Predicate Devices

Reference Devices

Not Found

AI/ML (Artificial Intelligence / Machine Learning)

No
The document describes a DNA sequencing instrument system and associated software for variant detection. While data analysis software is mentioned, there is no indication or mention of AI or ML being used in the process of sequencing, data analysis, or variant calling. The performance studies focus on traditional metrics like agreement and call rates, not metrics typically associated with AI/ML model evaluation.

Therapeutic

No.
The device is used for targeted sequencing of human genomic DNA and RNA to detect human variant sequences, which is a diagnostic purpose, not a therapeutic one.

Diagnostic

Yes

The "Intended Use / Indications for Use" states that the system is "intended for targeted sequencing of human genomic DNA (gDNA) from peripheral whole-blood samples and DNA and RNA extracted from formalin-fixed, paraffin-embedded (FFPE) samples" and the "Device Description" section states it is "used for detection of human variant sequences." Detecting variants in biological samples for diagnostic purposes clearly indicates its use as a diagnostic device.

SaMD (Software as a Medical Device)

No

The device description explicitly lists multiple hardware components as part of the system, including instruments, scanners, and servers, in addition to the software.

IVD (In Vitro Diagnostic)

Yes, this device is an IVD (In Vitro Diagnostic).

Here's why:

Intended Use: The "Intended Use / Indications for Use" section explicitly states that the system is "intended for targeted sequencing of human genomic DNA (gDNA) from peripheral whole-blood samples and DNA and RNA extracted from formalin-fixed, paraffin-embedded (FFPE) samples." This indicates that the device is used to examine specimens derived from the human body to provide information for the diagnosis, treatment, or prevention of disease.
Device Description: The "Device Description" further clarifies that the system is used for "detection of human variant sequences from DNA from whole blood samples or RNA and DNA from FFPE tissue samples." This directly relates to analyzing human biological samples for clinical purposes.
Performance Studies: The document includes detailed descriptions of performance studies such as Accuracy, Sample Reproducibility, Assay Reproducibility, Tissue Input, DNA and RNA Input, Interfering Substances, and Cross Contamination studies. These types of studies are typically conducted to demonstrate the analytical and clinical performance of IVD devices.
Key Metrics: The "Key Metrics" section lists metrics like Positive percent agreement (PPA), Negative percent agreement (NPA), Overall percent agreement (OPA), Call rate, False positive rate, etc. These are standard metrics used to evaluate the performance of diagnostic tests.
Intended User / Care Setting: The intended users are "professionals trained in laboratory techniques and procedures," and the implied setting is "Clinical Laboratories." This aligns with the typical use of IVD devices in a clinical laboratory environment.
Predicate Device: The mention of a "Predicate Device(s)" with a K number (K123989; Illumina MiSeqDx Platform) is a strong indicator that this device is being submitted for regulatory review as an IVD, as predicate devices are used for comparison in the regulatory process for new IVDs.

All these factors collectively point to the Ion PGM™ Dx Instrument System being an In Vitro Diagnostic device.

PCCP (Predetermined Change Control Plan) Authorized

N/A

Overview

Intended Use / Indications for Use

The Ion PGM™ Dx Instrument System is composed of a sequencing instrument that measures the hydrogen ions that are generated during the incorporation of nucleotides in the DNA sequencing reaction, and the ancillary instrumentation necessary for sample processing. This instrument system is used in conjunction with the instrument-specific Ion PGM™ Dx Library Kit, Ion OneTouch™ Dx Template Kit, Ion PGM™ Dx Sequencing Kit, and Ion 318™ Dx Chip Kit, and data analysis software. The Ion PGM™ Dx Instrument System is intended for targeted sequencing of human genomic DNA (gDNA) from peripheral wholeblood samples and DNA and RNA extracted from formalin-fixed, paraffinembedded (FFPE) samples. The lon PGM™ Dx Instrument System is not intended for whole genome or de novo sequencing.

Product codes

PFF

Device Description

The Ion PGM™ Dx System is used for detection of human variant sequences from DNA from whole blood samples or RNA and DNA from FFPE tissue samples. Detectable variants include substitutions, insertions, and deletions.

The Ion PGMTM Dx System consists of the following:

Ion OneTouch™ Dx Instrument
Ion OneTouch™ ES Dx Instrument
Ion OneTouch™ Rack Kit
· Ion PGM™ Dx Chip Minifuge
· Ion PGM™ Dx Sequencer
· Ion PGMTM Wireless Scanner
DynaMag™ Dx Kit—Tube & Plate
· Ion Torrent™ Server
Torrent Suite™ Dx Software

The Ion PGM™ Dx System is used in conjunction with the following kits:

Ion PGM™ Dx Library Kit
Ion OneTouch™ Dx Template Kit
· Ion PGM™ Dx Sequencing Kit
Ion 318™ Dx Chip Kit

The system should be used only by professionals trained in laboratory techniques and procedures and in the use of the system.

