Bio-Rad 12010873revA ATMOS C 051 Thorax Operating Instructions

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QXDx Automated Droplet Generator

12008019

QXDx Droplet Reader

12008020

QXDx AutoDG Droplet Digital PCR System

Operation Manual

April 2019 12010873revA

UNITED STATES, Bio-Rad Laboratories, Inc., 5731 W. Las Positas Blvd. Pleasanton, CA USA 94588, 510-724-7000

Translations

Product documents may be provided in additional languages on electronic media.

Symbols Lexicon

Manufacturer Lot Number

Use by For In Vitro Diagnostic Use

Temperature Limit Catalog Number

Consult Instructions for Use Number of Tests

For use with Serial Number

Prescription Use Only Contains Latex

Bio-Rad Technical Assistance

For help and technical advice, please contact the Bio-Rad Technical Support department. In the United States, the Technical Support department is open Monday–Friday, 5:00 AM–5:00 PM, Paciﬁc time.

Phone: 1-800-424-6723

Fax: 1-510-741-5802

Online technical support and worldwide contact information are available at www.consult.bio-rad.com.

Legal Notices

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage or retrieval system, without permission in writing from BioRad Laboratories.

Bio-Rad reserves the right to modify its products and services at any time. This instruction manual is subject to change without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors, or for any damages resulting from the application or use of this information.

Excel and Microsoft are trademarks of Microsoft Corporation. FAM and VIC are trademarks of Applera Corporation. TaqMan is a trademark of Roche Molecular Systems, Inc.

Bio-Rad’s thermal cyclers and real-time thermal cyclers are covered by one or more of the following U.S. patents or their foreign counterparts owned by Eppendorf AG: U.S. Patent Numbers 6,767,512 and 7,074,367.

This product and/or its use is covered by claims of U.S. patents, and/or pending U.S. and non-U.S. patent applications owned by or under license to Bio-Rad Laboratories, Inc. Purchase of the product includes a limited, non-transferable right under such intellectual property for use of the product for internal research and diagnostic purposes only.

No rights are granted for use of the product for commercial applications of any kind, including but not limited to manufacturing, quality control, or commercial services, such as contract services or fee for services. Information concerning a license for such uses can be obtained from Bio-Rad Laboratories. It is the responsibility of the purchaser/end user to acquire any additional intellectual property rights that may be required.

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual iiiii QXDx AutoDG Droplet Digital PCR System Instruction Manual 12010873revA

Safety and Regulatory Compliance

This instrument has been tested and found to be in compliance with all applicable requirements of the following safety and electromagnetic standards:

• IEC 61010-1:2010 (3rd ed.), EN61010-1:2010 (3rd ed). Electrical Equipment for Measurement, Control, and Laboratory Use — Part 1: General requirements

• EN 61326-1:2006 (Class A). Electrical equipment for measurement, control, and laboratory use. EMC requirements, Part 1: General requirements

• UL 61010-1:2004, Laboratory equipment, Test & Measurement Equipment and Industrial Process Controls

• CAN/CSA 22.2 No 61010-1-04, Safety Requirements for Electrical. Equipment for Measurement, Control, and Laboratory Use, Part I: General. Requirements

This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operation of this equipment

in a residential area is likely to cause harmful interference, in which case the user will be required to correct the interference at his own expense.

The CE mark indicates that the manufacturer ensures the product conforms with the essential requirements of the European Directive for in vitro diagnostic medical devices 98/79/EC

The CSA mark indicates that a product has been tested to Canadian and U.S. standards and it meets the requirements of those applicable standards.

This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment.

The Waste Electrical and Electronic Equipment Directive symbol indicates that when the enduser wishes to discard this product, it must be sent to separate collection facilities for recovery and recycling

This instrument is for use only by trained personnel.

Do not position the equipment so that it is difﬁcult to operate the plug of the power supply. The plug of the power supply is the disconnect device.

No serviceable parts inside.

Instrument Safety Warnings

Alteration of this instrument voids the warranty and safety certiﬁcation and creates a potential safety hazard.

This instrument is intended for laboratory use only. Bio-Rad Laboratories is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended, or by modiﬁcations of the instrument not performed by Bio-Rad Laboratories or an authorized agent. Follow the safety speciﬁcations listed here and throughout this manual. Use only the power cord supplied with the instrument, using only the plug adaptor that corresponds to the electrical outlets in your region.

NOTE: Use of unapproved supermixes may harm the instrument and voids the warranty.

PPE (Personal Protective Equipment) Training

Proper use of gloves is recommended with use of oils and sample plates. OSHA requirements for PPE are set forth in the Code of Federal Regulations (CFR) at 29 CFR 1910.132 (General requirements); 29 CFR 1910.138 (Hand protection); 29 CFR 1926.95 (Criteria for standard personal protective equipment). Any gloves with impaired protective ability should be discarded and replaced. Consider the toxicity of the chemicals and factors such as duration of exposure, storage, and temperature when deciding to reuse chemically exposed gloves. Features to aid glove selection for handling of machines, assays, oils, and cleaning solvents:

• Butyl gloves are made of a synthetic rubber and protect against peroxide, hydroﬂuoric acid, strong bases, alcohols, aldehydes, and ketones

• Natural (latex) rubber gloves are comfortable to wear and feature outstanding tensile strength, elasticity, and temperature resistance

• Neoprene gloves are made of synthetic rubber and offer good pliability, ﬁnger dexterity, high density, and tear resistance; they protect against alcohols, organic acids, and alkalis

• Nitrile gloves are made of copolymer and provide protection from chlorinated solvents such as trichloroethylene and tetrachloroethene; they offer protection when working with oils, greases, acids, and caustic substances

Transporting the Instrument

• Avoid dropping or subjecting the instrument to shock when transporting.

• This product weighs in excess of 50 lb. When lifting, two people are required. Grip from the underside with the people on opposite sides.

• After unpacking for placement of equipment, transport per lifting instructions above; place near grounded outlet with plug of power supply accessible.

Electrostatic Discharge

• Based on EMC testing, caution should be used if the intended use environment has low relative humidity, if the user wears synthetic clothing, or if there is synthetic carpeting. Under these conditions, the environment is more likely to make users susceptible to generating higher levels of electrostatic discharge.

• It is recommended to touch a metal door frame or other grounded metal surface to discharge static electricity before touching the equipment.

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual viv QXDx AutoDG Droplet Digital PCR System Instruction Manual 12010873revA

Radiated Emissions

QXDx Droplet Reader:

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual viivi QXDx AutoDG Droplet Digital PCR System Instruction Manual 12010873revA

QXDx Automated Droplet Generator:

Sensitivity to Electromagnetic Fields

Both the QXDx Droplet Reader and QXDx Automated Droplet Generator were tested for conducted immunity with no performance degradation. However as an added precaution, do not stack RF emitting devices (cell phones, other laboratory equipment, computers, microwave ovens) on top of, or very close to, the device to ensure proper performance.

