NP Screen is a semi-quantitative in vitro diagnostic test that uses real-time PCR to determine the level of Epstein-Barr Virus Nuclear Antigen-1 (EBNA-1) DNA in nasopharyngeal cellular specimens collected using the NP Screen Trans-Oral Nasopharyngeal Brush. The test is intended for use in conjunction with endoscopy and other clinical information to assess the likelihood that EBV-associated nasopharyngeal carcinoma (NPC) is present. The test is indicated for use in adults of Chinese descent with signs and symptoms of nasopharyngeal carcinoma.

Device Description

NP Screen is a semi-quantitative in vitro test for the detection of Epstein-Barr Virus Nuclear Antigen-1 gene (EBNA-1) in nasopharyngeal epithelial specimens are collected by the clinician, using the NP Screen Trans-Oral Collection Brush, and placed into the Transport Medium for shipping. The test is performed in a single laboratory, Primex Clinical Laboratories, Inc. Total nucleic acid is extracted from the specimen and the dsDNA is then quantitated. If the amount of extracted DNA does not meet the minimum required for testing, the specimen is rejected, and a new specimen must be collected. Extracted specimen DNA that meets the specification is normalized to a pre-defined concentration. The standardized DNA is tested in duplicate using real-time Polymerase Chain Reaction (real-time PCR) and nucleic acid hybridization for the detection of target EBV EBNA-1 DNA. Simultaneous amplification and detection of human RNAse P DNA serves as the internal control for assessing all steps of the NP Screen assay. Low and High Positive External Controls are included with each run.

AI/ML Overview

The provided text describes the evaluation of the NP Screen assay, a real-time PCR test for Epstein-Barr Virus Nuclear Antigen-1 (EBNA-1) DNA to assess the likelihood of EBV-associated nasopharyngeal carcinoma (NPC) in adults of Chinese descent with signs and symptoms of NPC.

Here's an analysis of the acceptance criteria and study details:

1. A table of acceptance criteria and the reported device performance:

The document doesn't explicitly define "acceptance criteria" in a typical table format with specific performance thresholds for sensitivity, specificity, or predictive values against a predefined benchmark. Instead, it focuses on the device's ability to provide clinically relevant risk stratification when used in conjunction with endoscopy. The performance is presented as post-test risks of NPC.

Therefore, I will present the key clinical performance data that demonstrates the device's utility in risk assessment, which can be interpreted as fulfilling its intended purpose and thereby meeting implicit "acceptance criteria" for a de novo classification:

Endoscopy (Degree of Suspicion)	NP Screen Result	Reported Device Performance (Risk of NPC)	Benefit/Impact on Risk (Compared to Pre-Test Risk)
High Suspicion (Pre-Test Risk: 79.6%)	Positive	100% (33/33) [95% CI: 91.4%; 100%]	Statistically significantly higher than pre-test risk, confirming high risk.
	Negative	10% (1/10) [95% CI: 0.7%; 37.8%]	Statistically significantly lower than pre-test risk, reducing estimated risk.
Intermediate Suspicion (Pre-Test Risk: 16.7%)	Positive	90.0% (9/10) [95% CI: 62.1%; 99.4%]	Statistically significantly higher than pre-test risk, increasing estimated risk.
	Negative	0.0% (0/40) [95% CI: 0.0%; 7.7%]	Statistically significantly lower than pre-test risk, reducing estimated risk to zero.
Low Suspicion (Pre-Test Risk: 1.7%)	Positive	66.7% (6/9) [95% CI: 39.4%; 88.0%]	Statistically significantly higher than pre-test risk, greatly increasing estimated risk.
	Negative	0.0% (0/342) [95% CI: 0.0%; 1.0%]	Statistically significantly lower than pre-test risk, reducing estimated risk to zero.
No Suspicion (Pre-Test Risk: 0.149%)	Positive	16.7% (1/6) [95% CI: 1.6%; 33.6%]	Statistically significantly higher than pre-test risk, indicating a notable increase despite low baseline.
	Negative	0.0% (0/640) [95% CI: 0.0%; 0.146%]	Statistically significantly lower than pre-test risk, reducing estimated risk to zero.
Combined (Pre-Test Risk: 4.8%)	Positive	84.5% (49/58) [95% CI: 74.0%; 91.7%]	Substantially increases risk estimation.
	Negative	0.10% (1/1,032) [95% CI: 0.01%; 0.91%]	Substantially decreases risk estimation.

2. Sample size used for the test set and the data provenance (e.g. country of origin of the data, retrospective or prospective)

Sample Size for Test Set: 1,138 evaluable patients. (A total of 1146 patients were enrolled, with 8 excluded due to invalid NP Screen results).
Data Provenance: Prospective clinical study. The collection site was located in Toronto, Canada.

