(142 days)
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.
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.
The provided text describes the acceptance criteria and the studies performed for the Ion PGM™ Dx System. Here's a structured breakdown of the requested information:
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria are not explicitly stated in a single section as "acceptance criteria," but rather derived from the "Special conditions statement for performance" for both gDNA from whole blood and DNA/RNA from FFPE samples. The "Reported Device Performance" is taken from the "Non-Clinical Performance Data" section.
| Feature / Metric | Acceptance Criteria (from "Special Conditions") | Reported Device Performance (from "Non-Clinical Performance Data") |
|---|---|---|
| gDNA from Whole Blood (SVA Panel) | ||
| Sequencing output | > 0.7 gigabases | Not explicitly reported for gDNA from whole blood in the performance data, but indicated as "validated to deliver" in the special conditions. |
| Reads | > 4 million | Not explicitly reported for gDNA from whole blood in the performance data, but indicated as "validated to deliver" in the special conditions. |
| Read length | up to 200 base pairs | Not explicitly reported for gDNA from whole blood in the performance data, but indicated as "validated to deliver" in the special conditions. |
| Mean Raw Read Accuracy | 99.0% when compared to hg19 | Not explicitly reported for gDNA from whole blood in the performance data, but indicated as "validated to deliver" in the special conditions. |
| SNV Detection Reproducibility | 100% reproducibility for 440 unique SNV positions | Not explicitly reported in the Non-Clinical Performance Data for gDNA from whole blood. This is stated as a system capability in the "Special conditions statement for performance derived from gDNA from whole blood." |
| Indel Detection Reproducibility | 100% reproducibility for various insertion/deletion lengths (1-4 bp insertions, 1-14 bp deletions) | Not explicitly reported in the Non-Clinical Performance Data for gDNA from whole blood. This is stated as a system capability in the "Special conditions statement for performance derived from gDNA from whole blood." |
| HPT limitation | Variants in homoploymer tracts exceeding 8 bases called as no calls | Not applicable; this is a known limitation, not a performance metric to be achieved. |
| Min coverage for germline DNA | >30X | Not explicitly reported in performance data. (This is a recommended use parameter) |
| FFPE Samples (Representative Assay) | ||
| Sequencing output | > 0.7 gigabases | Not explicitly reported for a representative assay in the performance data, but indicated as "validated to deliver" in the special conditions. |
| Reads | > 3 million | Not explicitly reported for a representative assay in the performance data, but indicated as "validated to deliver" in the special conditions. |
| Read length | up to 141 base pairs | Not explicitly reported for a representative assay in the performance data, but indicated as "validated to deliver" in the special conditions. |
| PPA (excluding no calls) | Not explicitly stated as a minimum. | Variant: 98.5% (195/198) |
| Bin: 97.2% (176/181) | ||
| Sample: 96.9% (158/163) | ||
| NPA (excluding no calls) | Not explicitly stated as a minimum. | Variant: 100.0% (118,155/118,159) |
| Bin: 99.8% (942/944) | ||
| Sample: 98.4% (124/126) | ||
| OPA (excluding no calls) | Not explicitly stated as a minimum. | Variant: 100.0% (118,350/118,357) |
| Bin: 99.4% (1,118/1,125) | ||
| Sample: 97.6% (282/289) | ||
| Repeatability (DNA variants, excl. no calls) | ≥97.5% (95% CI lower limit) | ≥98.8% (95% CI lower limit of ≥97.5%) |
| Repeatability (RNA variants, excl. no calls) | Not explicitly stated as a minimum for individual RNA variant locations, but overall ≥87.5% for positive variant location. | 94.4% for each RNA clinical variant location. (For a specific ROS1 RNA variant for Sample C, it was 87.5% with 95% CI lower bound of 61.7%). |
| Call Rate (DNA pos. variants, excl. no calls) | Not explicitly stated as a minimum. | Mean: 96.60%, Median: 97.10% |