Cybersecurity

The purpose of this Section is to provide a basic summary of Bio-Rad’s Cybersecurity policies as they pertain to the QXDx Software.

Accounts & Passwords

The QXDx Software 1.0 is conﬁgured as a domain environment and uses network accounts to access the computers and servers that make up the system. Using the Microsoft Windows Active Directory the software can be conﬁgured to set up and authenticate user roles, privileges, and set login timeouts. The passwords used for both the domain and local accounts meet typical minimum complexity requirements.

Customer/Site Responsibilities (Laptop Computer with QXDx Software):

It is recommended that the customer use anti-virus software and a network ﬁrewall to help prevent unauthorized internet users from accessing their private network.

In the event a user encounters any issues with the laptop that are potentially related to a virus or malware, it is recommended users contact Bio-Rad Laboratories Technical Service Department.

Only qualiﬁed personnel with privileged device access (in accordance with the Accounts & Passwords section above) are allowed to perform software or ﬁrmware updates on the laptop (including those affecting the operating system, applications, and anti-malware).

Hospital/Clinic Site’s IT Administration is responsible for password rules. This includes determining the necessary strength of password and time between changing of passwords.

Files:

Data backup, restore, and archive are all integrated into the software. For data recovery users should contact Bio-Rad Laboratories Technical Service Department.

Analysis protocol ﬁles that are generated with the QXDx™ Software are encrypted when exported/imported to prevent unauthorized personnel to alter critical protocol data used in results determination.

Network:

The Bio-Rad QXDx Software can be used on a stand-alone computer, or on the customer’s network. The Bio-Rad system shall be connected to the customer’s network only where required. Only authorized users (in accordance with the Accounts & Passwords section above) are able to access the QXDx™ Software applications.

Operating System Updates:

The system is updated at the time of deployment with all the relevant operating system patches.

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Contents

Legal Notices .............................................................................................................................iii

Safety and Regulatory Compliance .......................................................................................... iv

Instrument Safety Warnings ...................................................................................................... v

PPE (Personal Protective Equipment) Training ......................................................................... v

Transporting the Instrument ....................................................................................................... v

Electrostatic Discharge .............................................................................................................. v

Radiated Emissions .................................................................................................................. vi

Sensitivity to Electromagnetic Fields ....................................................................................... viii

1 QXDx AutoDG Droplet Digital PCR System .......................................................................1-1

1.1 Introduction ..........................................................................................................................................1-1

1.2 Intended Use and Indication for Use....................................................................................................1-1

1.3 Droplet Digital PCR Workﬂow ..............................................................................................................1-1

1.4 Setting Up and Operating the System .................................................................................................1-2

1.5 System Components ............................................................................................................................1-3

Technical Assistance .......................................................................................................................................1-4

2 About QXDx Automated Droplet Generator .......................................................................2-1

2.1 Sample Plate Layout ............................................................................................................................2-1

2.2 Loading a Bottle of Oil before Conﬁguring a Plate...............................................................................2-2

2.3 Starting a Run on AutoDG ...................................................................................................................2-3

2.4 Sealing the Plate after a Run on AutoDG ..........................................................................................2-13

2.5 Accessing Run Logs ..........................................................................................................................2-14

2.6 Exporting an AutoDG Run Log ..........................................................................................................2-16

3 Using the QXDx Droplet Reader ..........................................................................................3-1

3.2 Light Indicators .....................................................................................................................................3-3

4 About QXDx Software ..........................................................................................................4-1

4.1 Adding or Editing Lot Information ........................................................................................................4-2

4.2 Starting a New Run ..............................................................................................................................4-4

4.3 Using the Well Editor ............................................................................................................................4-4

4.4 Viewing and Printing of Results ...........................................................................................................4-5

4.5 Reports ................................................................................................................................................4-7

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual xi

Contents

5 Maintenance ..........................................................................................................................5-1

5.1 Updating the Software and Firmware ..................................................................................................5-3

5.2 Cleaning the Oil Purge Reservoir ........................................................................................................5-3

5.3 Replacing Droplet Reader Oil and Removing Waste ........................................................................... 5-4

5.4 Performing Maintenance Routines .......................................................................................................5-4

5.5 Quality Control .....................................................................................................................................5-5

6 Troubleshooting .................................................................................................................... 6-1

6.1 Restarting a Run on AutoDG after an Error .........................................................................................6-1

6.2 Restarting a Run on AutoDG After a System Error .............................................................................6-2

6.3 Instrument and Mechanical Errors .......................................................................................................6-3

6.4 User Actions During Run ...................................................................................................................6-12

6.5 Analysis Errors ...................................................................................................................................6-13

7 Speciﬁcations .......................................................................................................................7-1

7.1 QXDx AutoDG Speciﬁcations ..............................................................................................................7-1

7.2 QXDx Droplet Reader Speciﬁcations ...................................................................................................7-1

8 Advanced Administration ....................................................................................................8-1

8.1 Changing the Password .......................................................................................................................8-1

8.2 Adding, Editing and Deleting Users .....................................................................................................8-1

8.3 Managing Assays .................................................................................................................................8-1

8.4 Conﬁguring Database Connection .......................................................................................................8-2

8.5 Backing Up and Restoring Data ..........................................................................................................8-2

8.6 Lab Conﬁguration .................................................................................................................................8-2

8.7 Event Log .............................................................................................................................................8-3

Index ................................................................................................................................................I-1

1 QXDx AutoDG Droplet Digital

PCR System

1.1 Introduction

The QXDx AutoDG ddPCR System, performs accurate and precise digital PCR.

The system consists of two instruments, the QXDx Automated Droplet Generator and the QXDx Droplet Reader, and their associated consumables. The QXDx Automated Droplet Generator partitions samples into ~20,000 nanoliter-sized droplets and, after PCR on a thermal cycler, droplets from each sample are analyzed individually on the QXDx Droplet Reader.

1.2 Intended Use and Indication for Use

The QXDx AutoDG Droplet Digital PCR System with QXDx software is an in vitro diagnostic droplet digital PCR ampliﬁcation and detection test system. It is intended for the ampliﬁcation, detection (qualitative and quantitative), and analysis of nucleic acid samples, which have been partitioned into nanoliter droplets using ﬂuorescence detection methods. The QXDx AutoDG Droplet Digital PCR System is indicated for use in clinical laboratories with legally-marketed assays which specify its use.

1.3 Droplet Digital PCR Workﬂow

Droplet Digital PCR involves the following steps. The entire workﬂow takes about 5-6 hours to complete.

1.3.1 Procedure

1. Prepare PCR-ready samples. For RNA based assay - Extract RNA from sample medium, and run the RT reaction for cDNA. Refer to the Instruction Manual from your RT kit and Thermal Cycler for more information on performing RT reaction.

2. Use the QXDx Automated Droplet Generator(AutoDG) to generate droplets by partitioning the sample using microﬂuidics into nanoliter-sized droplets required for ddPCR analysis.

