Predicate Devices

Not Found

Reference Devices

AI/ML (Artificial Intelligence / Machine Learning)

No
The description focuses on chemical reagents and laboratory procedures for preparing RNA samples for microarray analysis. There is no mention of algorithms, data processing beyond signal measurement, or any characteristics indicative of AI/ML.

Therapeutic

No.
This device is for preparing labeled RNA targets from clinical tissue specimens for molecular analysis using microarrays, which is a diagnostic purpose, not a therapeutic one.

Diagnostic

Yes

The "Intended Use / Indications for Use" states that the reagents are "intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target... Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents." This indicates that the reagents are used as part of a system for analyzing clinical tissue specimens, which is a diagnostic purpose. The "Device Description" also explicitly states, "The Affymetrix® Gene Profiling Reagents were designed for in vitro diagnostic use as an accessory to the GeneChip® MicroArray Instrumentation System."

SaMD (Software as a Medical Device)

No

The device description explicitly states that the device consists of three kits containing reagents (chemicals and biological materials) for preparing and processing samples for microarray analysis. These are physical components, not software.

IVD (In Vitro Diagnostic)

Based on the provided information, the Affymetrix® Gene Profiling Reagents are indeed an IVD (In Vitro Diagnostic).

Here's why:

Explicit Statement: The "Device Description" section explicitly states: "The Affymetrix® Gene Profiling Reagents were designed for in vitro diagnostic use as an accessory to the GeneChip® MicroArray Instrumentation System."
Intended Use: The "Intended Use / Indications for Use" describes the reagents' purpose in preparing labeled RNA target from clinical tissue specimens for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents. This indicates their role in a diagnostic workflow.
Clinical Study: The "Summary of Performance Studies" includes a Clinical Study Summary comparing the performance of the IVD Gene Profiling Reagents to a research use only kit in the context of a Pathwork® Tissue of Origin-Frozen Test. This demonstrates their intended use in a clinical setting for diagnostic purposes.
Predicate Device: The listing of the Affymetrix GeneChip® Microarray Instrumentation System as a predicate device, which is cleared for RNA analysis, further supports the diagnostic context.

Therefore, the Affymetrix® Gene Profiling Reagents are clearly intended and described as an In Vitro Diagnostic device.

PCCP (Predetermined Change Control Plan) Authorized

N/A

Overview

Intended Use / Indications for Use

Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system.

Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

Product codes (comma separated list FDA assigned to the subject device)

OVA

Device Description

The Affymetrix® Gene Profiling Reagents were designed for in vitro diagnostic use as an accessory to the GeneChip® MicroArray Instrumentation System. Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system. Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

The Affymetrix Gene Profiling Reagents consist of three kits.

Kit 1 is the RNA Control Kit consisting of Poly-A Control and Dilution Buffer. These reagents are designed to provide exogenous positive controls to monitor the entire target labeling process. The Poly-A Control and Dilution Buffer are provided with the kit to prepare the appropriate serial dilutions. After the appropriate dilution of the Poly-A Control, they are added to the total RNA and then amplified and labeled together. Examining the hybridization intensities of these controls on the array helps to monitor the amplification and labeling processes.

Kit 2 is comprised of the Transcript Synthesis and Labeling Kits A and B and includes enzyme mixes, labeling reagent, reaction buffers and purification reagents for the preparation of the labeled cRNA target. Kit 2 is optimized specifically for producing amplified and biotinylated cRNA targets to hybridize to arrays for expression analysis.

Kit 3 is comprised of Transcript Detection Kits A, B and C and includes all of the reagents to perform fragmentation of the labeled cRNA target, prepare the hybridization cocktail (including Oligo B2 and hybridization controls) and process the arrays in the Affymetrix Fluidics Station 450. The arrays are then ready to be scanned by the Affymetrix GeneChip Scanner.