| Call Rate (RNA pos. variants, excl. no calls) | Not explicitly stated as a minimum. | Mean: 94.80%, Median: 95.50% |
| Call Rate (WT DNA, neg. calls, excl. no calls) | Not explicitly stated as a minimum. | Mean: 96.10%, Median: 95.00% |
| Call Rate (WT RNA, neg. calls, excl. no calls) | Not explicitly stated as a minimum. | Mean: 99.30%, Median: 99.30% |
| Tissue Input (% meeting conc.) | 98.3% (59/60) had DNA ≥0.83 ng/uL and RNA >1.43 ng/uL. (This is a study finding, implicitly demonstrating the ability to meet the given concentration requirements for the assay under specific tissue input conditions.) | 98.3% (59/60) met the concentration requirements (DNA ≥0.83 ng/uL, RNA >1.43 ng/uL). |
| DNA/RNA Input (Positive Call Rate) | 100% positive variant call rate within 5-15 ng input range for a representative assay. | 100% positive variant call rate within the input range tested (5-15 ng), supporting the 10 ng specified input. For clinical samples, one CD74-ROS1 fusion variant showed 100% positive calls at all input combinations, while the other showed rates as low as 50% at specific high input combinations (attributed to likely operator error). |
| DNA/RNA Input (Negative Call Rate) | Not explicitly stated as a minimum. | >95% for all except 4 sample/input combinations; cases with 95% negative call rates. The second CD74-ROS1 clinical sample showed 100% negative call rates for all test conditions where it was expected to be wild type. |
| Interfering Substances | Positive/Negative/Overall concordance with control was 100% (excluding no calls) for most interferents. For hemoglobin, positive concordance was 100%, negative 99.99%, overall 99.99%. (These are the observed results which met the study's goal of demonstrating non-interference). | For most interferents (Paraffin, Xylene, Ethanol, Protease, Wash buffer): 100% positive, negative, and overall concordance with control (excluding no calls). For Hemoglobin: 100% positive concordance, 99.99% negative concordance, 99.99% overall concordance (excluding no calls). |
| Cross Contamination Rate | Not explicitly stated as a specific rate, but the study aims to evaluate cross-contamination. | False-positive rate at DNA variant locations: 0% (0/100). False-positive rate at RNA variant locations: 1.25% (1/80), attributed to likely sample cross-contamination. |
| Minimal coverage needed for FFPE calling | ≥347X for SNV, MNV, deletion; ≥41X for fusion. | Not explicitly reported in performance data. (This is a recommended use parameter) |
2. Sample size used for the test set and the data provenance
- Accuracy Study (FFPE):
- Sample Size: 290 FFPE tumor samples.
- Data Provenance: The document implies these are clinical samples ("human specimens," "FFPE tumor samples") but does not specify country of origin. It is a retrospective study since variants were compared against "validated reference detection methods."
- Sample Reproducibility Study (FFPE):
- Sample Size: 2 WT (Wild Type) samples and 10 variant-positive samples. Each sample tested 8 times at each of 4 sites, for a total of 32 replicates per sample.
- Data Provenance: Not explicitly stated (e.g., country of origin, retrospective/prospective). These appear to be characterized samples used in a prospective, controlled study.
- Assay Reproducibility Study (FFPE):
- Sample Size: 18 DNA samples (6 plasmid/clinical DNA blends, 12 clinical DNA samples) and 9 RNA samples (1 WT, 8 with RNA variants). Each pre-extracted sample run in duplicate with 2 different reagent lots (3 sites) or 3 reagent lots (1 site), resulting in 72 test determinations per DNA sample and 144 per RNA sample, total of at least 1,296 sequencing reactions.
- Data Provenance: Mixtures of plasmid and clinical DNA/RNA. Not explicitly stated (e.g., country of origin, retrospective/prospective). This is a prospective, controlled study.
- Tissue Input Study (FFPE):
- Sample Size: 60 slide-mounted FFPE samples (30 resection with >20% tumor, 15 resection with
§ 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.