3. Perform PCR ampliﬁcation — Remove the plate from AutoDG and seal the plate with foil using

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual 1-1

QXDx AutoDG Droplet Digital PCR System

a PX1 Plate Sealer. Perform PCR to end point (~40 cycles) using a thermal cycler. Refer to the Instruction Manual of your thermal cycler for more information performing pcr. The thermal cycler must meet the following speciﬁcations:

Thermal Cycler (meeting the following speciﬁcations):

• Temperature accuracy: ±0.2°C

• Well-to-well temperature uniformity: ± 0.4°C within 10 seconds

• Adjustable ramp rate: at or adjustable to 2°C per second

• Temperature range: 0 - 100°C

4. Read droplets and analyze results: Load the plate into the QXDx Droplet Reader, IVD and start your run. The droplet reader sips each sample, singulates the droplets, and streams them in single ﬁle past a two-color detector. The detector reads the droplets to determine which contain a target (+) and which do not (–).1

NOTE: If reading or quantifying droplets and recovering material from droplets in parallel, prepare two sets of reactions, one for each application. For example, a set of eight wells in a single DG32 cartridge can be generated: four of these will be read after thermal cycling, and four will not be read.

The droplet reader connects to a laptop computer running QXDx Software. The software provides a complete set of tools for setting up and naming samples, running and controlling the instrument, and analyzing results. It also reads the positive and negative droplets in each sample and plots the ﬂuorescence droplet by droplet. The fraction of positive droplets in a sample determines the concentration of target in copies/μl

1.4 Setting Up and Operating the System

Set up and power-up the system before using it for acquisition and analysis.

1.4.1 About this task

The system consists of two instruments and associated software:

• QXDx Automated Droplet Generator (AutoDG) — utilizes proprietary reagents and microﬂuidics to

partition samples into ~20,000 nanoliter-sized droplets

• QXDx Droplet Reader — following PCR ampliﬁcation of the nucleic acid target in the droplets, this

instrument analyzes each droplet individually using a two-color detection system (set to detect FAM and VIC, HEX); PCR- positive and PCR-negative droplets are counted to provide absolute quantiﬁcation of target DNA in digital form using QXDx Software

1.4.2 Procedure

1. Connect the QXDx Automated Droplet Generator and QXDx Droplet Reader to a power source using the power cords and power adapter provided. Leave 10” (25 cm) clear space behind and 5” (12 cm) clear to the right and left of each instrument for proper ventilation. Position the instrument such that it can be easily disconnected from the power source should that become necessary for servicing the equipment.

2. Connect the QXDx Droplet Reader to the Bio-Rad provided system laptop using the USB 2.0

QXDx AutoDG Droplet Digital PCR System

cord provided. QXDx Software comes pre-installed on the laptop.

3. Power on both systems using the switch on the back. The status indicator turns solid green to indicate that the power is on.

4. Replace the droplet reader oil per the prescribed maintenance task. The droplet reader requires droplet reader oil (catalog #12002526).

1.4.3 Results

Your system is connected and ready for use.

1.5 System Components

Table 1: QXDx AutoDG Droplet Digital PCR System components. Items shipped with the QXDx AutoDG Droplet Digital PCR System (catalog # 12008019, 12008020). Catalog # refers to replacement items (quantities may be different).

Component Description Catalog#

QXDx Automated Droplet Generator

Cooling block accessory Prevents evaporation during droplet generation. 12002819

Oil waste reservoir Collects oil waste from priming and ﬂushing Call technical support

Power Cord

QXDx Droplet Reader Instrument used for droplet reading, data collection 12008020

Droplet reader plate holders (2)

USB 2.0 cable Connects QXDx Droplet Reader to PC Call technical support

Powercord Connects QXDx Droplet Reader to power source Call technical support

Laptop PC

QXDx USB QXDx Software(2 Modules)

QXDx Acquisition v.1.0 Acquisition controls instrument and data acquisition 12005824

QXDx Analysis v.1.0 Analysis performs assay speciﬁc analysis 12005825

Instrument used for droplet Generation 12008019

Positions and holds the droplet generator cartridge in the instrument for droplet generation

Position96-well PCR plate in the droplet reader droplet reader

Connects to the QXDX Droplet Reader for data acquisition and analysis

Contains Software images and manual 12010773

Call technical support

29711024

12010757

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QXDx AutoDG Droplet Digital PCR System

Table 2: Universal Kit

Component Catalog # Description

QXDx Universal Kit for AutoDG ddPCR System

QXDx AutoDG Consumable Pack 12001922 Includes ddPCR 96-Well Plates, ddPCR Pierceable

QXDx AutoDG Supermix Pack 12003031 Includes supermix required for Droplet Digital PCR

QXDx Droplet Reader Oil Pack 12002526 Includes Droplet Reader Oil required for Droplet

Table 3: Additional materials needed but not provided with the system

Component Recommended

Plate Sealer PX1 PCR Plate Sealer 181-4000

Thermal Cyclers with speciﬁcations equivalent to the following: Accuracy: +/- 0.2°C

Thermal Cycler

Uniformity: +/- 0.4°C well-to-well within 10 sec Adjustable ramp rate capability with required ramp rate: 2°C/sec Temperature range: 0-100°C

17001378

Foil Heat Seals, Automated Droplet Generation Oil for Probes, DG32 Cartridges, Pipet Tips, and instructions for use required for automated droplet generation

Digital PCR

Catalog# and

Supplier

N/A

Droplet reader waste bottle Empty waste bottle N/A

Technical Assistance

Bio-Rad Technical Support

The Bio-Rad Technical Support department is open Monday through Friday, 5:00 AM to 5:00 PM, Paciﬁc Time. Phone: 1-800-424-6723

Email: Support@Bio-Rad.com (U.S./Canada only)

For technical assistance outside the U.S. and Canada, contact your local technical support ofﬁce or click the Contact us link at www.bio-rad.com.

2 About QXDx Automated Droplet

Generator

Bio-Rad’s QXDx AutoDG ddPCR System combines water-oil emulsion droplet technology with microﬂuidics to perform accurate and precise digital PCR. The system consists of two instruments — an Automated Droplet Generator and a QXDx Droplet Reader — and associated consumables. The Automated Droplet Generator, IVD partitions each sample into ~20,000 uniform nanoliter-sized droplets in which nucleic acid molecules are distributed in a random fashion. Each droplet serves to partition the reactions.

The 96-well PCR plate of droplets is removed from the AutoDG Instrument, sealed, and PCR is performed to end point in a thermal cycler. Droplets from each sample are analyzed individually on the Droplet Reader; the droplets stream single ﬁle through the reader for ﬂuorescence analysis.

2.1 Sample Plate Layout

Use the sample layout provided here to prepare and ﬁll the wells as per the kit IFU.

