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The Vysis D7S486/CEP 7 FISH Probe Kit is a device intended for specimen characterization, and detects the LSI D7S486 probe target on chromosome 7q31 and the CEP 7 probe target on chromosome 7p11.1-q11.1 in bone marrow and peripheral blood specimens from patients with acute myeloid leukemia or myelodysplastic syndrome. The assay results are intended to be interpreted by a qualified pathologist or cytogeneticist. This device is not intended for high-risk uses such as selecting therapy, predicting therapeutic response or disease screening. The use of this device for diagnosis, prognosis, monitoring or risk assessment has not been established.

The Vysis D7S486/CEP 7 FISH Probe Kit is for specimen characterization and detects the LSI D7S486 (7q31) probe target on chromosome 7q31 and CEP 7 probe target chromosome 7p11.1-q11.1 in bone marrow and peripheral blood specimens.

DNA Probe Description

Vysis LSI D7S486 SpectrumOrange/ CEP 7 SpectrumGreen Probes:

The SpectrumOrange labeled LSI D7S486 probe is approximately 308 kb in length (chr7:115983468-115675366; February 2009 Assembly UCSC Human Genome Browser).

The SpectrumGreen labeled CEP 7 probe targets the D7Z1 alpha satellite sequence at the centromere of chromosome 7.

The Vysis D7S486/CEP 7 FISH Probe Kit (List No. 04N78-020) consists of a mixture of two DNA FISH probes and four general reagents sufficient to process 20 assays.

• . Vysis LSI D7S486 SpectrumOrange/ CEP 7 SpectrumGreen Probes
• . Vysis LSI/WCP Hybridization Buffer
• . DAPI II Counterstain
• NP-40 .
• . 20X SSC

The Vysis D7S486/CEP 7 FISH Probe Kit is designed for specimen characterization, specifically detecting the LSI D7S486 probe target on chromosome 7q31 and the CEP 7 probe target on chromosome 7p11.1-q11.1 in bone marrow and peripheral blood specimens from patients with acute myeloid leukemia or myelodysplastic syndrome.

Here's an analysis of the acceptance criteria and the study that proves the device meets them:

1. Table of Acceptance Criteria and Reported Device Performance

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

• Analytical Specificity: 4 male and 1 female karyotypically normal specimen slides.
• Analytical Sensitivity and Verification of Upper Reference Limit: 25 bone marrow and 25 peripheral blood specimens. These were from either karyotypically normal individuals or patients lacking monosomy 7 and loss of 7q. The provenance is not explicitly stated (e.g., country of origin, retrospective/prospective).
• Reproducibility (Site-to-Site & Lot-to-Lot): The panel members for the reproducibility studies were prepared by mixing positive cells with normal cells. The exact number of individual patient samples from which these positive and normal cells originated is not specified. The study used 2 high-positive, 2 low-positive, and 2 negative panel members for each specimen type (bone marrow and peripheral blood). The data provenance is not specified as retrospective or prospective, nor is the country of origin explicitly mentioned.

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

• Analytical Specificity: 1 technologist for evaluating metaphase chromosomes.
• Analytical Sensitivity and Verification of Upper Reference Limit: 2 technologists for evaluating interphase nuclei.
• Reproducibility: The ground truth for the reproducibility studies (negative, low positive, high positive categories) was established by mixing positive cells with normal cells to achieve desired levels of positivity, implying a predefined "known status" based on these mixtures. The expertise used to determine the initial "positive cells" or "normal cells" is not detailed.

The qualifications of these technologists/experts are not explicitly stated (e.g., years of experience, specific certifications like "radiologist with 10 years of experience").

4. Adjudication Method (e.g., 2+1, 3+1, none) for the Test Set

For Analytical Sensitivity and Verification of Upper Reference Limit, the document states that each technologist evaluated 100 nuclei per specimen, implying independent scoring. There is no mention of an adjudication method (like 2+1 or 3+1) if scores differed between the two technologists, nor is an adjudication method specified for other tests.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was Done, What Was the Effect Size of How Much Human Readers Improve with AI vs. Without AI Assistance?

No MRMC comparative effectiveness study was done. This device is a FISH probe kit, not an AI-assisted diagnostic tool. Therefore, there is no discussion of human reader improvement with or without AI assistance.