Mentions image processing

Not Found

Mentions AI, DNN, or ML

Not Found

Input Imaging Modality

Not Found

Anatomical Site

Not Found

Indicated Patient Age Range

Not Found

Intended User / Care Setting

Professionals trained in laboratory techniques and procedures.
Clinical Laboratories

Description of the training set, sample size, data source, and annotation protocol

Not Found

Description of the test set, sample size, data source, and annotation protocol

Not Found

Summary of Performance Studies

Non-Clinical Performance Data:

a. Accuracy study:

Study type: Accuracy
Sample size: 290 FFPE tumor samples
Data source: Somatic variants in human specimens
Reference methods: A validated NGS assay (for SNV and deletion hotspot variants) and a ROS1 FISH reference test (for ROS1 fusions).
Key results:
- PPA (excluding no calls): Variant 98.5% (195/198), Bin 97.2% (176/181), Sample 96.9% (158/163)
- PPA (including no calls): Variant 98.5% (195/198), Bin 97.2% (176/181), Sample 96.9% (158/163)
- NPA (excluding no calls): Variant 100.0% (118,155/118,159), Bin 99.8% (942/944), Sample 98.4% (124/126)
- NPA (including no calls): Variant 96.8% (118,155/122,012), Bin 70.0% (657/939), Sample 23.4% (29/124)
- OPA (excluding no calls): Variant 100.0% (118,350/118,357), Bin 99.4% (1,118/1,125), Sample 97.6% (282/289)
- OPA (including no calls): Variant 96.8% (118,350/122,210), Bin 74.4% (833/1,120), Sample 65.2% (187/287)

b. Sample Reproducibility study:

Study type: Reproducibility and repeatability of variant detection
Sample size: 2 WT samples and 10 variant-positive samples
Testing sites: 4 testing sites, each with 4 Ion PGM™ Dx instrument systems and 4 operators.
Replicates: Each sample tested 8 times at each site, total of 32 replicates per sample.
Key results:
- Negative call rate: 100% at each clinical variant location for all samples (including no calls and excluding known positive variant locations).
- Positive call rates: >84% (including no calls from positive variant locations).
- Repeatability (excluding no calls): 100% for DNA variants, 87.5% for RNA variant. 95% CI lower limit exceeded 96% at all variant locations.
- Repeatability (including no calls): 100% at 218/605 variant locations, 94-99.9% at 186/605 variant locations, 71.6-93.9% at 184/605 variant locations. 95% CI lower limit exceeded 64.6% at all variant locations.

c. Assay Reproducibility Study:

Study type: Reproducibility and repeatability for 30 representative variants
Sample size: 18 DNA samples and 9 RNA samples.
Replicates: 72 test determinations per DNA sample, 144 test determinations per RNA sample. Total of at least 1,296 sequencing reactions.
Key results:
- Call rate (excluding no calls):
  - DNA positive variants: Mean 96.60%, Median 97.10%
  - RNA positive variants: Mean 94.80%, Median 95.50%
  - WT DNA variant locations: Mean 96.10%, Median 95.00%
  - WT RNA variant locations: Mean 99.30%, Median 99.30%
- Call rate (including no calls):
  - DNA positive variants: Mean 94.50%, Median 95.80%
  - RNA positive variants: Mean 94.80%, Median 95.50%
  - WT DNA variant locations: Mean 96.10%, Median 95.00%
  - WT RNA variant locations: Mean 99.30%, Median 99.30%
- Repeatability (excluding no calls): ≥98.8% for each DNA variant location (95% CI lower limit of ≥97.5%), 94.4% for each RNA clinical variant location.
- Coefficient of variation (CV) (excluding no calls): DNA clinical variants ranged from 9.8% to 39%. RNA locations ranged from 72% to 78%.

d. Tissue Input Study:

Study type: Evaluation of DNA and RNA concentration yield from FFPE samples.
Sample size: 60 slide-mounted FFPE samples (30 resection samples with >20% tumor, 15 resection samples with 1.43 ng/uL.

e. DNA and RNA Input Study:

Study type: Evaluation of variant call rates at various DNA and RNA input-level combinations.
Sample size: 8 cell-line samples (FFPE sections) and 4 clinical samples (FFPE sections).
DNA and RNA input: 5-15 ng for cell-line blends and clinical samples; positive controls and NTC controls.
Replicates: 6 replicate libraries each for DNA and RNA per test condition for cell-line samples.
Key results:
- Cell-line samples: 100% positive variant call rate within the input range tested. Negative variant call rate >95% for all but 4 combinations (due to no calls, mostly at 5 ng input). No false-positive calls.
- Clinical samples: >95% positive and negative call rates for DNA variants at all input combinations. 100% for one CD74-ROS1 fusion variant. The second CD74-ROS1 sample showed some false negatives at higher input concentrations.
- Conclusion: Supports the 10-ng input requirement for DNA and RNA.

f. Interfering Substances Study:

Study type: Evaluation of 5 potentially interfering substances.
Sample size: 8 FFPE samples (1 WT, 7 mutants) with 6 replicates each.
Substances tested: Paraffin, Xylene, Ethanol, Hemoglobin, Protease, Wash buffer.
Key results:
- Excluding no calls: Positive and negative concordance with control condition was 100% for most interferents.
- Hemoglobin: Positive concordance 100%, negative concordance 99.99%, overall concordance 99.99%.
- Necrotic tissue (from clinical studies): 10-20% necrotic tissue does not appear to interfere.

g. Cross Contamination Study:

Study type: Determination of false positive rate due to cross-contamination and carryover contamination.
Sample size: 8 FFPE cell line samples.
Data points analyzed: 100 DNA and 80 RNA data points.
Key results:
- False positive rate for DNA variants: 0% (0/100).
- False positive rate for RNA variants: 1.25% (1/80) (one false positive in a ROS1 fusion variant attributed to cross-contamination from an adjacent well).

