global uniformity is within the <10% range for individual scanners, but slightly higher when comparing across scanners at later time points.
    Scanner Uniformity (Local): CV for local uniformity < 1% (each 400 uM2 gridded cell with surrounding 4 cells; averaged over alternating cells of the 32x32 array)Scanner Uniformity (Local): Not explicitly reported with a specific numerical value. The study mentions demonstrating uniformity of scanner performance by calculating CVs but only provides global CVs for the scanner performance. The overall average of CVs for 72 images for hybridized control oligonucleotide (reflecting cumulative variability of all system components) was 8.0%.
    Feature Position Check (Scanner): Displacement introduced by scanner (No explicit criterion, but implied to be minimal)Feature Position Check (Scanner): The scanner introduced no more than 2.5 microns of feature displacement.
    Overall System Reproducibility (Hybridization Uniformity): Signal %CV (cumulative variability of all system components)Overall System Reproducibility (Hybridization Uniformity): The overall average of CVs for 72 images for the control oligonucleotide was 8.0%. Hybridization uniformity was consistent across 36 arrays.
    Chip-to-Chip Variability (PM Features): Signal CV for perfect match featuresChip-to-Chip Variability (PM Features): One perfect match feature had a signal CV > 13%. (No explicit criterion provided, but performance is specified).
    Chip-to-Chip Variability (MM Features): Signal CV for mismatch featuresChip-to-Chip Variability (MM Features): No mismatch features had signal variation > 15%. (No explicit criterion provided, but performance is specified).
    Discrimination Score Reproducibility: Discrimination scores within 95% confidence intervalDiscrimination Score Reproducibility: 36 average discrimination scores from all arrays fell within 95% confidence interval (average = ave of 2 scanned images/array x 36 arrays).
    System Component Variability (ANOVA): No statistically significant variability introduced by FS, FS port, or scannerSystem Component Variability (ANOVA): P-values >0.05 for FS, FS port, and scanner, indicating no statistically significant variability introduced.

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

    • Sample Size (for comprehensive system reproducibility study):
      • Arrays: 36 individual GeneChip microarrays (12 chips on 3 Fluidics Stations, each chip scanned in duplicate on each of 3 scanners).
      • Scans: 72 total scans of the same test material (6 scans per chip: 2 duplicates x 3 scanners).
      • Fluidics Stations: 3
      • Scanners: 3
    • Data Provenance: Not explicitly stated (e.g., country of origin). The data appears to be prospective as it describes a specific study designed and executed to assess the device's performance.

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

    Not applicable. This study is focused on the analytical performance (reproducibility and consistency) of the instrumentation system itself, not on the clinical interpretation of results from specific assays. Therefore, there is no "ground truth" derived from expert review of patient data in the context of this submission. The "ground truth" for this study is essentially the known concentration and design of the control probes and target samples used for the reproducibility assessment.

    4. Adjudication Method for the Test Set

    Not applicable. As there is no expert interpretation of clinical data or qualitative assessments requiring adjudication, no adjudication method was used. The study relies on quantitative measurements (fluorescence intensity, CVs, discrimination scores).

    5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done

    No, a MRMC comparative effectiveness study was not done. This study evaluates the instrumentation's ability to consistently generate raw data, not the diagnostic performance of an AI algorithm or the improvement of human readers with AI assistance. The device is an instrument system, not an AI diagnostic tool.

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

    Yes, in essence, a standalone performance assessment of the instrument system was conducted. The study explicitly evaluates the performance of the FS450Dx Fluidics Station, GCS3000Dx Scanner, and GCOSDx Software in generating consistent and reproducible raw data (CEL files). The "algorithm" here refers to the GCOSDx software's image processing and cell intensity calculation algorithms. The study measures the output of the system (intensity readings, CVs, discrimination scores) as an objective assessment of its analytical capabilities, independent of human interpretation of those results.

    7. The Type of Ground Truth Used

    The ground truth used for this analytical performance study consists of:

    • Known concentrations: Two target sets (for control and discrimination) at specific known concentrations (0.1, 0.5, 1, and 3nM).
    • Known array design: The precisely designed array with specific probe sequences (control probes, discrimination controls, PM/MM pairs) located in specific patterns.
    • Known chip lot: A single chip lot was used to minimize chip-to-chip variability as a source of error.

    Essentially, the "ground truth" is the expected and designed behavior of the system when processing known, controlled inputs, focusing on the system's ability to consistently and accurately (in terms of reproducibility) detect and quantify these known elements.

    8. The Sample Size for the Training Set

    Not applicable. This document describes the performance validation of a hardware and software system, not a machine learning or AI model that requires a training set. The GCOSDx software contains algorithms for image processing and data analysis, but these are likely deterministic algorithms, not adaptive machine learning models that would be "trained" on data in the modern sense.

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

    Not applicable. Since there is no "training set" for an AI model, the concept of establishing ground truth for it does not apply in this context.

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