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts (e.g. radiologist with 10 years of experience)

The document primarily relies on biopsy results to establish the ground truth for NPC diagnosis, especially for patients with High Suspicion endoscopy findings or those for whom biopsy was recommended at follow-up. For patients with Intermediate or Low Suspicion who did not receive a biopsy after 3 months, or patients with No Suspicion at baseline, their clinical status was considered negative for NPC based on the observed clinical course without further intervention.

While endoscopy findings categorized by "degree of suspicion" were used as a pre-screening step and part of the clinical study design, the ultimate determination of NPC presence for analysis relied on biopsy. The endoscopy examinations were performed by "ENT surgeon[s]" according to "standard clinical practice," implying qualified medical professionals, but specifically states "biopsy" results are the definitive ground truth where applicable. The number of ENT surgeons or pathologists involved in reading slides for biopsy is not specified.

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

The document does not describe an explicit adjudication method for reconciling disagreements between readers or interpretations, primarily because the clinical status (ground truth) for patients who underwent biopsy was determined by the biopsy result itself. For patients not biopsied, their clinical status was determined by the absence of further recommendations for biopsy after observation or discharge.

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, a multi-reader multi-case (MRMC) comparative effectiveness study was not done. This device is an in-vitro diagnostic (IVD) test measuring EBV DNA levels, not an AI-powered image analysis tool that would typically involve human readers. The study evaluates the NP Screen assay in conjunction with endoscopy (human assessment), but not how human readers' performance changes with or without AI assistance from this specific device.

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

Yes, the NP Screen assay essentially performs as a standalone algorithm in terms of generating its quantitative EBV DNA Detection Level (EDL) and then categorizing it into "Positive," "Equivocal," or "Negative." The clinical study then integrates these standalone assay results with human endoscopy findings to present post-test risks. The performance figures (Risks of NPC given an NP screen result) represent the direct output of the assay (alone or in combination with endoscopy category), demonstrating its standalone diagnostic utility within the context of the clinical pathway.

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

The primary type of ground truth used for determining the presence of NPC was pathology (biopsy results). For patients who were not biopsied (e.g., those discharged or considered negative after follow-up), the ground truth was effectively outcomes data / clinical follow-up, where the absence of a confirmed NPC diagnosis over time was considered as negative for NPC.

8. The sample size for the training set

The document does not explicitly describe a separate "training set" for the NP Screen assay in the context of a machine learning or AI model development. The assay is an in-vitro diagnostic (real-time PCR) with established cut-off points. These cut-off points were determined using dilutions of a material traceable to the 1st WHO International Standard (Section L.1.f) and were "clinically validated in the clinical study." This implies that the clinical study described (N=1138 evaluable patients) served as the primary validation set to demonstrate the clinical utility of the pre-defined cut-offs, rather than a dataset used for iterative model training.

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

As noted above, a distinct "training set" in the machine learning sense is not described. The cut-off points for the NP Screen assay were established based on EBV concentrations traceable to the 1st WHO International Standard for Epstein-Barr Virus for Nucleic Acid Amplification Techniques. This is an analytical method rather than a clinical ground truth establishment for a training set. The clinical study then validated the performance of these pre-defined cut-offs against biopsy and clinical follow-up outcomes.

Summary

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EVALUATION OF AUTOMATIC CLASS III DESIGNATION FOR NP SCREEN DECISION SUMMARY

A. DEN Number:

DEN190031

B. Purpose for Submission:

De Novo request for evaluation of automatic class III designation for the NP Screen assay

C. Measurand:

Epstein-Barr Virus DNA

D. Type of Test:

Real-Time PCR

E. Applicant:

Advance Sentry Corporation

F. Proprietary and Established Names:

NP Screen

G. Regulatory Information:

1. Regulation section:
  21 CFR 866.3236
1. Classification:
  Class II
1. Product code:
  OJY

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4. Panel:

Microbiology (83)

H. Intended Use:

1. Intended use(s):
  NP Screen is a semi-quantitative in vitro diagnostic test that uses real-time PCR to determine the level of Epstein-Barr Virus Nuclear Antigen-1 (EBNA-1) DNA in nasopharyngeal cellular specimens collected using the NP Screen Trans-Oral Nasopharyngeal Brush. The test is intended for use in conjunction with endoscopy and other clinical information to assess the likelihood that EBV-associated nasopharyngeal carcinoma (NPC) is present. The test is indicated for use in adults of Chinese descent with signs and symptoms of nasopharyngeal carcinoma.