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

Not Found

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 (study type, sample size, AUC, MRMC, standalone performance, key results)

Non-Clinical Test Summaries:

Precision/Reproducibility:
- Study Type: Reproducibility studies.
- Sample Size: Three lots of Gene Profiling Reagents tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate by three different operators. One lot of Gene Profiling Reagents tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate, repeated on three different days. For comparison, three lots of Pathwork® Expression 3'-Amplification One-Cycle Target Reagents were tested using 1000 ng of MAQC A and B total RNAs in quadruplicate by three different operators.
- Key Results: The median probeset signal %CV from detected probesets was calculated both between lots and between days within a lot. The acceptance criterion of %CV less than 20% was met for all combinations.
Repeatability:
- Study Type: Repeatability studies.
- Sample Size: Same samples as reproducibility studies. Also, testing at two external sites with eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples.
- Key Results: The median probeset signal %CV from detected probesets for the replicates was calculated. The acceptance criterion for %CV less than 10% was met for all conditions and for both external sites.
Input Total RNA:
- Study Type: Testing of input material range.
- Key Results: The range for the amount of starting material was determined to be between 100 ng to 1000 ng (1ug) of total RNA. Reagents performed as expected using 100 ng and 1000 ng of input total RNA, producing sufficient cRNA (≥ 20 µg) for one microarray. When tested with 200 ng, sufficient cRNA (≥ 15μg) was produced for one Pathchip™ microarray.
cRNA Yield:
- Study Type: Internal and external testing to demonstrate cRNA yield.
- Sample Size: Internal testing: 100 ng of total RNA from ten commercially available human tissues run in triplicate. External testing at two sites: eight replicates using 100 ng and 1000 ng of MAQC A and MAQC B total RNAs in batches of a minimum of 8 samples.
- Key Results: Internal testing: 100% (30/30) of samples yielded ≥ 20 µg cRNA and a cRNA concentration ≥0.625 µg/µL. External testing: 100% (32/32) of samples at both sites achieved yields of ≥ 20 µg cRNA and cRNA concentration of ≥0.625 µg/µL.
Performance of the Controls:
- Study Type: Evaluation of Poly-A Control, Oligo B2, and hybridization controls.
- Sample Size: Internal testing: three lots of Gene Profiling Reagents tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate. External testing: eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples. Clinical studies: 45 total RNA samples at each of 3 clinical sites (total 135 samples), and 16 total RNA samples from 16 frozen tissues at one site (total 32 samples).
- Key Results: For both internal and external studies, .CEL files were generated by successful automatic gridding, demonstrating Oligo B2 performance. Poly-A Control spikes were present, and signal intensities and r-squared values for correlation met acceptance criteria (≥ 0.900). Hybridization controls followed expected concentration gradients. 100% (80/80) of samples passed acceptance criteria in the internal study and 100% (64/64) in the external study. In clinical studies, 100% (135/135) and 100% (32/32) passed acceptance criteria for all controls.
Stability Studies:
- Study Type: Real-time, open-vial, and freeze-thaw stability studies.
- Key Results: Results support the established shelf life, freeze-thaw, and open-vial stability recommended in the package inserts.
Shipping Studies:
- Study Type: Shipping studies under actual and simulated conditions.
- Key Results: Confirmed that products maintain transport storage conditions and packaging integrity.

Clinical Study Summary:

Study Type: Comparison study (Method Comparison).
Sample Size:
- Part 1: 16 frozen tissues tested twice with Gene Profiling Reagents and One-Cycle Reagent Kit.
- Part 2: 45 total RNA samples prepared with Gene Profiling Reagents. 39 of these had been tested with One-Cycle Kit reagents in a previous reproducibility study, and 6 additional samples had also been tested with One-Cycle Kit reagents.
Key Results:
- Acceptance criteria for both prospective studies included meeting specimen processing specifications, overall success rate for generating Tissue of Origin Test - Frozen results greater than 90%, and no significant difference (α = 0.05) in observed percent correct between Gene Profiling Reagents and One-Cycle Reagent Kit when combined.
- The integrated clinical analysis showed that the observed percent correct when using the Affymetrix Gene Profiling Reagents was no different (α = 0.05) from the expected percent correct when using the One-Cycle Reagent Kit (95% bootstrap confidence limits (-5.9%, 3.4%)).
- The acceptance criteria were achieved, supporting substantial equivalence. The combined data demonstrated the performance of the TOO assay was comparable with both sets of reagents.

Key Metrics (Sensitivity, Specificity, PPV, NPV, etc.)

