TISSUE OF ORIGIN TEST KIT FFPE

K120489 · Pathwork Diagnostics, Inc. · OIW · May 17, 2012 · Clinical Toxicology

Device Facts

• Record ID: K120489
• Device Name: TISSUE OF ORIGIN TEST KIT FFPE
• Applicant: Pathwork Diagnostics, Inc.
• Product Code: OIW · Clinical Toxicology
• Decision Date: May 17, 2012
• Decision: SESE
• Submission Type: Traditional
• Regulation: 21 CFR 862.3100
• Device Class: Class 2
• Attributes: AI/ML

AI Performance

Output	Acceptance	Observed	Dev DS	Test DS
Tissue of Origin Similarity Scores	Not explicitly stated as a threshold, but performance was validated by comparing results of modified procedure (30-150 ng RNA) to original procedure (>=150 ng RNA).	97.7% concordance (95% CI: 87.7%, 99.9%) between modified and original procedures.	Database of 2,196 specimens, divided into independent training and test datasets.	Non-clinical validation study: 45 tumors (3 of each tumor type), with 43 tumors successfully analyzed and compared between the original and modified methods.

Indications for Use

The Pathwork® Tissue of Origin Test is an in vitro diagnostic intended to measure the degree of similarity between the RNA expression patterns in a patient’s formalin-fixed, paraffin-embedded (FFPE) tumor and the RNA expression patterns in a database of fifteen tumor types (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. This test should be evaluated by a qualified physician in the context of the patient’s clinical history and other diagnostic test results. Limitations: The Pathwork® Tissue of Origin Test is not intended to establish the origin of tumors (e.g. cancer of unknown primary) that cannot be diagnosed according to current clinical and pathological practice. It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork® Tissue of Origin Test database may have RNA expression patterns that are similar to patterns in the database. Therefore, results cannot be used to distinguish tumor types in the database from tumor types not in the database.

Device Story

Pathwork Tissue of Origin Test Kit-FFPE is an in vitro diagnostic kit for gene expression-based tumor classification. Input: RNA extracted from FFPE tumor specimens (minimum 30ng). Process: RNA is processed using Pathchip microarrays (Affymetrix-manufactured, 500,000+ features, 2000 gene probesets); Pathwork System Software performs quality control and executes a machine-learning-based algorithm to compare specimen expression patterns against a 15-tumor-type database. Output: 15 Similarity Scores (0-100 scale) provided in a report via secure website. Used in clinical settings; interpreted by physicians to aid diagnosis of poorly differentiated/metastatic tumors. Modification (K120489) allows lower RNA input (30-150ng) and adds ethanol to purification process. Benefits: Enables molecular classification of difficult-to-diagnose tumors using smaller tissue samples.

Clinical Evidence

No clinical data provided. Bench testing only: 45 tumor specimens (3 per 15 tumor types) were analyzed to validate the modified extraction procedure. 43 specimens were successfully compared; 42 were concordant, resulting in 97.7% concordance (95% CI: 87.7%, 99.9%). Regression analysis of similarity scores yielded a slope of 0.91, intercept of 0.61, and R=0.94.

Technological Characteristics

Kit includes Pathchip microarray (custom Affymetrix design, 18-micron features, 2000 gene probesets), reagents for extraction/amplification/hybridization, and analysis software. Sensing principle: gene expression measurement via microarray hybridization. Connectivity: secure password-protected website for report access. Software: ML-based algorithm for similarity scoring. Sterilization: N/A (reagents/microarray).

Indications for Use

Indicated for patients with poorly differentiated, undifferentiated, or metastatic tumors to measure similarity of tumor RNA expression patterns against a 15-tumor-type database. For use by qualified physicians in conjunction with clinical history and diagnostic results. Not for establishing origin of tumors undiagnosable by standard practice, subclassification, predicting disease course/treatment efficacy, or distinguishing primary from metastatic tumors.

Regulatory Classification

Identification

An amphetamine test system is a device intended to measure amphetamine, a central nervous system stimulating drug, in plasma and urine. Measurements obtained by this device are used in the diagnosis and treatment of amphetamine use or overdose and in monitoring levels of amphetamine to ensure appropriate therapy.