Key Metrics

Sensitivity: Not explicitly provided in Isolation, but PPA (Positive Percent Agreement) is given.
Specificity: Not explicitly provided in Isolation, but NPA (Negative Percent Agreement) is given.
PPV: Not Found
NPV: Not Found

From Accuracy Study:

PPA (Positive Percent Agreement) (excluding no calls):
- Variant: 98.5% (195/198) with 95% CI (95.6%, 99.7%)
- Bin: 97.2% (176/181) with 95% CI (93.7%, 99.1%)
- Sample: 96.9% (158/163) with 95% CI (93.0%, 99.0%)
NPA (Negative Percent Agreement) (excluding no calls):
- Variant: 100.0% (118,155/118,159) with 95% CI (99.99%, 100.0%)
- Bin: 99.8% (942/944) with 95% CI (99.2%, 100.0%)
- Sample: 98.4% (124/126) with 95% CI (94.4%, 99.8%)
OPA (Overall Percent Agreement) (excluding no calls):
- Variant: 100.0% (118,350/118,357) with 95% CI (99.99%, 100.0%)
- Bin: 99.4% (1,118/1,125) with 95% CI (98.72%, 99.75%)
- Sample: 97.6% (282/289) with 95% CI (95.07%, 99.02%)

Predicate Device(s)

Illumina MiSeqDx Platform, K123989 (DEN130011)

Reference Device(s)

Not Found

Predetermined Change Control Plan (PCCP) - All Relevant Information

Not Found

Regulation Number and Section

§ 862.2265 High throughput genomic sequence analyzer for clinical use.

(a)
Identification. A high throughput genomic sequence analyzer for clinical use is an analytical instrument system intended to generate, measure and sort signals in order to analyze nucleic acid sequences in a clinical sample. The device may include a signal reader unit; reagent handling, dedicated instrument control, and other hardware components; raw data storage mechanisms; data acquisition software; and software to process detected signals.(b)
Classification. Class II (special controls). 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. The special controls for this device are:(1) The labeling for the instrument system must reference legally marketed pre-analytical and analytical reagents to be used with the instrument system and include or reference legally marketed analytical software that includes sequence alignment and variant calling functions, to be used with the instrument system.
(2) The labeling for the instrument system must include a description of the following information:
(i) The specimen type(s) validated as an appropriate source of nucleic acid for this instrument.
(ii) The type(s) of nucleic acids (
e.g., germline DNA, tumor DNA) validated with this instrument.(iii) The type(s) of sequence variations (
e.g. single nucleotide variants, insertions, deletions) validated with this instrument.(iv) The type(s) of sequencing (
e.g., targeted sequencing) validated with this instrument.(v) The appropriate read depth for the sensitivity claimed and validation information supporting those claims.
(vi) The nucleic acid extraction method(s) validated for use with the instrument system.
(vii) Limitations must specify the types of sequence variations that the instrument cannot detect with the claimed accuracy and precision (
e.g., insertions or deletions larger than a certain size, translocations).(viii) Performance characteristics of the instrument system must include:
(A) Reproducibility data generated using multiple instruments and multiple operators, and at multiple sites. Samples tested must include all claimed specimen types, nucleic acid types, sequence variation types, and types of sequencing. Variants queried shall be located in varying sequence context (
e.g., different chromosomes, GC-rich regions). Device results shall be compared to reference sequence data with high confidence.(B) Accuracy data for all claimed specimen types and nucleic acid types generated by testing a panel of well characterized samples to query all claimed sequence variation types, types of sequencing, and sequences located in varying sequence context (
e.g., different chromosomes, GC-rich regions). The well-characterized sample panel shall include samples from at least two sources that have highly confident sequence based on well-validated sequencing methods. At least one reference source shall have sequence generated independently of the manufacturer with respect to technology and analysis. Percent agreement and percent disagreement with the reference sequences must be described for all regions queried by the instrument.(C) If applicable, data describing endogenous or exogenous substances that may interfere with the instrument system.
(D) If applicable, data demonstrating the ability of the system to consistently generate an accurate result for a given sample across different indexing primer combinations.
(ix) The upper and lower limit of input nucleic acid that will achieve the claimed accuracy and reproducibility. Data supporting such claims must also be summarized.

Summary

0

Image /page/0/Picture/1 description: The image shows the logo for the U.S. Department of Health & Human Services. The logo consists of a stylized caduceus symbol, which is often associated with healthcare. The caduceus is depicted with three intertwined snakes and a staff. The text "DEPARTMENT OF HEALTH & HUMAN SERVICES - USA" is arranged in a circular pattern around the caduceus symbol.

Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002

June 22, 2017

LIFE TECHNOLOGIES CORPORATION EMILY FINNEGAN, REGULATORY ANALYST 5781 VAN ALLEN WAY CARLSBAD CA 92008

Re: K170299

Trade/Device Name: Ion PGM Dx System Regulation Number: 21 CFR 862.2265 Regulation Name: High throughput genomic sequence analyzer for clinical use Regulatory Class: II (special controls); exempt from the premarket notification procedures in subpart E of part 807 of this chapter subject to 862.9. Product Code: PFF Dated: June 20, 2017 Received: June 21, 2017

Dear Ms. Finnegan:

We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food, Drug, and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. The general controls provisions of the Act include requirements for annual registration, listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.

If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21, Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.

Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Parts 801 and 809); medical device reporting (reporting of medical device-related adverse events) (21 CFR 803); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.

1

If you desire specific advice for your device on our labeling regulations (21 CFR Parts 801 and 809), please contact the Division of Industry and Consumer Education at its toll-free number (800) 638 2041 or (301) 796-7100 or at its Internet address

http://www.fda.gov/MedicalDevices/Resourcesfor You/Industry/default.htm. Also, please note the regulation entitled. "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to

http://www.fda.gov/MedicalDevices/Safety/ReportaProblem/default.htm for the CDRH's Office of Surveillance and Biometrics/Division of Postmarket Surveillance.

You may obtain other general information on your responsibilities under the Act from the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address

http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm.