Not Found (For clinical studies, "percent correct" was the metric used for comparison)

Predicate Device(s): If the device was cleared using the 510(k) pathway, identify the Predicate Device(s) K/DEN number used to claim substantial equivalence and list them here in a comma separated list exactly as they appear in the text. List the primary predicate first in the list.

Affymetrix GeneChip® Microarray Instrumentation System

Reference Device(s): Identify the Reference Device(s) K/DEN number and list them here in a comma separated list exactly as they appear in the text.

K080896, K080995

Predetermined Change Control Plan (PCCP) - All Relevant Information for the subject device only (e.g. presence / absence, what scope was granted / cleared under the PCCP, any restrictions, etc).

Not Found

Regulation Number and Section

§ 862.2570 Instrumentation for clinical multiplex test systems.

(a)
Identification. Instrumentation for clinical multiplex test systems is a device intended to measure and sort multiple signals generated by an assay from a clinical sample. This instrumentation is used with a specific assay to measure multiple similar analytes that establish a single indicator to aid in diagnosis. Such instrumentation may be compatible with more than one specific assay. The device includes a signal reader unit, and may also integrate reagent handling, hybridization, washing, dedicated instrument control, and other hardware components, as well as 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 control is FDA's guidance document entitled “Class II Special Controls Guidance Document: Instrumentation for Clinical Multiplex Test Systems.” See § 862.1(d) for the availability of this guidance document.

Summary

0

K103112

Image /page/0/Picture/1 description: The image shows the Affymetrix logo, which includes the company name in a stylized font and a graphic element above it. Below the logo, the text "Gene Profiling Reagents Premarket Notification" is displayed. The text is in a smaller font size compared to the company name.

April 28, 2011

Summary of Safety and Effectiveness

MAY - 4 2011

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

Submitter: Affymetrix, Inc. 3420 Central Expressway Santa Clara, CA 95051

Establishment Registration No: 3003314809 '

Contact:

Phone: Fax:

E-mail:

Chief Medical Officer, Affymetrix

:

Phone: 408-731-5967

Fax: 408-731-5755

E-mail: Rick_Hockett@Affymetrix.com

Rick Hockett

Regulatory Contact: Maureen Mende

MyRAQA, Inc. 3 Lagoon Drive, Suite 280 Redwood Shores, CA 94065 650-730-5020 650-730-5005 Maureen@myraqa.com

April 17, 2011 Date Prepared:

II. Name of Device and Classification - 21 CFR 807.92(a)(2):

Affymetrix Gene Profiling Reagents Name:

Class II Classification:

OVA Product Code:

AFFYMETRIX, INC.

1

Image /page/1/Picture/0 description: The image shows the Affymetrix logo, which includes a stylized DNA double helix and the company name in bold, sans-serif font. Below the logo, the text "Gene Profiling Reagents Premarket Notification" is displayed in a smaller, regular font. The text indicates that the image is related to the regulatory submission of gene profiling reagents by Affymetrix.

III. Predicate Device - 21 CFR 807.92(a)(3):

Affymetrix GeneChip® Microarray Predicate Device:

Instrumentation System

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

The Affymetrix® Gene Profiling Reagents were designed for in vitro diagnostic use as an accessory to the GeneChip® MicroArray Instrumentation System. Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system. Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

The Affymetrix Gene Profiling Reagents consist of three kits.

Kit 1 is the RNA Control Kit consisting of Poly-A Control and Dilution Buffer. These reagents are designed to provide exogenous positive controls to monitor the entire target labeling process. The Poly-A Control and Dilution Buffer are provided with the kit to prepare the appropriate serial dilutions. After the appropriate dilution of the Poly-A Control, they are added to the total RNA and then amplified and labeled together. Examining the hybridization intensities of these controls on the array helps to monitor the amplification and labeling processes.

Kit 2 is comprised of the Transcript Synthesis and Labeling Kits A and B and includes enzyme mixes, labeling reagent, reaction buffers and purification reagents for the preparation of the

2

labeled cRNA target. Kit 2 is optimized specifically for producing amplified and biotinylated cRNA targets to hybridize to arrays for expression analysis.