Make sure that the wells are ﬁlled as per the following example layout. The assay requires preset position for calibrators and controls positioned on the plate as indicated in the layout. Additionally, the plate must hold minimum of 8 wells worth of materials at a minimum in a column. The run cannot be initiated unless all 8 wells contain reagents. For blank wells, that contain no sample, control, or calibrator, use 2x control buffer diluted with a 1:1 ratio of water and buffer.

NOTE: If the total number of samples and controls are not in multiples of 8 (such as 8,16, 24 and so forth then ﬁll the remaining wells with 25 μL ddPCR control buffer or excess reagents. Droplets will not form if the wells are left empty.

Table 4: Sample Plate Layout Template.

1 2 3 4 5 6 7 8 9 10 11 12

A NTC NTC S1 S1

B Hi Hi S2 S2

C N N S3 S3

D Lo Lo S4 S4

E 0.1%IS 0.1%IS S5 S5

F 10%IS 10%IS S6 S6

G Buf Buf S7 S7

H Buf Buf S8 S8

NOTE: This is just a sample layout. The layout for QXDx Assays may vary depending on the assay speciﬁcations.

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual 2-1

About QXDx Automated Droplet Generator

2.2 Loading a Bottle of Oil before Conﬁguring a Plate

2.2.1 About this task

To save time at the beginning of a run, a bottle of Automated Droplet Generation Oil can be loaded into the instrument, and the oil delivery system primed, at any point. When there is no bottle of oil loaded into the instrument, the Oil Level display on the screen will appear gray to indicate it is empty. The Oil Type display on the screen will not display an oil type.

2.2.2 Procedure

1. Open the door of the AutoDG Instrument by lifting up on the handle until it clicks into a locked position.

2. Remove the cap from the bottle of AutoDG Oil and insert the bottle into the tower of the oil delivery system at the front left corner of the instrument.

3. Touch the Oil Type button on the home screen to bring up the Select Oil Type display.

4. Touch the droplet to indicate which type of oil has been loaded. To help differentiate, the AutoDG Oil for Probes bottle has a yellow label and contains a yellow straw, while the AutoDG Oil for EvaGreen bottle has a green label and contains a green straw.

5. The instrument will check that there is oil in the bottle. If you did not load a bottle (or insert the bottle completely) as described in step 2, you will be prompted to load a bottle of the oil type that you selected in the previous screen. Once correctly loaded, the AutoDG Instrument will begin the ﬂush and prime routine. A, display while checking for the bottle; B, display while priming the oil delivery system with AutoDG Oil for Probes. Once complete, the instrument will display a screen conﬁrming successful priming of the selected and loaded oil.

A B C

About QXDx Automated Droplet Generator

6. Touch OK to return to the home screen. The Oil Level icon will now reﬂect the amount of oil in the bottle, and the Oil Type icon will reﬂect the type of oil loaded and primed. The example below shows the home screen displaying a full bottle of AutoDG Oil for Probes loaded.

2.3 Starting a Run on AutoDG

2.3.1 About this task

The Automated Droplet Generator (AutoDG) is designed to remain powered on in order to preserve positive airﬂow inside of the instrument and track consumable use. The instrument stays in an idle state when not being used.

If the instrument deck is empty, the indicator lights on the deck of the AutoDG should be off, indicating that no consumables are present. The corresponding areas of the touch screen will be gray.

When a new or different bottle of oil is loaded, or when power is lost, the AutoDG will perform a small volume ﬂush and prime of the oil delivery system. If the AutoDG Instrument has not been used for an extended time period (a week or more) but left powered on, it is recommended to perform a ﬂush and prime routine before running a plate

If consumables were present in the instrument when power was lost or disconnected, an error message will appear prompting you to check and reset the consumables if necessary. The cartridges, gaskets, tips, and plates are all single- use consumables and should be discarded after use. If the consumables in the instrument are of questionable use after power loss, please remove and discard.

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About QXDx Automated Droplet Generator

ATTENTION: The AutoDG accepts either a sealed or open 96-well PCR plate containing 25 μl prepared ddPCR reactions. Detailed sample preparation and reaction setup information can be found in the QXDx Supermix product inserts.

2.3.2 Procedure

1. Touch the screen to bring the AutoDG out of idle mode.

NOTE: When powering on the AutoDG, IVD, you will see a startup screen while the instrument powers on and performs a self-check. The door will automatically close.

Figure 1: Home screen, no consumables loaded

2. Check the indicator lights on the deck of the AutoDG Instrument nd the consumable icons on the touch screen. Refer to the table below to familiarize with the deck lighting statuses, touch screen icons statuses, and their descriptions.

Table 5: AutoDG Instrument deck lighting and touch screen status indicators

Deck Lighting

Status

Off Gray, Empty Ready to conﬁgure a new run

Off Gray, Used Ready to conﬁgure a new run;

Green Green, Ready Ready to conﬁgure a new run;

Yellow Yellow, Load Run conﬁgured, load consumables

Touch Screen Icon Status Indication

instrument will prompt for consumable replacement in used positions when the next run is conﬁgured

consumables in the green positions are ready to be used

as prompted (this status occurs only during run setup).

About QXDx Automated Droplet Generator

Deck Lighting

Status

Blue Blue, Complete Run complete and droplets ready;

Red Red, ? Consumables status unknown after

3. To create a plate of droplets with the Automated Droplet Generator, IVD:

a. Touch the Conﬁgure Sample Plate button at the bottom center of the screen.

Figure 2: AutoDG Home Screen

Touch Screen Icon Status Indication

occurs only at droplet plate position

power loss, please conﬁrm manually

b. Optional: Enter the plate name and plates notes. Touch the ﬁelds to bring up a keyboard on

the screen.

Figure 3: Plate Layout Screen

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About QXDx Automated Droplet Generator

c. Touch or swipe across the screen to select the columns in which your samples are located

on the sample plate. Touching a selected column deselects it. You can touch any orientation of columns.

d. Conﬁgure Sample Plate screen with A, full plate of samples selected; B, half plate of

samples selected; C, alternating columns of samples selected.

A B C

e. Click OK when done.

In the example below, a full plate has been selected

Based on the number of columns selected the consumable icons on the screen will begin to blink yellow to indicate where new consumables need to be loaded into the instrument.

4. Depending on the indication on the screen do one of the following:

• If the blinking yellow icon displays Load on the screen, remove the previously used consumable (if applicable) and load a new consumable into the designated area of the instrument.

• If the icon remains gray on the screen, that consumable is not needed to complete the currently conﬁgured run.

5. Open the door on the AutoDG Instrument by lifting up on the handle at the front of the instrument. The electronic braking system will assist you in this task and prevent the lid from closing accidentally.

ATTENTION: The Automated Droplet Generator, IVD door will close to preserve HEPAﬁltered enclosure if left open for longer than 20 minutes while in idle mode (not generating droplets). There is an audible click when the door brake releases, and the door closes slowly. Observe caution around the pinch points of the instrument and keep your hands clear. To avoid

About QXDx Automated Droplet Generator

contamination, load the consumables from the back to the front of the instrument. Do not plate anything on the instrument deck outside of the dedicated consumable holders.