Sincerely yours,

Kellie B. Kelm -S

for Courtney H. Lias, Ph.D. Director Division of Chemistry and Toxicology Devices Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health

Enclosure

2

Indications for Use

510(k) Number (if known) K170299

Device Name Ion PGM™ Dx System

Indications for Use (Describe)

The Ion PGM™ Dx Instrument System is composed of a sequencing instrument that measures the hydrogen ions that are generated during the incorporation of nucleotides in the DNA sequencing reaction, and the ancillary instrumentation necessary for sample processing. This instrument system is used in conjunction with the instrument-specific Ion PGM™ Dx Library Kit, Ion OneTouch™ Dx Template Kit, Ion PGM™ Dx Sequencing Kit, and Ion 318™ Dx Chip Kit, and data analysis software. The lon PGM™ Dx Instrument System is intended for targeted sequencing of human genomic DNA (gDNA) from peripheral whole-blood samples and DNA and RNA extracted from formalin-fixed, paraffin-embedded (FFPE) samples. The lon PGM™ Dx Instrument System is not intended for whole genome or de novo sequencing.

Type of Use (Select one or both, as applicable)
-------------------------------------------------

X Prescription Use (Part 21 CFR 801 Subpart D)

Over-The-Counter Use (21 CFR 801 Subpart C)

CONTINUE ON A SEPARATE PAGE IF NEEDED.

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3

510(k) Summary

Submitter Information - 21 CFR 807.92(a)(1):

| Submitter: | Life Technologies Corporation
5781 Van Allen Way
Carlsbad, CA 92008 |
|----------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|
| Manufacturer: | Life Technologies Holdings Pte Ltd
Blk 33, #07-06, Marsiling Industrial Estate, Road 3
Singapore 739256 |
| Establishment Registration No: | 3003673482 |
| Contact: | Emily Finnegan, Regulatory Analyst |
| Phone: | 916-838-0714 |
| Fax: | 760-268-8393 |
| E-mail: | emily.finnegan@thermofisher.com |
| Alternate Contact: | Jody Schulz, Senior Manager, Regulatory Affairs |
| Phone: | 414-534-4809 |
| Fax: | 414-278-0688 |
| E-mail: | jody.schulz@thermofisher.com |
| Date Prepared: | June 20, 2017 |
| Name of Device and Classification – 21 CFR 807.92(a)(2): | |
| Product Name: | Ion PGM™ Dx System |
| Common Name: | High-throughput DNA sequencing |

Device Classification: Class II, exempt from the premarket notification requirement

subject to the limitations in 21 CFR 862.9

Product Code: PFF - High throughput DNA sequence analyzer

4

Predicate Devices - 21 CFR 807.92(a)(3):

Predicates: Illumina MiSeqDx Platform, K123989 (DEN130011)

Device Description - 21 CFR 807.92(a)(4):

The Ion PGM™ Dx System is used for detection of human variant sequences from DNA from whole blood samples or RNA and DNA from FFPE tissue samples. Detectable variants include substitutions, insertions, and deletions.

The Ion PGMTM Dx System consists of the following:

Ion OneTouch™ Dx Instrument
Ion OneTouch™ ES Dx Instrument
Ion OneTouch™ Rack Kit
· Ion PGM™ Dx Chip Minifuge
· Ion PGM™ Dx Sequencer
· Ion PGMTM Wireless Scanner
DynaMag™ Dx Kit—Tube & Plate
· Ion Torrent™ Server
Torrent Suite™ Dx Software

The Ion PGM™ Dx System is used in conjunction with the following kits:

Ion PGM™ Dx Library Kit
Ion OneTouch™ Dx Template Kit
· Ion PGM™ Dx Sequencing Kit
Ion 318™ Dx Chip Kit

The system should be used only by professionals trained in laboratory techniques and procedures and in the use of the system.

Intended Use/Indications for Use - 21 CFR 807.92(a)(5):

Ion PGM Dx System intended use and special conditions statement:

5

Intended use:

The Ion PGM™ Dx Instrument System is composed of a sequencing instrument that measures the hydrogen ions that are generated during the incorporation of nucleotides in the DNA sequencing reaction, and the ancillary instrumentation necessary for sample processing. This instrument system is used in conjunction with the instrument-specific Ion PGM™ Dx Library Kit, Ion OneTouch™ Dx Template Kit, Ion PGM™ Dx Sequencing Kit, and Ion 318TM Dx Chip Kit, and data analysis software. The Ion PGM™ Dx Instrument System is intended for targeted sequencing of human genomic DNA (gDNA) from peripheral wholeblood samples and DNA and RNA extracted from formalin-fixed, paraffinembedded (FFPE) samples.

The Ion PGMTM Dx Instrument System is not intended for whole genome or de novo sequencing.

Indications for use:

Same as intended use.

Special conditions statement

For in vitro diagnostic use. For prescription use only.

Special conditions statement for performance derived from gDNA from whole blood:

1. The Ion PGM™ Dx System has been validated to deliver the following using the
  System Variant Assay (SVA) panel:
· Sequencing output > 0.7 gigabases
Reads > 4 million
· Read length up to 200 base pairs
· Mean Raw Read Accuracy of 99.0% when compared to hg19

Note:

· Mean Raw Read Accuracy is defined as the average raw accuracy across each individual base position in a read, where raw read accuracy is calculated as 100 * (1 - (sum(per base error)/sum(per base depth)))
· The 632 primer pairs of the SVA panel are designed to amplify regions across 23

6

chromosomes in the two well-characterized cell lines. The regions were selected based on the presence of well characterized insertions/deletions (Indels) and singlenucleotide variant (SNV) positions. The amplicons produced range in size from 80 to 200 base pairs, with a GC content of 20-80%.