Kit 3 is comprised of Transcript Detection Kits A, B and C and includes all of the reagents to perform fragmentation of the labeled cRNA target, prepare the hybridization cocktail (including Oligo B2 and hybridization controls) and process the arrays in the Affymetrix Fluidics Station 450. The arrays are then ready to be scanned by the Affymetrix GeneChip Scanner.

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

Affymetrix® Gene Profiling Reagents are intended for the preparation of labeled complementary RNA target from purified total RNA from fresh or frozen clinical tissue specimens for hybridization to Affymetrix® GeneChip® microarrays and the measurement of fluorescence signals of labeled RNA target using the Affymetrix GeneChip microarray instrumentation system.

Special Conditions For Use Statement(s):

Intended for use with separately FDA-cleared Affymetrix GeneChip microarray assays specifying the use of the Affymetrix Gene Profiling Reagents.

VI. Performance Data - 21 CFR 807.92(b):

A. Non-Clinical Test Summaries 21 CFR 807.92(b)(1):
- i. Analytical Performance:
  - 1. Precision/Reproducibility
    - To demonstrate reproducibility studies were conducted in which three lots of Gene Profiling Reagents were tested

AFFYMETRIX, INC.

3

using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate by three different operators. Three lots of Pathwork® Expression 3'-Amplification One-Cycle Target Reagents were tested using 1000 ng of MAQC A and B total RNAs in quadruplicate by three different operators for comparison.

In addition, one lot of the Gene Profiling Reagents was tested using 100 ng and 1000 ng of MAQC A and B total RNAs in quadruplicate. One lot of the One-Cycle Reagent Kit was tested using 1000 ng of MAQC A and B total RNAs in quadruplicate for comparison. The testing was repeated on three different days.

The median probeset signal %CV from detected probesets was calculated both between lots and between days within a lot and is reported in Table 6-1 (a - d), The acceptance criterion of %CV less than 20% was met for all combinations.

Table 6-1

a - %CV between days within a lot for MAQC A
----------------------------------------------	--	--	--

| Data Sets | One-Cycle
Days 1, 2 and 3
MAQC A | Gene Profiling
1000 ng
Days 1, 2 and 3
MAOC A | Gene Profiling
100 ng
Days 1, 2 and 3
MAQC A |
|------------|----------------------------------------|--------------------------------------------------------|-------------------------------------------------------|
| Median CV% | 7.97 % | 7.17 % | 7.03 % |

b - %CV between days within a lot for MAQC B

| Data Sets | One-Cycle
Days 1, 2 and 3
MAQC B | Gene Profiling
1000 ng
Days 1, 2 and 3
MAQC B | Gene Profiling
100 ng
Days 1, 2 and 3
MAQC B |
|------------|----------------------------------------|--------------------------------------------------------|-------------------------------------------------------|
| Median CV% | 7.68 % | 7.24% | 9.33 % |

c - %CV between lots for MAQC A

Data Sets	Gene Profiling	Gene Profiling
One-Cycle Lots
1, 2 and 3
MAQC A	1000 ng
Lots 1, 2 and 3
MAQC A	100 ng
Lots 1, 2 and 3
MAQC A
Median CV%
8.70 %	9.54 %	8.74 %

4

d - %CV between lots for MAQC B
Data Sets	One-Cycle
Lots 1, 2 and 3
MAQC B	Gene Profiling
1000 ng
Lots 1, 2 and 3
MAQC B	Gene Profiling -
100 ng
Lots 1,2 and 3
MAQC B
Median CV%	9.52 %	9.93 %	11.72 %

2. Repeatability

To demonstrate repeatability, the samples described in the Reproducibility section of this summary were used to calculate the median probeset signal %CV from detected probesets for the replicates. Table 6-2 (a - f) shows the results for all sets of replicates using the Gene Profiling Reagents and the One-Cycle Reagent Kits. The acceptance criterion for %CV less than 10% for Repeatability was met for all conditions.

Table 6-2

a - %CV for the replicates of 3 lots of the One-Cycle Reagent Kit, and one lot tested on 3 different days using 1000 ng of MAQC A.

| Data Sets | Lot1 Day1
One-Cycle
MAQC A | Lot1 Day2
One-Cycle
MAQC A | Lot1 Day3
One-Cycle
MAQC A | Lot2 Day1
One-Cycle
MAQC A | Lot3 Day1
One-Cycle
MAQC A |
|------------|----------------------------------|----------------------------------|----------------------------------|----------------------------------|----------------------------------|
| Median CV% | 5.06% | 4.55% | 4.85% | 3.67% | 4.30% |

b - %CV for the replicates of 3 lots of the Gene Profiling Reagents, and one lot tested on 3 different days using 100 ng of MAQC A.