Special Controls

*Classification.* Class II (special controls). An amphetamine test system is not exempt if it is intended for any use other than employment or insurance testing or is intended for Federal drug testing programs. The device is exempt from the premarket notification procedures in subpart E of part 807 of this chapter subject to the limitations in § 862.9, provided the test system is intended for employment and insurance testing and includes a statement in the labeling that the device is intended solely for use in employment and insurance testing, and does not include devices intended for Federal drug testing programs (*e.g.,* programs run by the Substance Abuse and Mental Health Services Administration (SAMHSA), the Department of Transportation (DOT), and the U.S. military).

Predicate Devices

• Pathwork® Tissue of Origin Test Kit – FFPE (k092967)

Submission Summary (Full Text)

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# 510(k) SUBSTANTIAL EQUIVALENCE DETERMINATION DECISION SUMMARY

A. 510(k) Number:
k120489

B. Purpose for Submission:
Modified device

C. Measurand:
Gene expression profile for 15 common tumor types

D. Type of Test:
Gene expression microarray

E. Applicant:
Pathwork Diagnostics Inc.

F. Proprietary and Established Names:
Pathwork® Tissue of Origin Test Kit – FFPE (Origin Test Kit-FFPE)

G. Regulatory Information:

1. Regulation section:
21 CFR § 862.3100 Amphetamine Test System

2. Classification:
Class II

3. Product code:
OIW, Software, similarity score algorithm, tissue of origin for malignant tumor types

4. Panel:
Toxicology (91)

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H. Intended Use:

1. Intended use(s):

The Pathwork® Tissue of Origin Test is an in vitro diagnostic intended to measure the degree of similarity between the RNA expression patterns in a patient’s formalin-fixed, paraffin-embedded (FFPE) tumor and the RNA expression patterns in a database of fifteen tumor types (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. This test should be evaluated by a qualified physician in the context of the patient’s clinical history and other diagnostic test results.

Limitations: The Pathwork® Tissue of Origin Test is not intended to establish the origin of tumors (e.g. cancer of unknown primary) that cannot be diagnosed according to current clinical and pathological practice. It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork® Tissue of Origin Test database may have RNA expression patterns that are similar to patterns in the database. Therefore, results cannot be used to distinguish tumor types in the database from tumor types not in the database.

2. Indication(s) for use:

Same as intended use

3. Special conditions for use statement(s):

For prescription use only

4. Special instrument requirements:

Affymetrix GeneChip® Microarray Instrumentation System (k080995)

I. Device Description:

The modified and the predicate device (k092967) are both in vitro diagnostic product consisting of a reagent kit and instructions, plus a microchip and software, for the comparison of the RNA expression pattern of a patient’s tumor sample to a database of expression patterns of 15 known tumor tissues. Equipment required but not provided are an Affymetrix GeneChip Fluidics Station FS450Dx and an Affymetrix GeneChip Scanner GCS3000Dx, attached to an Affymetrix Workstation with GeneChip Operating System (GCOS). Additional equipment required but not provided is commonly available laboratory equipment.

J. Substantial Equivalence Information:

1. Predicate device name(s) and 510(k) number(s):

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Pathwork® Tissue of Origin Test Kit – FFPE, k092967

2. Comparison with predicate:

| Similarities | | |
| --- | --- | --- |
| Item | Device | Predicate |
| Intended Use | The Pathwork® Tissue of Origin Test is an in vitro diagnostic intended to measure the degree of similarity between the RNA expression patterns in a patient’s formalin-fixed, paraffin-embedded (FFPE) tumor and the RNA expression patterns in a database of fifteen tumor types (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. This test should be evaluated by a qualified physician in the context of the patient’s clinical history and other diagnostic test results. | Same |
| Limitations in the Intended Use | The Pathwork® Tissue of Origin Test is not intended to establish the origin of tumors (e.g. cancer of unknown primary) that cannot be diagnosed according to current clinical and pathological practice. It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork® Tissue of Origin Test database may have RNA expression patterns that are similar to patterns in the database. Therefore, results cannot be used to distinguish tumor types in the database from tumor types not in the database. | Same |
| Technology | Comparison of the RNA expression pattern of a patient’s tumor sample to a database of expression patterns of 15 known tumor tissues. Algorithm as described in k092967 and report graphic presentation of similarity scores for 15 tissues of origin | Same |

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| Differences | | |
| --- | --- | --- |
| Item | Device | Predicate |
| Purification of biotinylated cDNA | Ethanol | No Ethanol added |
| Minimum RNA Required | A minimum of 30 ng total RNA at a concentration of 10 ng/μl (±0.5 ng/μl) is required. If the specimen has an area <25mm², commonly employed techniques for manual dissection under a microscope need to be followed to obtain at least 60% tumor and a recommended tissue volume of at least 0.05mm³. | 150 ng |

## K. Standard/Guidance Document Referenced (if applicable):

Not applicable.