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

This is a laboratory diagnostic kit (FISH probe) that requires human interpretation (a qualified pathologist or cytogeneticist). Therefore, a standalone algorithm-only performance assessment is not applicable and was not performed. The performance studies evaluate the kit's analytical characteristics.

7. The Type of Ground Truth Used (Expert Consensus, Pathology, Outcomes Data, etc.)

• Analytical Specificity: Karyotypically normal specimens were used, with the "correct locus" pre-defined based on known chromosomal locations.
• Analytical Sensitivity and Verification of Upper Reference Limit: Karyotypically normal individuals or patients lacking the specific abnormalities (monosomy 7 and loss of 7q) were used. The expected typical signal pattern (2R2G) served as the ground truth for normalcy. The "atypical" patterns (1R1G, 1R2G) were defined based on the biological expectation of monosomy 7 or 7q deletion.
• Reproducibility: The ground truth for the panel members was established by preparing mixtures of positive and normal cells to achieve predefined "negative," "low positive," and "high positive" statuses. The origin of the "positive cells" would implicitly be from samples with confirmed deletion 7q or monosomy 7, likely established through standard cytogenetic or FISH methods.

8. The Sample Size for the Training Set

This document describes a diagnostic kit and its analytical validation. It does not refer to a machine learning or AI algorithm development pipeline, so there is no specific mention of a "training set" in the context of algorithm development. The studies performed are for analytical validation.

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

As there is no mention of a "training set" for an algorithm, this question is not applicable. The kit is based on established FISH technology, and its performance is validated through analytical studies.

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The Vysis EGR1 FISH Probe Kit - SC detects the LSI EGR1 probe target on chromosome 5q in bone marrow specimens. The Vysis EGR1 FISH Probe Kit -SC assay results characterize bone marrow specimens from patients with acute myeloid leukemia or myelodysplastic syndrome. The assay results are intended to be interpreted by a qualified pathologist or cytogeneticist. This device is not intended for high-risk uses such as selecting therapy, predicting therapeutic response or disease screening. The use of this product for diagnosis, monitoring or risk assessment has not been established.

The Vysis EGR1 FISH Probe Kit - Specimen Characterization uses fluorescence in situ hybridization (FISH) DNA probe technology to detect probe target LSI EGR1 (containing early growth response 1 gene; location chromosome 5g31). The LSI D5S23, D5S721 probe (location chromosome 5p15.2) serves as a control.

The Vysis EGR1 FISH Probe Kit – SC (List No. 04N37-001) consists of the following components which are sufficient to process 20 assays:

1. Vysis LSI EGR1 SpectrumOrange/D5S23, D5S721 Spectrum Green Probes
2. Vysis LSI/WCP Hybridization Buffer
3. DAPI II Counterstain
4. NP-40
5. 20X SSC Salt

Items 2 through 5 above are general purposes reagents.

DNA Probes: Vysis LSI EGR1 SpectrumOrange/ D5S23, D5S721 SpectrumGreen.

a. The SpectrumOrange-labeled LSI EGR1 probe, approximately 209 kb in length (chr5:137654208-137862738; February 2009 Assembly; UCSC Human Genome Browser) is located at 5g31 and contains the complete EGR1 gene.
b. The SpectrumGreen-labeled LSI D5S23, D5S721 probe, approximately 561 kb in length (chr5:9397109-9958407; February 2009 Assembly; UCSC Human Genome Browser) is located at 5p15.2.

Here's a summary of the acceptance criteria and the studies performed for the Vysis EGR1 FISH Probe Kit - SC, based on the provided text:

Acceptance Criteria and Device Performance for Vysis EGR1 FISH Probe Kit - SC

1. Table of Acceptance Criteria and Reported Device Performance:

2. Sample sizes used for the test set and the data provenance:

• Precision/Reproducibility (Intra-Day, Inter-Day, Inter-Site, Lot-to-Lot):
  • Test Set Sample Size: 6 bone marrow specimens (2 high positive, 2 low positive, 2 negative).
  • Nuclei evaluated: 200 nuclei per panel member (100 by each of 2 technologists) for a total of 1200 nuclei per study type (e.g., Intra-day, Inter-day, etc.).
  • Data Provenance: Not explicitly stated (e.g., country of origin). Appears to be prospective analytical testing conducted by the manufacturer.
• Analytical Sensitivity:
  • Test Set Sample Size: 25 bone marrow specimens (karyotypically normal or 5p15 and 5q31 deletion-free).
  • Nuclei evaluated: 200 nuclei per specimen (100 by each of 2 technologists) for a total of 5000 scoreable nuclei.
  • Data Provenance: Not explicitly stated. Appears to be prospective analytical testing.
• Analytical Specificity:
  • Test Set Sample Size: Metaphase chromosomes prepared from peripheral blood cultures of five karyotypically normal males (pooled).
  • Nuclei evaluated: 100 consecutive metaphase nuclei by one technologist, for a total of 200 target loci (100 for each probe).
  • Data Provenance: Not explicitly stated. Appears to be prospective analytical testing.
• Reference Range Validation:
  • Test Set Sample Size: 25 bone marrow specimens (karyotypically normal or 5p15.2 and 5q31 deletion-free).
  • Nuclei evaluated: 200 nuclei per specimen (100 by each of 2 technologists).
  • Data Provenance: Not explicitly stated. Appears to be prospective analytical testing.
• Clinical Supportive Data (Clinical Validity):
  • Test Set Sample Size:
    • Data Source 1 (Sun et al.): 320 bone marrow specimens
    • Data Source 2 (Galvan et al.): 28 bone marrow specimens
    • Data Source 3 (Vance et al.): 181 bone marrow specimens
  • Data Provenance: Retrospective, derived from peer-reviewed published literature (implicitly based on patient data from the respective study locations, not specified).

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts:

• Analytical Performance Studies (Precision, Sensitivity, Specificity, Reference Range):
  • "Two technologists" or "one technologist" were involved in evaluating nuclei. Their specific qualifications (e.g., "cytogeneticist with X years of experience") are not explicitly stated, beyond being referred to as "technologists."
  • The overall interpretation is intended for a "qualified pathologist or cytogeneticist."
• Clinical Supportive Data:
  • Ground truth for the clinical studies would have been established by the methods described in those published papers, likely involving consensus diagnostics by pathologists and/or cytogeneticists based on conventional cytogenetics and clinical information. The number and qualifications of these experts are not detailed in this summary document.

4. Adjudication method (e.g., 2+1, 3+1, none) for the test set:

• For the analytical performance studies where two technologists evaluated slides (e.g., Precision, Analytical Sensitivity, Reference Range Validation), the text states "each technologist evaluated 100 nuclei per panel member" or "100 nuclei per specimen." It does not explicitly describe an adjudication method (e.g., 2+1, 3+1) if their readings disagreed. It simply reports aggregated results.

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 described as an assay (FISH probe kit) intended to be interpreted by a qualified pathologist or cytogeneticist, not an automated system or AI-assisted diagnostic tool. The text explicitly states: "These devices do not include automated systems that directly report results without review and interpretation by a qualified pathologist or cytogeneticist." Therefore, the concept of human readers improving with AI assistance is not applicable to this submission.

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

• No, a standalone (algorithm only) performance study was not done.
• As noted above, this is a FISH probe kit, which is a laboratory assay requiring manual interpretation by human experts. It is not an algorithm that performs standalone analysis.

7. The type of ground truth used (expert consensus, pathology, outcomes data, etc.):

• Analytical Performance Studies:
  • Expected signal pattern: This serves as the ground truth for parameters like precision and sensitivity. It's based on the known genetic characteristics of the specimens (e.g., high positive, low positive, negative, normal karyotype).
  • Known chromosomal location: For analytical specificity, the ground truth is the established chromosomal location of the gene targets.
• Clinical Supportive Data:
  • The ground truth for the clinical studies (validation of clinical utility) was likely established through a combination of pathology reports, conventional cytogenetics, and clinical diagnoses of AML or MDS as carried out in the respective peer-reviewed studies. The "percentage of cells with 1R2G signal pattern" would have been correlated with these clinical states.

8. The sample size for the training set:

• Not applicable. The Vysis EGR1 FISH Probe Kit is a diagnostic assay (chemical reagents and probes), not a machine learning algorithm. Therefore, there is no "training set" in the context of AI/ML. All samples discussed are for analytical or clinical validation/support.

9. How the ground truth for the training set was established:

• Not applicable, as there is no "training set" for this type of device.

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