6. To load the DG32 AutoDG Cartridges along the back row of the instrument, remove the plastic wrapping from the DG32 cartridges and place with the green gaskets to the right, into the three plate holders. The holders are keyed for proper orientation of each DG32 cartridge to prevent incorrect loading.

A, DG32 Cartridge holders on the AutoDG deck in the “Load” state, indicated by yellow lights; B, green lights indicate the DG32 Cartridge has been correctly loaded and is ready; C, DG32 consumables have been correctly loaded. The Ready status appears on the DG32 icons on the screen.

Table 6: Example indicators

A B C

The lights on the DG32 plate holders will change from yellow to green when the DG32 cartridges are inserted correctly. If a light remains yellow, try repositioning the plate in a different orientation. As the lights turn green on the deck, the corresponding icons on the touch screen will go from blinking yellow to solid green, and Ready will be displayed.

7. To load the AutoDG Pipet Tips along the center row of the instrument:

ATTENTION: Only AutoDG Pipet Tips should be used; other tips can damage the instrument.

a. Remove the plastic wrapping and box lids from the tip boxes and place into the plate

holders in the middle of the deck. Only full tip boxes should be loaded.

Remove the tip waste bin containing any tips from a previous run and replace with a clean waste bin.

The example shows that the pipet tip boxes have been correctly loaded. The Ready status appears on the Pipet Tip icons on the screen.

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About QXDx Automated Droplet Generator

The lights on the tip box holders will change from yellow to green when the tip boxes are inserted correctly. As the lights turn green on the deck, the corresponding areas of the touch screen will go from blinking yellow to solid green, and Ready will be displayed.

8. To load the 96-well PCR plate containing your prepared ddPCR reactions into the front row of the instrument: Please note that a sample plate is required for every run, regardless of the number of columns selected.

a. The sample plate can be sealed with a PX1 Plate Sealer and heat-sealing foil in advance

of loading into the AutoDG Instrument. Each well should contain 25 μl of your prepared ddPCR reaction. See the supermix product insert for more detailed information on ddPCR reaction setup.

b. Place the plate into the front left plate holder, labeled on the screen as Sample Plate. The

holder is keyed for proper orientation and contains plate clips to support sealed plates. In the example, the sample plate has been correctly loaded. The Ready status appears on the Sample Plate icon on the screen.

The light on the Sample Plate holder will change from yellow to green when the plate is inserted correctly. If the light remains yellow, try repositioning the plate in a different orientation. As the light turns green on the deck, the corresponding icon on the touch screen will go from blinking yellow to solid green, and Ready will be displayed.

About QXDx Automated Droplet Generator

9. To load the Droplet Plate assembly:

ATTENTION: The cooling block should be placed in a –20°C freezer for at least 2 hours before conﬁguring a run on the AutoDG Instrument and inserting the Droplet Plate assembly into the instrument. The block goes from a pink color at room temperature to a dark purple color when properly cooled.

NOTE: The AutoDG Instrument uses a cooling method to prevent droplet evaporation, much like the Droplet Generator requires you to cover the wells once droplets are transferred.

a. Remove the cooling block from the freezer and place into the front right plate holder, labeled

on the screen as Droplet Plate. The holder is keyed for proper orientation of the cooling block. The block should be a dark purple color, indicating it is at the proper temperature. If the block is pink, it has warmed up and should not be used.

A, purple - ready for use; B, pink - freeze before use.

As the light turns green on the deck, the corresponding area of the screen will go from blinking yellow to solid green, and Ready will be displayed.

b. Place a clean 96-well PCR plate for droplet collection into the cooling block accessory. The

cooling block is also keyed for proper orientation of the plate. In the example, the droplet plate and cooling block assembly have been correctly loaded. The Ready status appears on the Droplet Plate icon on the screen. A clean droplet plate is required for every run, regardless of the number of columns selected. Once generated, the droplets will be dispensed into the same plate orientation as the ddPCR reactions were taken from the sample plate.

10. To load Automated Droplet Generation Oil into the instrument: If a bottle of Automated Droplet Generation Oil was previously loaded, you may be prompted to conﬁrm the type of oil currently loaded into the instrument. If the last plate was run on the AutoDG Instrument with a different oil type than the one being currently loaded and selected, the instrument will perform a small volume purge of the oil through the delivery system and into the oil waste reservoir. The total run time will be a few minutes longer when this occurs, but droplet generation will not be impacted. To prevent this operation in the future, see advanced oil loading and switching.

a. Remove the cap from the bottle of Automated Droplet Generation Oil and twist the bottle

into the tower of the oil delivery system at the front left corner of the instrument. Turn the bottle until it does not move; the label on the bottle should face out.

b. Touch Probes oil, to select the type of Automated Droplet Generation Oil that was loaded

into the instrument.

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About QXDx Automated Droplet Generator

Figure 4: Select Oil Type Dialog

c. After the droplet you select will turn blue; touch OK to set the oil type.

The Oil Level icon on the screen will turn blue and display the current oil level of the bottle. The system will display the oil type at the bottom left of the screen as well.

11. After all of the consumables are loaded and the corresponding lights are green on the deck and touch screen, a blue Start button appears at the bottom right of the screen. Touch Start to bring up a conﬁrmation window indicating the type of Droplet Generation Oil loaded, the number and orientation of columns selected for droplet generation, and any plate name and details entered during conﬁguration of the sample plate. Home screen; all consumables are correctly loaded and the system is ready to start droplet generation.

12. Run conﬁrmation screen with A, full plate of samples selected; B, half plate of samples selected; C, alternating columns of samples selected.

A B C

• Once you have conﬁrmed the plate setup, touch the Start Run button to begin droplet generation. The door will automatically close at the beginning of the run and must remain closed during the run. Opening the door before the Droplets Ready message appears may cause the instrument to terminate the run and samples to be lost.

• If the selected columns on the conﬁrmation screen do not match the location of samples in your sample plate, touch Back to make any changes. Touch the sample plate to bring up the Conﬁgure Sample Plate window and change your selections as needed.

• The AutoDG door automatically closes at the start of each run and must remain closed until droplet generation is complete.

About QXDx Automated Droplet Generator

• After a brief initialization, the AutoDG displays a countdown timer on the screen with time remaining until the plate of droplets is ready. No additional action is needed until the plate is ready. The initialization can take 1–5 min, depending on whether the oil type has been changed or not. If you want to abort, skip to the next step.

Table 7: A, initializing display with progress bar at the beginning of a run; B, countdown timer

display indicates the time remaining until droplet generation is complete and the Droplet Plate can be removed.

A B

• Once the plate of droplets is ready, the screen displays a ﬁnalizing window followed by a blue Droplets ready message with the time taken for the run to complete.