1. The system has been evaluated for the detection of single-nucleotide variants (SNVs) and insertions and deletions of various lengths on 23 chromosomes. The system identified 440 unique SNV positions in the SVA panel with 100% reproducibility.
  The following tables illustrate the lengths and locations of insertions and deletions in the SVA panel that were detected with 100% reproducibility.

| Insertion Length
(base pairs) | Total Number of
Distinct chromosomal
locations | Total Number of Unique
chromosomes |
|----------------------------------|------------------------------------------------------|---------------------------------------|
| 1 | 14 | 10 |
| 2 | 4 | 4 |
| 3 | 5 | 4 |
| 4 | 5 | 4 |

| Deletion Length
(base pairs) | Total Number of
Distinct chromosomal
locations | Total Number of Unique
chromosomes |
|---------------------------------|------------------------------------------------------|---------------------------------------|
| 1 | 15 | 11 |
| 2 | 10 | 6 |
| 3 | 3 | 3 |
| 4-14[1] | 7 | 7 |

[1] Deletions of ≥ 4 bp have been grouped for clarity

1. The system may exhibit a limitation in detecting one-base insertions or deletions in homoploymer tracts (e.g., polyA). Variants in homopolymer runs exceeding 8 bases are called as no calls in the VCF file.
1. The system is designed to deliver qualitative (i.e., genotype) results.
1. As with any hybridization-based workflow, underlying polymorphisms or mutations in primer-binding regions can affect the regions being sequenced and, consequently, the calls made.
1. The recommended minimal coverage per amplicon needed for accurate variant calling

7

for germline DNA is >30X.

1. Special instrument requirements for the Ion PGM™ Dx Library Kit, Ion OneTouch™ Dx Template Kit, Ion PGMTM Dx Sequencing Kit, and Ion 318™ Dx Chip Kit: For use with the Ion PGM™ Dx System.

Special Conditions statement for performance derived from a representative assay using RNA and gDNA from FFPE samples:

1. The Ion PGM™ Dx System has been validated to deliver the following using a representative assay:
- Sequencing output > 0.7 gigabases .
- Reads > 3 million .
- Read length up to 141 base pairs .
1. A representative assay, consisting of two sets of primer panels was used to detect DNA and RNA variants in key regions of cancer-related genes. The Ion PGM™ Dx System has been evaluated for the detection of SNVs, multi-nucleotide variants (MNVs), and deletions of various lengths in FFPE tissue samples using this representative assay. The types and numbers of variants detected by the assay are listed below.

| Type of | Number of variants
detected with a
representative assay | Number of samples tested for detection by sample type | | |
|----------------|---------------------------------------------------------------|-------------------------------------------------------|----------------------------------------------|-------------------------|
| Variant | | Plasmid/FFPE
Sample Blend | FFPE Cell Line or
FFPE Cell Line
Blend | FFPE Clinical
Sample |
| MNV | 9 | 9 | 0 | 2 |
| SNV | 326 | 329 | 8 | 113 |
| 3-bp deletion | 4 | 6 | 0 | 0 |
| 6-bp deletion | 4 | 8 | 0 | 0 |
| 9-bp deletion | 4 | 8 | 0 | 1 |
| 12-bp deletion | 7 | 7 | 0 | 0 |
| 15-bp deletion | 7 | 10 | 3 | 23 |
| 18-bp deletion | 7 | 8 | 0 | 11 |

1. The following studies were used to evaluate the performance of the Ion PGMTM Dx System using a representative assay:

8

Accuracy ●
Sample reproducibility ●
Assay reproducibility ●
Tissue input ●
DNA and RNA input ●
. Interfering substances
1. The system is designed to deliver qualitative results.
1. As with any hybridization-based workflow, underlying polymorphisms or mutations in primer-binding regions can affect the regions being sequenced and, consequently, the ability to make calls.
1. The minimal coverage required to call an SNV, MNV or deletion variant is ≥347X. The minimal coverage required to call a fusion variant is ≥41X.
1. Special instrument requirements for the Ion PGM™ Dx Library Kit, Ion OneTouch™ Dx Template Kit, Ion PGM™ Dx Sequencing Kit, and Ion 318TM Dx Chip Kit: For use with the Ion PGM™ Dx System.

Summary of technological characteristics of the device compared to the predicate devices-21 CFR 807.92(a)(6):

The Ion PGM™ Dx System ("Subject Device") and the legally marketed device Illumina MiSeqDx Platform are compared and contrasted as described in the table below:

| Item for Comparison | Proposed Device:
Ion PGM Dx
System | Predicate Device:
MiSeqDx
Platform | Comparison |
|--------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Intended Use | The Ion PGMTM Dx
System is composed
of a sequencing
instrument that
measures the
hydrogen ions that
are generated during
the incorporation of
nucleotides in the | The MiSeqDx
Platform is a
sequencing
instrument that
measures
fluorescence
signals of labeled
nucleotides through
the use of | The intended uses are
different due to the
expansion of the Ion PGM
Dx System sample input to
include DNA and RNA
extracted from FFPE
samples, however the two
devices continue to use the
same basic technology and |
| Item for Comparison | Proposed Device:
Ion PGM Dx
System | Predicate Device:
MiSeqDx
Platform | Comparison |
| | sequencing reaction
and the ancillary
instrumentation
necessary for sample
processing. This
instrument system is
used in conjunction
with the instrument
specific
Ion PGMTM Dx
Library Kit, Ion
OneTouchTM Dx
Template Kit, Ion
PGMTM Dx
Sequencing Kit, Ion
318TM Dx Chip Kits,
and data analysis
software. The Ion
PGMTM Dx
System is intended
for targeted
sequencing of
human RNA and
DNA derived from
FFPE tissue samples
and human gDNA
from peripheral
whole blood
samples. The
Ion PGMTM Dx
System is not
intended for whole
genome or de novo
sequencing. | instrument specific
reagents and flow
cells (MiSeqDx
Universal Kit 1.0),
imaging hardware,
and data analysis
software. The
MiSeqDx Platform
is intended for
targeted sequencing
of human genomic
DNA from
peripheral whole
blood samples. The
MiSeqDx Platform
is not intended for
whole genome or
de novo
sequencing. | are therefore under the
same regulation (21 CFR
Part 862.2265). |
| Environment of Use | Clinical Laboratories | Clinical
Laboratories | The environment of use is
the same. |
| Specimen Type | whole-blood or
formalin fixed
paraffin embedded
(FFPE) samples | whole-blood
samples | The specimen type is
different with the inclusion
of FFPE samples |
| Input Sample | Genomic DNA and
cDNA | Genomic DNA | The input sample is
different with the inclusion
of cDNA as an option for
use on the Ion PGM Dx
system. However, genomic
DNA and cDNA are
biochemically equivalent as
they are both made up of
Deoxyribonucleic acid and
are interpreted in the same
manner by the PGM Dx
sequencer to generate |
| Item for Comparison | Proposed Device:
Ion PGM Dx
System | Predicate Device:
MiSeqDx
Platform | Comparison |
| Regulation/Classification | 21 CFR 862.2265
Class II, exempt
from the premarket
notification
requirement subject
to the limitations in
21 CFR 862.9 | 21 CFR 862.2265
Class II, exempt
from the premarket
notification
requirement subject
to the limitations in
21 CFR 862.9 | The
regulation/classification is
the same. For the purpose
of this 510(k), Ion PGM Dx
system is not exempt from
premarket notification
requirements due to the
expansion in the intended
use to add FFPE and RNA. |
| Technology | A sequencing
instrument that
measures the
hydrogen ions that
are generated during
the incorporation of
nucleotides in the
DNA sequencing
reaction and the
ancillary
instrumentation
necessary for sample
processing. | A sequencing
instrument that
measures
fluorescence
signals of labeled
nucleotides through
the use of
instrument specific
reagents and flow
cells (MiSeqDx
Universal Kit 1.0),
imaging hardware,
and data analysis
software. | The technology used for
DNA sequencing are
equivalent NGS
technologies. Both the Ion
PGM Dx system and the
MiSeqDx platform detect
the incorporation of
nucleotides by DNA
polymerases. However,
they differ in that the Ion
PGM Dx system measures
the incorporation of
hydrogen ions, while the
MiSeqDx platform
measures the fluorescence
signal. The differences in
the signal measured during
DNA sequencing do not
raise questions to the safety
and effectiveness of the Ion
PGM Dx system. |
| Software Description
Comparison | Combined Functions
software with Assay
Development mode
for Research Use
Only | Combined
Functions software
with ability to use
Research Use Only
mode | The software description is
equivalent. |
| Equipment included in
the device system | • Ion OneTouch™
Dx Instrument
• Ion OneTouch™
ES Dx Instrument
• Ion PGM™ Dx
Chip Minifuge
• Ion PGM™ Dx
Sequencer
• Ion PGM™
Torrent Server
• Torrent Suite™ Dx
Software | • MiSeqDx
Instrument
• MOS -
MiSeqDx
Operating
Software
• RTA - Realtime
Analysis
Software
• MiSeq
Reporter | The equipment included in
the device system is
different as the technology
characteristics differ. |

Table 1. Predicates Comparison - Thermo Fisher Scientific Ion PGM™ Dx System and Illumina MiSeqDx Platform

9

10

11

Performance Data – 21 CFR 807.92(b):

This section provides a summary of the non-clinical and clinical performance studies with DNA and RNA from FFPE samples using a representative assay, which demonstrates instrument performance when using the Ion PGM™ Dx system.

Non-Clinical Performance Data– 21 CFR 807.92(b)(1):

a. Accuracy study
To evaluate the ability of a representative assay DNA and RNA panels to identify somatic variants in human specimens, 290 FFPE tumor samples were analyzed using a representative assay to demonstrate positive percent agreement (PPA) and negative percent agreement (NPA) concordance with validated reference detection methods. The following reference detection methods were used:
· A validated NGS assay, to detect SNV and deletion hotspot variants
A ROS1 FISH reference test, to detect ROS1 fusions

Variants detected by a representative assay that were not covered by the reference methods were not included in the PPA/NPA concordance calculation. Variants detected by arepresentative assay test for which the reference method testing failed and did not yield a valid result were not included in the PPA/NPA calculation.

Accuracy data was analyzed by the following:

Each variant location
· Bins (or categories) of variants: RNA fusions , simple SNVs, complex SNVs, and deletions
Each FFPE sample

12

| PPA

Measure	Excluding no calls
	Percent
agreement	95% CI	Percent
agreement	95% CI
Variant	98.5% (195/198)	95.6%,
99.7%	98.5% (195/198)	(95.6%,
99.7%)
Bin	97.2% (176/181)	93.7%,
99.1%	97.2% (176/181)	(93.7%,
99.1%)
Sample	96.9% (158/163)	93.0%,
99.0%	96.9% (158/163)	(93.0%,
99.0%)

Table 2. PPA Results

Table 3. NPA results

| NPA

Measure	Excluding no calls		Including no calls
	Percent
agreement	95% CI	Percent
agreement	95% CI
Variant	100.0%
(118,155/118,159)	99.99%,100.0%	96.8%
(118,155/122,012)	(96.7%, 96.9%)
Bin	99.8% (942/944)	99.2%, 100.0%	70.0% (657/939)	(66.9%, 72.9%)
Sample	98.4% (124/126)	94.4%, 99.8%	23.4% (29/124)	(16.3%, 31.8%)

Table 4. OPA Results

	Excluding no calls		Including no calls
OPA
Measure	Percent
agreement	95% CI	Percent
agreement	95% CI
Variant	100.0%
(118,350/118,357)	99.99%,100.0%	96.8%
(118,350/122,210)	(96.74%,
96.94%)
Bin	99.4% (1,118/1,125)	98.72%,99.75%	74.4% (833/1,120)	(71.71%,
76.91%)
Sample	97.6% (282/289)	95.07%,99.02%	65.2% (187/287)	(59.34%,70.66%)

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b. Sample Reproducibility study

The reproducibility and repeatability of variant detection using a representative assay were assessed with 2 WT samples and 10 variant-positive samples at 4 testing sites. Each site had 4 Ion PGM™ Dx instrument systems and 4 operators.