## L. Test Principle:

The test uses curls from a formaldehyde-fixed, paraffin-embedded (FFPE) block. The Origin Test Kit-FFPE test can be performed on a single 10-μm-thick curl cut from the block, or on up to five curls, to obtain tissue area of at least 25 mm². The specimen must contain at least 60% viable tumor. It can also use specimens that are manually dissected under a microscope (up to 4 manual dissected specimens). The manually dissected specimen must contain at least 60% viable tumor with a recommended tissue volume of at least 0.05mm³. The tissue must be de-paraffinized and total RNA must be isolated per the Pathwork Specimen Processing Guide (SPG). Thirty (30) nanograms of total RNA at a concentration of 10 ng/μl (±0.5 ng/μl) are required to perform the test.

The procedural steps include total RNA extraction, reverse transcription, cDNA purification, microarray gene expression analyses, and determination of similarity of 15 tissues of origin and generation of the report. Each specimen analyzed will produce 15 Similarity Scores, one for each tissue on the panel. Each Similarity Score is a measure of the similarity of the gene expression profile of the specimen to the profile of the indicated tissue, ranging from 0 (very low similarity) to 100 (very high similarity). Similarity Scores for all 15 tissues sum to 100. For each Origin Test Kit-FFPE test performed, a test report is generated that quantifies the similarity of the RNA expression pattern found in a tumor specimen (poorly or un-differentiated primary tumors, as well as metastatic tumors) to expression patterns found in tumor specimens from 15 known tissues of origin and provided back to the laboratory over a secure internet connection in pdf format.

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M. Performance Characteristics (if/when applicable):

1. Analytical performance:
a. Precision/Reproducibility:
Established under k092967
b. Linearity/assay reportable range:
Not applicable.
c. Traceability, Stability, Expected values (controls, calibrators, or methods):
Established under k092967
d. Detection limit:
Established under k092967
e. Analytical specificity:
Established under K092967
f. Assay cut-off:
Established under k092967

2. Comparison studies:
a. Method comparison with predicate device:
Forty-five FFPE specimens representing 15 tumor types with three samples per tumor type were used for the method comparison study. They were selected from reserves of specimens used in the analytical studies of the predicate device k092967. Multiple areas (2 - 10 mm²) were manually dissected under a microscope from 5-μm sections of each tumor specimen. RNA was extracted from each manually dissected sample. The amount of RNA was determined spectroscopically. If a single manually dissected sample did not provide between 30 and 150 ng at a concentration of at least 9.5 ng/μL required for the assay, multiple extractions were combined. These total RNA samples were tested with the modified assay and results were compared to those obtained with the larger amounts of total RNA for the same specimens which have available diagnosis.

Among 45 FFPE specimens, two specimens were excluded from the comparison. One failed the overall quality control criteria (signal threshold of 10); the other was erroneously chosen and no data from a paired specimen in the ≥150 ng RNA category was available. Therefore, comparison was based on 43 tumors. The concordance between ≥150 ng RNA specimens processed without ethanol, and 30-150 ng of RNA

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extracted and processed with ethanol was 97.7% (42/43) and the 95% confidence interval was 87.7-99.9%. One sample tested using modified device (30-150 ng of RNA and processed with ethanol) had discordant result with the available diagnosis.

| Comparison | Concordance | | Discordance | |
| --- | --- | --- | --- | --- |
| | Ratio | Percent [95% CI] | Ratio | Percent [95% CI] |
| ≥ 150 ng and ethanol absent vs. 30 to 150 ng and ethanol present | 42/43 | 97.7% [87.7, 99.9] | 1/43 | 2.3% [0.1, 12.3] |

b. Matrix comparison:
Not applicable.

3. Clinical studies:
a. Clinical Sensitivity:
Established under k092967
b. Clinical specificity:
Established under k092967
c. Other clinical supportive data (when a. and b. are not applicable):
None

4. Clinical cut-off:
Established under k092967

5. Expected values/Reference range:
Not applicable

N. Proposed Labeling:
The labeling is sufficient and it satisfies the requirements of 21 CFR Part 809.10.

O. Conclusion:
The submitted information in this premarket notification is complete and supports a substantial equivalence decision.