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About QXDx Automated Droplet Generator

• The Droplet Plate at the front right corner of the instrument illuminates in blue. The corresponding icon on the touch screen will also pulses blue. The instrument door unlocks for the droplet plate to be removed. Wait to remove the oil bottle as noted on the screen; the unused oil is being returned to the bottle.

If any errors were encountered during the run, an error notiﬁcation appears below the count-up timer. Touch the Errors encountered button to bring up the run logs and identify the error.

13. Optional: If for any reason you need to stop the run, touch the Abort button on the countdown timer screen. In the conﬁrmation window that appears, touch Yes to abort the run or No to return to the countdown timer.

IMPORTANT: Stopping the AutoDG during a run can result in loss of the current column of samples being processed. The example shows, A, abort conﬁrmation screen; B, terminated message

About QXDx Automated Droplet Generator

A B

After conﬁrmation, the system conﬁrms with time when run was terminated.

2.3.3 What to do next

• Seal the plate before performing PCR ampliﬁcation.

• Remove any consumables from the AutoDG Instrument that have been completely used and discard. You must not reuse DG32 cartridges, tips, and plates, as they are single-use consumables only. The AutoDG will remember the status of the consumables as long as it remains powered on; if a consumable has been only partially used, leave it in the AutoDG for the next run.

2.4 Sealing the Plate after a Run on AutoDG

2.4.1 Before you begin

You must remove the droplet plate containing ddPCR droplets.

2.4.2 About this task

You must seal the plate within 30 min of droplet generation using the PX1 PCR Plate Sealer and foil seals listed under system components. For more details, see also instructions in the PX1 PCR Plate Sealer Instruction Manual (part number 10023997). Here

2.4.3 Procedure

1. Set the plate sealer temperature to 180°C and time to 5 sec.

2. Touch the arrow to open the PX1 tray door. Position the support block on the tray with the 96well side facing up. Place the 96-well plate onto the support block and ensure that all plate wells are aligned with the support block.

3. Cover the 96-well plate with one sheet of pierceable foil seal. (The red stripe on the foil seal should face up towards the user.) Do not attempt to place the frame over the foil-covered plate. The frame is only for use with other seals.

4. Once the 96-well plate is secured on the support block and covered with the pierceable foil seal, touch the Seal button. The tray will close and heat sealing will initiate.

5. When heat sealing is complete, the PX1 door will open automatically. Remove the plate from the block for thermal cycling. Remove the block from the PX1 Sealer.

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About QXDx Automated Droplet Generator

6. Check that all the wells in the plate are sealed; the depressions of the wells should be visible on the foil.

2.4.4 Results

Once sealed, the plate is ready for thermal cycling.

2.4.5 What to do next

After the 96-well plate containing the droplets is sealed, place it into the thermal cycler for PCR ampliﬁcation within 30 min of sealing the plate, or store the plate at 4°C for upto 24hrs prior to thermal cycling.

Refer to the assay/supermix product inserts for cycling conditions.

After the PCR ampliﬁcation is complete, remove the 96-well plate from the thermal cycler and read the droplets using the QXDx Droplet Reader. If the goal is to read or quantify droplets and recover material from droplets in parallel, prepare two sets of reactions, one for each application.

For example, a set of eight wells in a single DG32 cartridge can be generated: four of these will be read after thermal cycling, and four will not be read.

2.5 Accessing Run Logs

2.5.1 About this task

The AutoDG stores information about each run, including consumables used, rows of reactions processed, and any errors that may have occurred.

To access the run log:

About QXDx Automated Droplet Generator

2.5.2 Procedure

1. Touch the Run Log button on the home screen.

2. To display detailed information about a run, touch the run.

• Example showing AutoDG Instrument run log with system summary of runs (completed or terminated).

• Example of Run Details for a run terminated by the system due to a pipet tip box lid being left on when placed in the instrument. The run details are displayed on the left of the screen and the error details on the right.

3. Touch OK to return to the run log (and to export run log or exit).

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About QXDx Automated Droplet Generator

2.6 Exporting an AutoDG Run Log

2.6.1 Before you begin

Open the run log before you can export it. Have a USB key connected and ready for receiving the exported ﬁle.

2.6.2 About this task

Use this procedure to export the AutoDG run logs to a USB drive.

2.6.3 Procedure

1. Touch the Run Log button on the home screen.

2. Remove the AutoDG Instrument’s side panel to the right of the touch screen. Slide the magnetic panel down to release, then pull straight out to remove the panel.

3. Insert a USB key into the USB port on the side of the instrument.

4. Touch the Export All button at the bottom left of the screen. Wait while the system exports the run logs to the USB key. When ﬁnished, Run logs successfully exported will be displayed on the screen. It is now safe to remove the USB key.

5. If the USB key is not connected, the AutoDG Instrument will display the message USB key not found. Please insert it and try again. Insert the USB key and touch Retry to proceed.

6. Replace the side panel.

3 Using the QXDx Droplet Reader

3.1.1 Before you begin

NOTE: You must have performed PCR ampliﬁcation and must be ready to load the plate for reading.

3.1.2 Procedure

1. Power on the QXDx™ Droplet Reader using the switch at the back. Allow it to warm up.

2. Check the indicator lights on the front of the droplet reader.

3. The ﬁrst two lights at left should be solid green. This indicates that the power is turned on, there is sufﬁcient oil in the designated oil reservoir, and there is less than 700 ml in the waste bottle. If the lights are ﬂashing amber, the run cannot be started; clean out the waste bottle or replace the oil.

4. After the instrument has warmed up, switch on the PC.

5. Open and login to the QXDx Acquisition Software.

6. Place the prepared 96-well PCR plate into the plate holder.

Figure 3-1: Placing the 96-well plate into the plate holder

a. Place the 96-well PCR plate containing the ampliﬁed droplets into the base of the plate

holder. Well A1 of the PCR plate must be in the top left position.

b. Move the release tabs of the top of the plate holder into the “up” position and place the

top on the PCR plate. Firmly press both release tabs down to secure the PCR plate in the holder.

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Using the QXDx Droplet Reader

Figure 3-2: Tabs down to lock the plate in place

7. Press the button on the green lid to open the droplet reader. Load the plate holder into the droplet reader, and press the button on the lid again to close the cover. Conﬁrm the ﬁrst three indicator lights are green

Figure 3-3: Push button to open/close

Figure 3-4: Placing the plate holder into the droplet reader

After loading the plate, you are ready to start the run on the QXDx Acquisition software.

Using the QXDx Droplet Reader

3.2 Light Indicators

Table 8: Status indicator lights on the QXDx™ Droplet Reader, IVD and its meaning.

Solid green Power on Bottle levels OK* Plate in place Run complete

Flashing green — Oil <30% or waste

>70%**

Flashing amber — Oil <10% or waste

>90%***

Off Power off — No plate Idle

* There is sufﬁcient oil and room in the waste bottle to run 96 wells.

** The run can be started if <96 wells are run (for example, only 19% oil is required for 24 wells); if there is

not enough oil for the run, the software will not allow you to start the run.