Each sample was tested 8 times at each site, for a total of 32 replicates per sample. After repeat testing, the final number of invalid reactions was 15/768 (1.95%), possibly due to low sample quality or lack of sample, though the cause was not definitively determined.

The call rate, no call rate, positive call rate, negative call rate, and within-run repeatability were computed at each variant location of interest. Including no calls and excluding known positive variant locations, the negative call rate at each clinical variant location for all samples was 100%.

The results at positive variant locations are shown in Table 5. Including no calls, all positive call rates from positive variant locations were >84%.

Excluding no calls and combining data across all study samples, the estimate of repeatability was 100% for DNA variants and 87.5% for the RNA variant. The lower limit of the 95% two-sided confidence interval (CI) for repeatability exceeded 96% at all variant locations.

Including no calls from the data, the estimate of repeatability was 100% at 218 out of 605 variant locations, 94-99.9% at 186 out of 605 variant locations, and 71.6-93.9% at 184 out of 605 variant locations. Including no calls, the lower limit of the 95% two-sided confidence interval for repeatability exceeded 64.6% at all variant locations.

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95% CI | | Negative call rate
95% CI | | Within-run repeatability + 95% CI | |
|--------|---------------------------|---------------------|----------------------------------------|-------------------------------|---------------------------------------|----------------------------|--------------------------------|------------------------------------|--------------------------------|------------------------------------|-----------------------------------|----------------------------|
| | | | | | | | Including no
calls (A/N) | Excluding
no calls
(A/(A+B)) | Including no
calls (B/N) | Excluding no
calls
(B/(A+B)) | Including no calls | Excluding no calls |
| B | COSM6223 | EGRF
Exon19del | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| B | COSM763 | PIK3C
A
E545K | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| C | ROS1 | N/A | 32 | 30 | 2 | 0 | 93.8%
(79.2%,
99.2%) | 93.8%
(79.2%,
99.2%) | 6.3%
(0.8%,
20.8%) | 6.3%
(0.8%,
20.8%) | 87.5%
(61.7%,
98.4%) | 87.5%
(61.7%,
98.4%) |
| D | COSM6225 | EGFR
Exon19del | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| E | COSM476 | BRAF V600E | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| F | COSM521 | KRAS G12D | 32 | 30 | 0 | 2 | 93.8%
(79.2%,
99.2%) | 100%
(88.4%,
100%) | 0% (0%,
10.9%) | 0% (0%,
11.6%) | 87.5%
(61.7%,
98.4%) | 100%
(76.8%,
100%) |
| | | | | | | | Positive call rate
95% CI | | Negative call rate
95% CI | | Within-run repeatability + 95% CI | |
| Sample | Variant
identification | Variant
location | # of valid
sample
results
(N) | # of
positive
calls (A) | # of
negat
ive
calls
(B) | # of
No
Calls
(C) | Including no
calls (A/N) | Excluding
no calls
(A/(A+B)) | Including no
calls (B/N) | Excluding no
calls
(B/(A+B)) | Including no calls | Excluding no calls |
| F | COSM29313 | PIK3C
A M1043I | 32 | 30 | 0 | 2 | 93.8%
(79.2%,
99.2%) | 100%
(88.4%,
100%) | 0% (0%,
10.9%) | 0% (0%,
11.6%) | 87.5%
(61.7%,
98.4%) | 100%
(76.8%,
100%) |
| G | COSM6224 | EGFR L858R | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| J | COSM87298 | KRAS Q61K | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| J | COSM172423 | ERBB3
V104M | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |
| K | COSM775 | PIK3 H1047R | 30 | 29 | 0 | 1 | 96.7%
(82.8%,
99.9%) | 100%
(88.1%,
100%) | 0% (0%,
11.6%) | 0% (0%,
11.9%) | 93.3%
(68.1%,
99.8%) | 100%
(76.8%,
100%) |
| M | COSM715 | FGR3 S249C | 32 | 32 | 0 | 0 | 100%
(89.1%,
100%) | 100%
(89.1%,
100%) | 0% (0%,
10.9%) | 0% (0%,
10.9%) | 100%
(79.4%,
100%) | 100%
(79.4%,
100%) |

Table 5. Call Rates at Positive Variant Locations

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16

c. Assay Reproducibility Study

The reproducibility and repeatability of a representative assay was evaluated for 30 representative variants from 18 DNA and 9 RNA samples.

The study was designed to evaluate within-run precision performance (repeatability) and variability across sites, operators, and instrument platforms (reproducibility). Six of the 18 DNA samples were mixtures of plasmid and clinical DNA. Seven of the 12 deletion variants were represented by these plasmid blends. All other variant types were represented by clinical sample DNA.