Data Sets	Lot1	Lot2	Lot3	Lot3	Lot3
	100ng	100ng	100ng	100ng	100ng
	Day1	Day1	Day1	Day2	Day3 -
	MAOC A	MAQC A	MAQC A	MAQC A	MAOC A
Median CV%	5.31%	5.81%	5.41%	4.24%	4.04%

5

Image /page/5/Picture/0 description: The image shows the Affymetrix logo, which includes the company name and a symbol resembling a DNA strand made of squares. Below the logo, the text "Gene Profiling Reagents Premarket Notification" is displayed. The text indicates that the image is related to the premarket notification of gene profiling reagents produced by Affymetrix.

c - %CV for the replicates of 3 lots of the Gene Profiling Reagents, and one lot tested on 3 different days using 1000 ng of MAQC A.

Data Sets	Lot1	Lot2	. Lot3	Lot3	Lot3
	1000ng	1000ng	1000ng	1000ng	1000ng
	Day1 -	Day1 -	Day1 -	Day2 -	Day3 -
	MAQCA	MAQCA	MAQCA	MAQCA	MAQCA
Median CV%	5.5%	4.38%	5.88%	4.54%	5.44%

d - %CV for the replicates of 3 lots of the One-Cycle Reagent Kit, and one lot tested on 3 different days using 1000 ng of MAQC B.

| Data Sets | Lot1 Day1
One-Cycle
MAQC B | Lot1 Day2
One-Cycle
MAQCB | Lot1 Day3
One-Cycle
MAQC B | Lot2 Day1
One-Cycle
MAQC B | Lot3 Day1
One-Cycle
MAQC B |
|------------|----------------------------------|---------------------------------|----------------------------------|----------------------------------|----------------------------------|
| Median CV% | 4.57% | 4.11% | 4.35% | 4.88% | 4.64% |

e - %CV for the replicates of 3 lots of the Gene Profiling Reagents, and one lot tested on 3 different days using 100 ng of MAQC B.

| Data Sets | Lot1
100ng
Day1
MAQC B | Lot2
100ng
Day1
MAQC B | Lot3
100ng
Day1
MAQC B | Lot3
100ng
Day2
MAQC B | Lot3
100ng
Day3
MAQC B |
|------------|---------------------------------|---------------------------------|---------------------------------|---------------------------------|---------------------------------|
| Median CV% | 8.77% | 4.42% | 5.15% | 5.46% | 4.79% |

f - %CV for the replicates of 3 lots of the Gene Profiling Reagents, and one lot tested on 3 different days using 1000 ng of MAQC B.

| Data Sets | Lot1
1000ng
Day1
MAQCB | Lot2
1000ng
Day1
MAQCB | Lot3
1000ng
Day1
MAQCB | Lot3
1000ng
Day2
MAQCB | Lot3
1000ng
Day3
MAQCB |
|------------|---------------------------------|---------------------------------|---------------------------------|---------------------------------|---------------------------------|
| Median CV% | 5.74% | 5.33% | 4.23% | 4.37% | 5.64% |

Repeatability was also demonstrated in the testing conducted at two external sites where eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples were tested. The median probeset signal %CV from detected probesets was calculated for the replicates and the acceptance criteria of % CV of 20 µg cRNA and cRNA concentration ≥0.625 µg/µL. 'All 32 samples (100%) at both sites achieved yields of ≥ 20 µg cRNA and cRNA concentration of ≥0.625 µg/µL.