*** The software will not allow you to start the run.

— Run in progress

— Error during run

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Using the QXDx Droplet Reader

4 About QXDx Software

QXDx Software has two application interfaces, QXDx Acquisition (p/n 12005824) and QXDx Analysis (p/n

12005825). The dual application design enables simplistic approach for end user to perform a run and analyze the data generated from the run separately.

This also allows enables Bio-Rad to update the applications without impacting instrument controls.

The QXDx Acquisition software is designed with instrument control and run setup as the primary function of this

application.

The QXDx Analysis Software is designed with the ﬂexibility to analyze, annotate run data and generate reports.

The software workﬂow can be described as follows:

In the QXDx Acquisition software you perform

• Instrument controls – perform instrument functions outside of starting a run.

• Manage Assays – Add/Remove application programmable ﬁle speciﬁcs to assays

• Plate Setup — enter information about the samples, assays, and experiments.

• Run — start the run with pre-deﬁned plate setup and apf.

• Maintenance – Perform maintenance tasks

In the QXDx Analysis software you perform

• Load Raw data – load data generated in QXDx Acquisition with (.ddpcrx) ﬁle.

• Analyze the automated data analysis from raw .ddpcrx ﬁle to nucleic acid concentration.

• Review Results — view results based on Assay speciﬁc rules (deﬁned in the apf).

• PDF reports – sample, patient, summary and trend reports.

• Comma-separated values (*.csv) — analyzed data in a format that can be assessed using other programs, such as Microsoft Excel

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About QXDx Software

4.1 Adding or Editing Lot Information

As a lab assistant, before you can start a new acquisition on the QXDx Acquisition software, you must add or edit the universal and test-speciﬁc kit lot information.

4.1.1 About this task

Use the Edit/Add Kit Lot Information dialog to add a new kit lot information for both universal and test-speciﬁc kits for running QXDx data acquisition. You can also edit existing kit lot information that you had previously entered.

4.1.2 Procedure

1. Open the Edit/Add Kit Lot Information dialog one of the following ways:

• Select Configure System > Kit Lot Manager

• Click the Add/Edit Lot button on the Run Setup/Status dialog.

2. Click the Universal Kits tab to open it.

You can simply click on a row to start adding new lot information or click on any column of an existing kit lot row to starting editing it.

NOTE: A pencil icon appears in the ﬁrst column to indicate the edit mode for that row.

a. Enter the Lot Number for the kit.

b. Enter the Part Number.

c. Enter a valid Lot Expiry Date. The date cannot be current date or in the past.

d. Select the Used check box to indicate if the kit is a previously used lot.

3. Click the Test-specific Kits tab to open it.

About QXDx Software

You can simply click on a row to start adding new lot information or click on any column of an existing kit lot row to starting editing it.

NOTE: A pencil icon appears in the ﬁrst column to indicate the edit mode for that row.

a. Simply click on a row to start adding lot information.

b. Select the Test Name from the drop-down.

c. Enter the Lot Number for the kit.

d. Enter the Part Number.

e. Enter a valid Lot Expiry Date. The date cannot be current date or in the past.

f. Select the Used check box to indicate if the kit is a previously used lot.

g. Enter the Conversion Factor for the kit lot.

h. For each Test-speciﬁc kit added, also add the following information about the kit.

In this column Enter

Expected % Ratio Minimum The minimum expected % ratio for both ~0.1%IS and~10%IS

calibrators. The value must be in the valid range.

Expected % Ratio Maximum The maximum expected % ratio for both ~0.1%IS and~10%IS

calibrators. The value must be in the valid range.

4. Select the Show Expired & Used Lots check box to show expired and used lots during the run for selection. This option is not selected by default.

5. Click Save to save changes and exit the dialog.

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4.2 Starting a New Run

As a lab assistant, start a new acquisition on the QXDx Acquisition software.

4.2.1 Before you begin

You have loaded the sealed 96-well plate into the QXDx Droplet Reader. You have opened and logged into the QXDx Acquisition software. You have added the universal kit and test-specific kit lot information.

4.2.2 Procedure

1. In the QXDx Acquisition software, click on New Run.

2. Select the test name from the list of tests.

3. Click New Plate to load a fresh plate, or click on Open Plate to open an existing plate. The plate screen opens.

4. Conﬁgure the plates using the well editor. See section, “Using the Well Editor” in Chapter 4.

5. After the plate is setup, click Run. On the screen, a visual indicator with a list of mechanical checks are listed with green check marks indicating successful instrument status. Failures are also indicated in which case you must ﬁx issues before proceeding with the run. For a list of instrument and mechanical errors, see Chapter 6, Troubleshooting.

6. On the Run Start Dialog, select the lot information for both Universal Kit and Test-Specific

Kit.

NOTE: See Section 4.1, Adding or Editing Lot Information for more information.

7. Optional: Enter comments speciﬁc to the run in the Run Notes text ﬁeld.

8. When ready, click Start Run to initiate the data acquisition.

4.2.3 Results

The run status indicator appears showing the progress and estimated time for completion. Depending on the number of samples in the plate, data acquisition typically takes about a 2.5 minutes per test and approximately 120 minutes per plate (fully ﬁlled). After a successful run completion, the QXDx Analysis software opens automatically.

4.3 Using the Well Editor

4.3.1 About this task

Use the well editor to deﬁne the settings (samples, experiment type, and detection type) for the plate. Sample and experiment types are color-coded and can be customized for easy reference in the plate map. The plate map in the software must be conﬁgured exactly the way the wells were ﬁlled.

Settings appear in the Applied Well Settings box as you enter them. When you are done, click Apply to save the information. The settings appear in the well in the plate map.

About QXDx Software

4.3.2 Procedure

1. To open the well editor, double-click on the well(s) you wish to edit. Selected wells are highlighted, and the well editor opens in the edit mode.

a. To select multiple wells, hold Ctrl and select the wells.

b. To select wells in a continuous series (horizontal or vertical), hold Shift and select the ﬁrst

and last wells.

c. To select all wells, double-click in the top left corner of the plate.

d. To select a row or column, double-click the letter or number for that row or column.

2. For samples, enter the sample name and select the experiment from the drop-down menu.

For each sample, two neighboring wells are ﬁlled. Thus two contiguous wells with the same sample must be conﬁgured on the plate layout matching the ﬁlled well location on the plate.

NOTE: To ensure traceable, and accurate results for each sample, scan or enter the ID in the correct well location as ﬁlled in the wells on the plate.

a. All saved experiments appear in the drop-down menu.

b. The sample name is case-sensitive; only wells with identical sample names can be treated

as merged wells during data analysis.

c. To create or edit an experiment, use the experiment editor.

3. Select the Supermix from the drop-down menu (required; selection cannot be changed after data collection).

4. Assign each assay a Name and sample Type.

4.4 Viewing and Printing of Results

4.4.1 About this task

The results are generated automatically by the QXDx Analysis Software including measured droplet counts, ﬂuorescent signals, and embedded calculation algorithms and displayed in the View Results.