The NP Screen assav is a single-site assay performed at Primex Clinical Laboratories. Inc.

1. Indication(s) for use:
  Same as Intended Use
1. Special conditions for use statement(s):
  For prescription use only.

For in vitro diagnostic use.

1. Special instrument requirements:
- . Roche MagNA Pure 96 System (for nucleic acid extraction)
- Thermo Scientific Fluoroskan Ascent (for pre-analytical DNA standardization) .
- Applied Biosystems OuantStudio 12K Flex Real-Time PCR System (for EBV DNA . amplification)

I. Device Description:

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DNA is tested in duplicate using real-time Polymerase Chain Reaction (real-time PCR) and nucleic acid hybridization for the detection of target EBV EBNA-1 DNA. Simultaneous amplification and detection of human RNAse P DNA serves as the internal control for assessing all steps of the NP Screen assay. Low and High Positive External Controls are included with each run.

The NP Screen assay requires the following reagents and materials:

. Specimen Collection and Transport
- · Trans-Oral Nasopharyngeal Specimen Collection Kit
  - . Instruction sheet
  - . Trans-Oral Collection Brush, packaged separately (sterile)
  - I Vial with Transport Medium - 0.5 mL
  - . Vial labels for patient information and specimen identification
  - . Biohazard specimen transport bag
  - . Disposable scissors
. DNA Extraction
- 0 MagNA Pure 96 DNA and Viral NA Small Volume Kit
DNA Standardization .
- Quant-iT dsDNA Assay Kit, broad range
. Real-Time PCR
- EBV DNA TagMan Primers and Probe o
- TaqMan RNase P Detection Kit O
- TaqMan Universal Master Mix II with UNG O
- o External Controls
  - . Low Positive
  - . High Positive

J. Standard/Guidance Document Referenced (if applicable):

CLSI EP05-A3: Evaluation of Precision of Quantitative Measurement Procedures: Approved Guideline - Third Edition

K. Test Principle:

Target sequences located in the EBV EBNA-1 gene and the human RNase P gene are detected and co-amplified during the real-time PCR reaction. For patient samples, EBNA-1 is the clinically relevant analyte, while RNase P serves as the internal control.

Uracil-N-glycosylase is included in each reaction to prevent amplification of products from previous PCR reactions. The Low Positive Control and High Positive Control are extracted

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and tested in duplicate with each run. A negative (no-template control) is tested in duplicate with each run,

For each specimen, the duplicate Ct results are averaged and then converted to an NP Screenspecific unit of Epstein-Barr Virus DNA Detection Level (EDL). Results of the NP Screen assay are reported as Positive, Equivocal, or Negative. The cut-off points for Negative and Positive results represent EBV DNA levels relevant in assessing the likelihood of nasopharyngeal carcinoma in adult patients of Chinese descent with signs and symptoms of nasopharyngeal carcinoma. The NP Screen result is intended to be used as a supplement to endoscopy, along with other clinical information. Result interpretation for the NP Screen assay is shown in Table 1.

NP Screen Result	Interpretation
Positive	EBV DNA was detected at a significantlyelevated level.
Equivocal	EBV DNA was detected at a low level.
Negative	EBV DNA was not detected or was detectedat a very low level.
Insufficient	Amount of DNA was not sufficient fortesting. Collect and submit a new specimen.

Table 1: NP Screen Result Interpretation

L. Performance Characteristics (if/when applicable):

1. Analytical performance:

a. Precision:
A panel of samples consisting of High Positive, Low Positive, Equivocal, High Negative and Negative levels of EBV DNA was tested at 60000 site. The panel was tested in runs per day 1014 operators per day x [ runs per operator), in 10149 replicates per sample, on 20 days, for a total of per replicates per sample. The study included bear reagent lots. Results are shown in Table 2.

Table 2: Precision of the NP Screen assay

			Repeatability		BetweenRun		BetweenLot		BetweenDay		WithinLab
Sample	MeanEDL	N	SD	%CV	SD	%CV	SD	%CV	SD	%CV	SD	%CV
HighPositive						(b)(4)

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			Repeatability		BetweenRun		BetweenLot		BetweenDay		WithinLab
Sample	MeanEDL	N	SD	%CV	SD	%CV	SD	%CV	SD	%CV	SD	%CV
LowPositive						(b)(4)
Equivocal
HighNegative

results are excluded from calculations because they were | |004 The finvalid result was excluded due to a failed Internal Control signal.

b. Linearity/assay reportable range: Not applicable
c. Traceability, Stability, Expected values (controls, calibrators, or methods): Traceability

The concentrations of EBV DNA detected at the NP Screen cut-off points for Negative and Positive result interpretations were determined using an EBV virus preparation traceable to the 1st WHO International Standard for Epstein-Barr Virus for Nucleic Acid Amplification Techniques, NIBSC code: 09/260. The Low and High Positive Controls are also traceable to the 1st WHO International Standard.