Due to the large number of variants detected by the test and the rarity of some of the variants, a representative variant approach was used. Variants were selected in the following categories:

| Variant Category | No. of Plasmid Blends
Used | No. of Clinical Samples
Used |
|-----------------------------|-------------------------------|---------------------------------|
| 6-bp deletion | 6 | 0 |
| 9-bp deletion | 4 | 2 |
| 15-bp deletion | 2 | 4 |
| 18-bp deletion | 2 | 4 |
| Simple SNV | 0 | 8 |
| Complex SNVs and
MNPs[1] | 0 | 6 |
| Fusion | 0 | 12 |

Table 6. Categories

[1] Including SNVs in di- or tri-nucleotide repeat regions and SNVs in high-GC (>60%) or low-

GC (1.43 ng/uL.

Thirty resection samples with >20% tumor content were prepared without macrodissection, 15 resection samples with 1.43 ng/uL. One CNB sample failed the minimum DNA and RNA concentration specifications, with values of 0.52 ng/uL and 1.23 ng/uL respectively. The low concentrations were likely caused by the small tissue size and low tumor content (5%).

e. DNA and RNA Input Study

Eight cell-line samples were prepared as FFPE sections, and DNA and RNA

19

were extracted and quantified from multiple sections from each cell line for blending and testing. Sample blends were prepared with known variants at various DNA and RNA input-level combinations within the range of 5-15 ng. The DNA and RNA blends had a target allele frequency of 15% for SNVs and deletions and target fusion reads of 300–600 for the ROS1 variant. A total of 540 individual DNA and RNA libraries were tested, including positive controls and NTC controls, with 6 replicate libraries each for DNA and RNA per test condition.

The study demonstrated a 100% positive variant call rate within the input range tested, supporting the specified input amount of 10 ng each for DNA and RNA for a representative assay.

The negative variant call rate was >95% for all except 4 sample and DNA/RNA input- level combinations. All cases with a negative variant call rate of 95% for the DNA variants at all input combinations, and 100% for one of the CD74-ROS1 fusion variants at all input combinations. The second CD74-ROS1 clinical sample showed 100% negative call rates for all test conditions, and 100% positive call rates except for Test Condition 4 (8.5 ng RNA/15 ng DNA), where the call rate was 83%, and Test Condition 6 (15 ng RNA/15 ng DNA), where the call rate was 50%. The false negatives for these test conditions were possibly due to

20

operator error during library preparation, since the remaining replicates in these test conditions had both high total mappable reads and fusion reads, but the cause was not definitively determined.

The results support the DNA and RNA 10-ng input requirement for a representative assay.

Interfering Substances Study f.

Five potentially interfering substances used to extract DNA and RNA from FFPE tissue samples were evaluated using a representative assay on the Ion PGM™ Dx System.

The guidelines for testing are defined in section 7.1 of CLSI EP07A2E, which describes testing substances at a relatively high concentration as an interference screen. One potentially interfering endogenous substance, hemoglobin, was tested at twice the concentration recommended in CLSI EP07A2E, Appendix D.

In addition to the substances tested in this study, data from the clinical studies demonstrated that 10-20% necrotic tissue in the region of interest in FFPE tissue samples does not appear to interfere with the assay. However, users should macrodissect highly necrotic areas or select alternate samples if possible.

| Potential
interfering

substance	Step	Amount of substance
Paraffin	At the deparaffinization step,
extra paraffin was added to the
xylene bath that contained 250
mL of xylene.	4X of normally expected levels
Xylene	Extra xylene was added into the
ethanol bath that contained 250
mL of ethanol.	6X of normally expected
residual volume

Table 8. Interfering substances and amounts

21

| Potential
interfering

substance	Step	Amount of substance
Ethanol	Extra ethanol was added into
the Protease digestion step
before digestion.	>4X of normally expected
residual volume
Hemoglobin	After deparaffinization,
hemoglobin was added to the
Digestion Buffer used to pre-
wet the tissue section	4 mg/mL
Protease	Extra Protease was added into
the reaction after the digestion
step and before column
purification.	>10X of expected residual
Protease after the heat-kill step
Wash buffer	Wash buffer used to isolate
DNA and RNA from
deparaffinized and digested
samples was added into an
aliquot of Dilution Solution,
which was subsequently used to
dilute the RNA and DNA to the
appropriate concentration before
library preparation.	1% wash buffer (equivalent to
~10% wash buffer carried over
into eluate)
Control	Tissue sections were processed
using the standard protocol,
without the addition of any
potentially interfering
substances.	N/A

A total of 8 FFPE samples (1 WT and 7 mutants) with 6 replicates each were processed through the entire assay workflow. The mutant samples included variants from all variant categories that can be detected by the test. The samples were spiked with additional concentrations or amounts of the listed substances at the relevant processing step, as shown in the table. Replicates of a control sample with no spiked substances were also analyzed. The concordance between variant calls in samples with and without interfering substances was computed for each substance under investigation.

22

With no calls excluded, for each potential interferent used in sample extraction, the positive and negative concordance with the control condition across all samples was 100%, and the overall concordance with the control condition across all samples was 100%

With no calls excluded, the results of testing with hemoglobin showed positive concordance with the control condition of 100% (only samples with a positive control condition were analyzed), negative concordance of 99.99%, and overall concordance of 99.99%.

g. Cross Contamination Study

A total of 8 FFPE cell line samples were evaluated to determine the percentage of false positive results caused by cross-contamination (contamination from one sample to another within the same sequencing run) and carryover contamination (contamination from a previous run on the same instrument system). Samples that were WT and mutant were tested in consecutive runs on the same instruments, and 5 DNA variant locations and 2 RNA variant locations that were expected to be WT for a sample were evaluated for contamination.

Out of 100 DNA and 80 RNA data points analyzed, no false positive results were reported in the DNA variants, and 1 false positive result was reported in a ROS1 fusion variant. The false positive was likely caused by sample crosscontamination from an adjacent well. Therefore, the false-positive rate at DNA variant locations was 0% (0/100) and the false-positive rate at RNA variant locations was 1.25% (1/80).