| Concentration | Adjusted
cRNA yields | Average
cRNA yields |
|-------------------- | Sample ID | Kidney Total RNA_R1 | Kidney Total RNA_R2 | Kidney Total RNA_R3 | Pancreas Total RNA_R1 | Pancreas Total RNA_R2 | Pancreas Total RNA_R3 | Heart Total RNA_R1 | Heart Total RNA_R2 | Heart Total RNA_R3 | MAQCB Total RNA_R1 | MAQCB Total RNA_R2 | MAQCB Total RNA_R3 | Liver Total RNA_R1 | Liver Total RNA_R2 | Liver Total RNA_R3 | Breast Total RNA_R1 | Breast Total RNA_R2 | Breast Total RNA_R3 | Testicle Total RNA_R1 | Testicle Total RNA_R2 | Testicle Total RNA_R3 | HeLa Total RNA_R1 | HeLa Total RNA_R2 | HeLa Total RNA_R3 | Thyroid Total RNA_R1 | Thyroid Total RNA_R2 | Thyroid Total RNA_R3 | Skeletal Muscle Total RNA | Sample ID Concentration
μg/μL | Adjusted
cRNA yields
(μg) | Average
cRNA yields
(μg) |
| Skeletal Muscle Total RNA
R2 | 2.043 | Skeletal Muscle Total RNA
R3 | 1.931 | cRNA
-------------|--------------------------------|---------------------------------|--------------------------------|
| μg/μL | (μg) | (μg) |
| 2.250 | 69.6 | |
| 2.112 | 65.4 | 67.1 |
| 2.141 | 66.3 | |
| 1.796 | 55.6 | |
| 1.792 | 55.5 | 54.2 |
| 1.664 | 51.5 | |
| 2.241 | 69.4 | |
| 2.338 | 72.4 | 69.2 |
| 2.126 | 65.8 | |
| 2.443 | 75.6 | |
| 2.441 | 75.6 | 74.4 |
| 3.009 | 72.1 | |
| 1.985 | 61.4 | |
| 1.843 | 57.0 | 57.1 |
| 1.705 | 52.8 | |
| 2.161 | 66.9 | |
| 1.844 | 58.9 | 62.2 |
| 1.965 | 60.8 | |
| 2.207 | 68.3 | |
| 2.268 | 70.2 | 69.5 |
| 2.261 | 70.0 | |
| 2.401 | 74.3 | |
| 2.277 | 72.8 | 73.7 |
| 2.390 | 74.0 | |
| 1.689 | 52.2 | |
| 1.562 | 48.3 | 50.5 |
| 1.644 | 50.8 | |
| | | 62.3 |
| cRNA
| 63.2 | |
| 59.8 | |

Table 6-3

AFFYMETRIX, INC.

8

Image /page/8/Picture/0 description: The image shows the logo for Affymetrix. The logo consists of the word "Affymetrix" in a sans-serif font, with a stylized double helix symbol above the letters "ff" and a series of black squares to the right of the helix. The squares are arranged in a pattern that resembles a grid or a barcode. The logo is simple and modern, and it is likely used to represent the company's focus on genomics and biotechnology.

Gene Profiling Reagents Premarket Notification

April 28, 2011

5. Linearity/Assay Reportable Range

Not Applicable.

Traceability, Stability Expected Values (controls, 6. calibrators or methods)

a. Performance of the Controls

Performance of the Poly-A Control, Oligo B2 and hybridization controls were evaluated by testing conducted internally at Affymetrix and at two external sites as part of Design Validation. The internal testing to evaluate the performance of the Poly-A Control, Oligo B2 and hybridization controls included three lots of Gene Profiling Reagents that were tested using 100 ng and 1000 ng of MAQC A and B total RNAs and tested in quadruplicate. The testing conducted at the two external sites included eight replicates using 100 ng and 1000 ng of MAQC A and B total RNAs in batches of a minimum of 8 samples.

In both studies .CEL files were generated by successful automatic gridding for all samples tested demonstrating that the Oligo B2 performed as expected. The analysis of the Poly-A Control showed the 3' AFFX-r2-Bs probe sets

9

Image /page/9/Picture/1 description: The image shows the Affymetrix logo and the text "Gene Profiling Reagents Premarket Notification". The Affymetrix logo is a stylized double helix with a series of squares above it. The text is in a simple, sans-serif font, with the company name in a larger size than the rest of the text.

for all three spikes (lys, phe and dap) were present. Signal intensities and r-squared values for the correlation of the 3' AFFX-r2-Bs signal intensities with the relative ratio for each spike, followed the relative concentration in the Poly-A Control mixture: lys