Reagent Stability

The reagents and the Controls used in the NP Screen assay are purchased from commercial vendors. Advance Sentry Corporation verified that the NP Screen reagents and Low and High Positive Controls are stable for up to seven months within the expiration date specified by the manufacturer of each reagent and control.

Specimen stability

(0) samples with EBV concentrations slightly above the cut-off for Positive results of the NP Screen assay were prepared from pooled NP Screen-negative clinical samples spiked with EBV. Immediately after preparation 1016 replicates of each sample were tested to establish the baseline results. All remaining aliquots were placed into storage. Storage conditions reflected temperature extremes that might be encountered during specimen transport as well as controlled temperatures in a laboratory setting. At each test time point, replicates of each of esamples were used for NP Screen testing.

Results of the study support the stability of specimens and extracted DNA stored under the following conditions:

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Specimen storage prior to extraction with the NP Screen assay:

. Up to 3 weeks, from time of collection, at either at 2 - 8℃ or at Room Temperature 22 - 25℃
Extracted DNA storage:
Up to 2 weeks at 2 8ºC after storage of the specimen for up to 3 weeks, from . time of collection, either at 2-8ºC or at Room Temperature 22 - 25ºC

Controls

Run controls .
- · Low Positive Control (purified EBV) is run in For each replicate, the Ct (FAM) must fall within the established range.
- o High Positive Control (purified EBV) is run in (D)(4) For each replicate, the Ct (FAM) must fall within the established range.
- Negative (no-template) PCR control (sterile, molecular grade water 0 10)(4) replaces DNA template) is run in Results must show no amplification.
Sample-specific controls patient samples are run in .
- o Internal Control Detection of human RNase P. The Ct (VIC) of each replicate must fall within the established range and the difference between the Ct values must be within the established acceptable limit.

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EBV EBNA-1 result. The Ct (FAM) of each replicate must fall within the o established range and the difference between the Ct values must be within the established acceptable limit.
d. Detection limit:

The Limit of Detection (LoD) was determined by testing a panel of | Samples. The samples were prepared from quantified EBV diluted in a matrix of pooled negative clinical specimens. The samples were tested in 100 replicates per run, 1040 runs per day, over | 0 days, for a total of replicates per sample. The LoD determined by the study is well below the established EBV concentration detected at the clinically validated NP Screen cut-off point for discriminating Negative from Equivocal specimen results.

e. Analytical specificity:

Cross-reactivity

Cross-reactivity studies were performed with a panel of microorganisms. For microorganisms sourced as viable virus or bacteria, the samples were thawed, or resuspended in sterile water if lyophilized, and extracted. For microorganisms sourced as purified DNA or RNA, the nucleic acid was added directly to the PCR reaction. For each panel member . I uL of purified nucleic acid from the microorganism plus uL of purified nucleic acid from a pool of NP Screen-negative samples were added to the PCR reaction. Each microorganism was tested in 1014) with the NP Screen

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assay. No cross-reactivity was observed with the microorganisms tested at the concentrations shown in Table 3.

Microorganism	Sample Type	Concentration*
Adenovirus (HAdv)	DNA	(5)(4)
Bordetella pertussis	culture
Chlamydia pneumoniae	culture
CMV (HHV5)	culture
Corynebacterium sp.	culture
E. coli	DNA
Enterovirus D68	RNA
Haemophilus influenzae	DNA
HHV6	culture
Human coronavirus 229E	RNA
Human parainfluenza	RNA
HPV Type 16‡	DNA
HPV Type 18‡	DNA
HSV I	culture
HSV II	culture
Influenza A (H1N1)‡	culture
Influenza A (H3N2)‡	culture
Influenza B‡	culture
Klebsiella pneumoniae	DNA
Lactobacillus sp.	culture
Legionella pneumophila	culture
Mumps virus	RNA
Mycobacterium sp.	DNA
Neisseria meningitidis	DNA
Pseudomonas aeruginosa	DNA
Respiratory syncytial virus	RNA
Rhinovirus	RNA
Staphylococcus aureus	DNA
Staphylococcus epidermidis	DNA
Streptococcus pneumoniae	DNA
Streptococcus pyogenes	DNA
Streptococcus salivarius	DNA

Table 3: Microorganisms tested for cross-reactivity in the NP Screen assay

For culture samples, this is the concentration of the sample input to the extraction step. For nucleic acid samples, this is the concentration of DNA or RNA input to the PCR reaction.

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- 10 uL of microorganism DNA were added to the PCR reaction without the addition of nucleic acid from a pool of NP Screen-negative samples.
  In addition, an in silico analysis was performed using the NP Screen assay primers and probe as input sequences for BLAST searches against the NCBI Public DNA Database. No significant sequence matches were detected in the in silico analysis.

Interfering Substances

A study was performed to evaluate the performance of the NP Screen assay in the presence of potentially interfering substances that might be found in the nasopharynx. A matrix of pooled NP Screen specimens was divided and spiked with EBV to obtain samples at two EBV concentrations, one just above the cutoff for Positive results and one in the range of Negative results for the NP Screen assay. An NP Screen Trans-Oral Collection Brush was submerged in the full-strength interfering substance and then placed in an aliquot of each sample. A control sample was prepared with Phosphate Buffered Saline (PBS), in place of the interfering substance. The samples were extracted and tested with the NP Screen assay. The potentially interfering substances evaluated are listed in Table 4.

Table 4: Potentially Interfering Substances Tested in the NP Screen Assay

Potentially Interfering Substances
Drixoral Nasal Spray
Taro-Mupirocin Antibiotic, nasal ointment
Mylan Belco AQ - nasal corticosteroid
Avamys Fluticasone - nasal corticosteroid
Lidodan - topical anesthetic
Relenza - inhaled antiviral medication
Blood

No interference was observed with the substances listed in Table 4, i.e., all positive replicates produced positive results and all negative replicates produced negative results.

f. Assay cut-off:

The EBV concentrations detected at the cut-off points for Positive and Negative results were determined by testing dilutions of a material traceable to the 1st WHO International Standard for Epstein-Barr Virus for Nucleic Acid Amplification. Techniques, NIBSC code: 09/260. The cut-off points for Positive and Negative results of the NP Screen assay indicate clinically relevant levels of EBV DNA and

+ Concentration information was not available.

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were validated in the clinical study.

g. Analytical accuracy:
Samples prepared from the pooled negative clinical specimens spiked with quantified EBV traceable to the 181 WHO International Standard were tested (see 1.d above).
h. Carryover
A series of EBV negative samples, with EDL=0, and high positive samples, with EDL were tested in a checkerboard pattern with the NP Screen assay. A total of high positive and 10 negative samples were processed on each of [0] plates by different operators in separate runs. All negative samples produced negative NP Screen results with EDL=0. No carryover was observed.
1. Comparison studies:
- a. Method comparison:

Not applicable

b. Matrix comparison:
Not applicable; the NP Screen assay is intended for use only with the NP Screen Trans-Oral Nasopharyngeal Specimen Collection Brush and Transport Media.
1. Clinical studies:
- a. Clinical Sensitivity:

The NP Screen Test is a semi-quantitative test; therefore, clinical sensitivity is not applicable. Clinical performance was evaluated by calculating risks for Positive, Equivocal and Negative results; refer to section M.3.c.

b. Clinical specificity:
The NP Screen Test is a semi-quantitative test; therefore, clinical specificity is not applicable. Clinical performance was evaluated by calculating risks for Positive. Equivocal and Negative results refer to section M.3.c.
c. Other clinical supportive data (when a. and b. are not applicable):

Clinical Validation Study

Overview

Patients with signs or symptoms of NPC are often referred by family physicians to an

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ear, nose, and throat (ENT) specialist for clinical examination and assessment of the nasopharynx using an endoscope. Depending on the findings of the endoscopy exam and other clinical information, the patient may be advised to have a biopsy. A clinical study was performed to determine the risk of nasopharyngeal carcinoma associated with different combinations of endoscopy findings and NP Screen results.

Study Design

The study included adult patients of Chinese descent with signs and symptoms of NPC. All patients who fulfilled the inclusion criteria and provided written consent in accordance with the IRB approved protocol were enrolled in the study. The collection site was located in Toronto. Canada. Upon enrollment, each patient received detailed clinical and endoscopy examinations at an ENT clinic, according to standard clinical practice. Following endoscopy, the ENT surgeon collected a nasopharyngeal specimen from each patient using the NP Screen Trans-Oral Collection Brush and collection procedure. The specimen was shipped to Primex Clinical Laboratory for NP Screen testing.

The endoscopy findings for each patient were categorized, based on commonly described endoscopic features of NPC, by degree of suspicion for NPC, as follows: High Suspicion, Intermediate Suspicion, Low Suspicion, or No Suspicion.

Expected Values

A total of 1146 patients were enrolled in the study. Of those, eight (0.7%) had invalid NP Screen results and were excluded from the analysis. There were 1,138 patients enrolled in the study with evaluable results. The percent of patients with Positive. Equivocal, and Negative NP Screen results, stratified by endoscopy at baseline, are presented in Error! Reference source not found ..

Endoscopy	N	NP Screen Results
(Degree ofSuspicion forNPC)		%Positive	%Equivocal	%Negative
High Suspicion	49	67.3%(33/49)	12.2%(6/49)	20.4%(10/49)
IntermediateSuspicion	54	18.5%(10/54)	7.4%(4/54)	74.1%(40/54)
Low Suspicion	363	2.5%(9/363)	3.3%(12/363)	94.2%(342/363)
No Suspicion	672	0.9%(6/672)	3.9%(26/672)	95.2%(640/672)
Combined	1,138	5.1%(58/1,138)	4.2%(48/1,138)	90.7%(1,032/1,138)

Table 5: Expected NP Screen Results

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Clinical Performance

Patients with abnormal endoscopy findings of High Suspicion were recommended for biopsy. Patients whose endoscopy findings showed No Suspicion for NPC were recommended for discharge from the clinical study. Patients with abnormal endoscopy findings of Intermediate or Low Suspicion were recommended for followup with repeat endoscopy at 3 months. At the 3-month follow-up visit, based on the findings of the repeat endoscopy and other clinical information, the patient was discharged, or biopsy was recommended.

The clinical study design is summarized in Figure 1.

Figure 1: Clinical study design

Image /page/10/Figure/4 description: This image is a flowchart outlining a medical procedure. The process starts with enrollment, followed by an endoscopy and NP screen. If the endoscopy findings are suspicious for NPC, the next step depends on the level of suspicion: high suspicion leads to a recommended biopsy, while intermediate or low suspicion results in a follow-up endoscopy in 3 months, after which a biopsy may be recommended or the patient is discharged. If the initial endoscopy findings show no suspicion for NPC, the patient is discharged.

Clinical Status

The clinical status for each patient was determined as follows:

1. For patients with High Suspicion endoscopy findings at baseline, biopsy is recommended, and clinical status is determined by results of the biopsy.

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1. For the patients with Intermediate or Low Suspicion endoscopy findings at baseline, clinical status was determined at the 3-month follow-up visit. If biopsy was recommended for the patient at the 3-month follow-up visit (because of endoscopy findings) then clinical status for the patient was determined by results of the biopsy. If biopsy was not recommended for the patient based on the endoscopy findings at 3 months, then clinical status for the patient is considered as negative for NPC.
1. For the patients with endoscopy findings of No Suspicion at baseline, clinical status for the patient is considered as negative for NPC.

Data Analysis

Performance of the NP Screen assay with three results (Positive, Equivocal, Negative) is described by risks for each result along with 95% confidence intervals.

Risks

The pre-test risk and post-test risks of NPC for patients with Positive, Equivocal, and Negative NP Screen results were calculated for each category of baseline endoscopy findings, as presented in Table 6.

Table 6. Risks of NPC for Different Combinations of Endoscopy and NP Screen Results

Endoscopy(Degree ofSuspicion)	N	Pre-TestRisk of NPC(Prevalence)	PositiveNP Screen Result		EquivocalNP Screen Result		NegativeNP Screen Result
			Risk ofNPC	95% CI	Risk ofNPC	95% CI	Risk ofNPC	95% CI
HighSuspicion	49	79.6%(39/49)	100%(33/33)	(91.4%; 100%)	83.3%(5/6)	(47.7%;98.4%)	10%(1/10)	(0.7%; 37.8%)
IntermediateSuspicion	54	16.7%(9/54)	90.0%(9/10)	(62.1%; 99.4%)	0.0%(0/4)	(0.0%; 45.5%)	0.0%(0/40)	(0.0%; 7.7%)
LowSuspicion	363	1.7%(6/363)	66.7%(6/9)	(39.4%; 88.0%)	0.0%(0/12)	(0.0%; 18.9%)	0.0%(0/342)	(0.0%; 1.0%)
No Suspicion	672	0.149%(1/672)	16.7%(1/6)	(1.6%; 33.6%)	0.0%(0/26)	(0.0%; 4.0%)	0.0%(0/640)	(0.0%; 0.146%)
Combined	1138	4.8%(55/1,138)	84.5%(49/58)	(74.0%; 91.7%)	10.4%(5/48)	(3.6%; 21.1%)	0.10%(1/1,032)	(0.01%; 0.91%)

Risks of 0.0% in the table mean small positive risks because patients with endoscopy findings not suspicious for NPC are considered as negative for NPC in the data analysis.

Conclusions for patients with High Suspicion endoscopy findings:

Data for 49 patients with High Suspicion endoscopy findings demonstrated that:
Patients with NP Screen Positive results have NPC risk of 100% and the risk is . statistically significantly higher than the pre-test risk of 79.6%.
Patients with NP Screen Negative results have NPC risk of 10% and the risk is . statistically significantly lower than the pre-test risk of 79.6%.

Conclusions for subjects with Intermediate Suspicion endoscopy findings:

Data for 54 subjects with Intermediate Suspicion endoscopy findings demonstrated:

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Patients with NP Screen Positive results have NPC risk of 90.0% and the risk is . statistically significantly higher than the pre-test risk of 16.7%.
. Patients with NP Screen Negative results have NPC risk of 0.0% and the risk is statistically significantly lower than the pre-test risk of 16.7%.

Conclusions for subjects with Low Suspicion endoscopy findings:

Data for 363 subjects with Low Suspicion endoscopy findings demonstrated that:
Patients with NP Screen Positive results have NPC risk of 66.7% and the risk is . statistically significantly higher than the pre-test risk of 1.7%.
Patients with NP Screen Negative results have NPC risk of 0.0% and the risk is . statistically significantly lower than the pre-test risk of 1.7%.

Conclusions for subjects with endoscopy findings of No Suspicion:

Data for 672 subjects with endoscopy findings of No Suspicion demonstrated that:
Patients with NP Screen Positive results have NPC risk of 16.7% and the risk is . statistically significantly higher than the pre-test risk of 0.149%.
Patients with NP Screen Negative results have NPC risk of 0.0% and the risk is . statistically significantly lower than the pre-test risk of 0.149%.
1. Clinical cut-off:

The NP Screen test has two cutoffs: one cutoff is for Negative results and the second cutoff is for Positive results.

1. Expected values/Reference range:
  For Expected values, see Table 5 above. Reference range is not applicable.

M. Instrument Name:

Not applicable.

N. System Descriptions:

1. Modes of Operation:
  Does the applicant's device contain the ability to transmit data to a computer, webserver, or mobile device?

Yes and or Nor No a x 1 - 1

Does the applicant's device transmit data to a computer, webserver, or mobile device using wireless transmission?

Yes of the for Not x x 1 - 1

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2. Software:

FDA has reviewed applicant's Hazard Analysis and software development processes for this line of product types:

Yes x x - or No ---------------------------------------------------------------------------------------

1. Specimen Identification:
  Specimen Identification labels are provided in the NP Screen Trans-Oral Nasopharyngeal Specimen Collection Kit.
1. Specimen Sampling and Handling:
  A nasopharyngeal specimen is collected by the clinician using the Trans-Oral Nasopharyngeal Brush and placed into the vial of Transport Medium. The specimen is shipped at ambient temperature to the laboratory.

Information on specimen collection is provided in the package insert of the NP Screen Trans-Oral Nasopharyngeal Specimen Collection Kit.

1. Calibration:
  Not applicable.
1. Quality Control:
  Refer to section L.1.c for a description of the assay and sample controls.

O. Other Supportive Instrument Performance Characteristics Data Not Covered In The "Performance Characteristics" Section above:

Not applicable.

P. Proposed Labeling:

The labeling supports the decision to grant the De Novo request for this device.

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Identified Risks to Health	Identified Mitigations
False test results	Use of certain specimen collection andtransport devices.Certain labeling information.Certain design verification andvalidation.
Failure to correctly interpret the testresults	Certain labeling information.

Q. Identified Risks to Health and Mitigation Measures

R. Benefit/Risk Analysis

Summary of the Assessment of Benefit

The benefit of the test, when used as a supplement to nasal endoscopy, along with other clinical information, would be aiding a clinician to assess the likelihood that EBV-associated nasopharyngeal carcinoma (NPC) is present in appropriate patients, namely adults of Chinese descent with signs and symptoms of NPC. The high prevalence of NPC in this population justifies authorizing use of this device. The clinical benefit of assessing the likelihood of EBV associated NPC would be the potential for initiation of further investigation and potentially intervention sooner than current medical practice to avoid the sequelae of untreated NPC, such as progression to more invasive disease requiring more aggressive treatment. Potentially, this device could result in reduced morbidity and improved survival in patients with undiagnosed NPC. The device is non-invasive and had favorable clinical performance characteristics in the clinical study. For patients with endoscopy findings in whom the recommendation to biopsy immediately would otherwise be uncertain, waiting 3 months for repeat evaluation is recommended as current standard of practice. The NP assay could be used in this population at the time of the first endoscopy to guide physicians to initiate further investigation and intervention.

Summary of the Assessment of Risk

The risks associated with the device, when used as intended, are those related to the risk of false test results and failure to correctly interpret the test results.

The risk of a false positive test result includes improper patient management, including biopsy, imaging, and/or treatment for nasopharyngeal cancer. A false positive will result in further assessment and biopsy of the site. Biopsies include the relatively rare risks of excessive bleeding and infection.

The risks of false negative tests include improper patient management, including missing an NPC diagnosis by a clinician choosing not to pursue further investigation and subsequently under-treating a patient with NPC in whom radiation with or without chemotherapy would otherwise be indicated. Untreated NPC can progress to more invasive disease requiring more aggressive treatment associated with increased morbidity and mortality.

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Summary of the Assessment of Benefit-Risk

The clinical benefits outweigh the probable risks for the proposed assay, considering the mitigations of the risks provided in the special controls as well as general controls. The special controls, including verification and validation documentation, a detailed explanation of the interpretation of results and acceptance criteria for evaluating the validity of results, and the limiting statements in device labeling will help to ensure that errors will be uncommon and will facilitate accurate assay implementation and interpretation of results.

Patient Perspectives

This submission did not include specific information on patient perspectives for this device.

S. Conclusion

The De Novo request for the NP screen device is granted and the device is classified under the following and subject to the special controls identified in the letter granting the De Novo request:

Product code: OJY Device Type: Device to detect or measure nucleic acid from viruses associated with head and neck cancers Class: II (special controls) Regulation: 21 CFR 866.3236

Regulation Number and Section

§ 866.3236 Device to detect or measure nucleic acid from viruses associated with head and neck cancers.

(a)
Identification. A device to detect or measure nucleic acid from viruses associated with head and neck cancers is an in vitro diagnostic test for prescription use in the detection of viral nucleic acid in nasopharyngeal or oropharyngeal cellular specimens from patients with signs and symptoms of head and neck cancer. The test result is intended to be used in conjunction with other clinical information to aid in assessing the clinical status of virus-associated head and neck cancers and/or the likelihood that head and neck cancer is present.(b)
Classification. Class II (special controls). The special controls for this device are:(1) Any device used for specimen collection and transport must be FDA-cleared, -approved, or -classified as 510(k) exempt (standalone or as part of a test system) for the collection of human specimens; alternatively, the sample collection device must be cleared in a premarket submission as a part of this device.
(2) The labeling required under § 809.10(b) of this chapter must include, as determined to be appropriate by FDA:
(i) An intended use statement that includes the following:
(A) The analyte(s) detected by the device;
(B) Data output of the device (qualitative, semiquantitative, or quantitative);
(C) The specimen types with which the device is intended for use;
(D) The clinical indications appropriate for test use (
e.g., in conjunction with endoscopy);(E) The intended use populations (
e.g., signs and symptoms, ethnicity); and(F) The intended use location(s) (
e.g., specific name and location of testing facility or facilities).(ii) A detailed device description, including reagents, instruments, ancillary materials, specimen collection and transport devices, controls, and a detailed explanation of the methodology, including all pre-analytical methods for processing of specimens.
(iii) A detailed explanation of the interpretation of results.
(iv) Limiting statements indicating:
(A) The device is not intended for use in screening for head and neck cancer in asymptomatic populations.
(B) Results of the device are not predictive of a patient's future risk of head and neck cancer.
(C) Patients who test negative for the virus should be managed in accordance with the standard of care, based on the assessment of endoscopy and/or other clinical information by a licensed healthcare professional.
(D) Results of the device are not intended to be used as the sole basis for determining the need for biopsy or for any other patient management decision.
(3) Design verification and validation must include the following:
(i) A detailed device description including pre-analytical specimen processing, assay technology, target region, primer/probe sequences, reagents, controls, instrument requirements, and the computational path from collected raw data to reported result.
(ii) Detailed documentation and results from analytical performance studies, including characterization of the cutoff(s), limit of detection, limit of quantitation, precision (including multisite reproducibility, if applicable), inclusivity, cross-reactivity, interference, carryover/cross-contamination, reagent stability, and specimen/sample stability, as determined to be appropriate by FDA.
(iii) Detailed documentation of a clinical performance study that includes patients from the intended use population, including the clinical study protocol, with a predefined statistical analysis plan, and a clinical study report with testing results and results of all statistical analyses.
(iv) A detailed description of the impact of any software, including software applications and software incorporated in hardware-based devices, on the device's functions.