4.4.2 Procedure

1. Upon completion, the Run Complete Dialog will appear and ask the user to go directly to QXDx Analysis Software for data review, or ask the user to logout and login to QXDx Analysis with the

active user.

2. In the QXDx Analysis Software select the Review Results button run to review, There will be 2 status buttons “In Review Runs” and “Reviewed Runs.”

a. In Review Runs – allows users to review the data, add notes, view sample reports, view

summary reports and release the results.

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About QXDx Software

NOTE: Reports are draft reports and water will not be removed until the run is Reviewed and Released.

b. Reviewed Runs – is the status that follows once a user reviews and releases the results for

distribution.

3. Once the run ﬁle is open, you will ﬁnd 2 tabs – Run Information and Table View

a. Run Information – allows the user to view runs 1 sample at time w/ 2D plot and sample

speciﬁc results. It also user to edit the sample/patient id in the event of transcription error.

b. Table View – allows the user to view the results in a tabular format and raw data supporting

the analysis.

4. Click on a link for a run from In Review Runs to open the data for analysis. You can perform one or more of the following functions to review results.

• Click on the sample on the plate layout to view the plot by Sample.

• Select a sample to review data and add notes to samples. Samples are two contiguous wells with the same information.

• Review each sample for analysis errors listed in the Errors section.

• You can also use the table view to review the data analysis summary.

• Refer to the IFU for interpretation of results

• The following is a sample screenshot of a well selected in the review screen.

5. Enter relevant comments in the Release Notes text ﬁeld.

NOTE: You must be an authorized user to perform this function.

6. To view reports, click one or more of the following options:

• Preview Sample Reports

• Preview Run Report

About QXDx Software

PDF reports are saved in the conﬁgured folder.

7. After completing your analysis, click Review button at the bottom right of the screen to release the ﬁnal report. The analysis data is moved to the Released Runs list.

4.5 Reports

Reports are generated by both user groups (admin, and standard user). The following reports are available to the user under the reports section of QXDx Analysis software.

4.5.1 Procedure

1. In the QXDx Analysis software, click on Reports.

2. Select desired report Sample, Patient, Control Trend, Event Log.

3. Select and Input required pararmeters to generate the reports.

See below for example reports.

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Example Sample Report - Passed

About QXDx Software

Example Sample Report – Failed

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Sample Summary Report

About QXDx Software

Sample Control Trend Report

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About QXDx Software

5 Maintenance

Recommended maintenance tasks for QXDx system and components.

Both QXDx™ Automated Droplet Generator and QXDx™ Droplet Reader are veriﬁed by Bio-Rad to be functioning to manufacturer speciﬁcations upon installation. Annual preventative maintenance offered by Bio-Rad is recommended to whichever comes ﬁrst, 365 runs on the system or 1 year from last PM to ensure that both instruments continue to function according to manufacturing speciﬁcations.

Maintenance Log is provided below for user to follow and track their daily, weekly, monthly and annual activities.

In the event of malfunction and/or changes in the analytical performance of the device, please contact Bio-Rad Technical Support (1-800-424-6723).

It is recommended to clean instrument surfaces regularly. Use deionized/ distilled water with a slightly dampened cloth to wipe down surfaces. For decontamination, use 10% bleach followed by 70% ethanol and/or deionized/ distilled water. Do not use acetone or tap water.

Inspect equipment regularly for damaged external components or wiring. Do not use if damaged.

Apply standard MSDS (Material Safety Data Sheet) and OSHA practices when handling and disposing of generated waste.

Bio-Rad droplet generation and reader ﬂuids are based on ﬂuorinated hydrocarbon chemistry and should be disposed of in accordance with institutional, state, and local regulations. These nonﬂammable ﬂuids are inert and have low environmental impact and low toxicity. Collect waste in a polyethylene container and discard within one month.

Droplets made with Bio-Rad master mix have antimicrobial properties, but microbial growth is possible. The waste proﬁle should contain the following: ﬂuorinated hydrocarbons, water, ﬂuorescent dye (from probes), intercalating dye, protein, and nucleic acids. The droplet generator is not intended to be used with bio hazardous material.

Do not replace detachable power cord with an uncertiﬁed or an inadequately rated cord.

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Maintenance

Maintenance Log

Maintenance

5.1 Updating the Software and Firmware

5.1.1 About this task

Perform the software and ﬁrmware upgrade using the upgrade USB key, if Bio-Rad informs you of a newer version of the AutoDG software and ﬁrmware.

5.1.2 Procedure

1. Remove AutoDG Instrument’s side panel to the right of the touch screen. Slide the magnetic panel down to release, then pull straight out to remove the panel.

2. Insert a USB key into the USB port on the side of the instrument.

3. Touch the Settings button on the home screen.

4. Scroll down to the Update section of the menu and touch Update Software and Firmware.

5. Touch the Update button and wait while the system completes the upgrade. When ﬁnished, a message will appear indicating it is safe to remove the USB key.

6. Replace the side panel and power cycle the instrument.

5.2 Cleaning the Oil Purge Reservoir

5.2.1 About this task

It is recommended that you clean the oil purge reservoir on a quarterly basis. The oil purge reservoir collects Droplet Generation Oil during the ﬂush and prime routine; it is unused oil that has not come into contact with the ddPCR™ reaction. To access the oil purge reservoir:

5.2.2 Procedure

1. Touch the Settings button on the home screen.

2. Under the System Maintenance section of the menu, touch Remove Oil Purge Reservoir.

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Maintenance

3. If the door is open it will close automatically and a message will appear. Touch OK to continue.

4. The droplet generation head of the AutoDG Instrument will slide out of the way, exposing the small oil purge reservoir. The screen will display a Moving droplet generation head message while this occurs.

5. Once complete, the onscreen instructions will prompt you to remove the oil purge reservoir, clean, and replace it. Open the door and remove the reservoir from the back left corner of the instrument deck. The reservoir is magnetic and can be lifted easily.

6. Wash the oil purge reservoir with distilled water, dry completely, and replace.

7. Touch the OK button to close the door and move the droplet generation head back into place. The Moving droplet generation head message will once again be displayed while this occurs.

5.2.3 Results

When ﬁnished, a complete message will appear, and you can touch OK to return to the Settings menu.

5.3 Replacing Droplet Reader Oil and Removing Waste

5.3.1 Before you begin

If the instrument has been unused for longer than a week, prime the system before running a plate.

5.3.2 Procedure

1. Replace the droplet reader oil and empty the waste receptacle as needed.

2. Use the handle built into the side compartment to slide the carriage out.

3. Use empty oil supply bottles as new waste bottles.

4. Add 50 ml 10% bleach to the waste bottle to prevent microbial growth

5. Place a label on the waste bottle at this time.

6. Place the new bottle of oil in the oil position and screw the cap into place.

7. In QXDx Software™, click Maintenance > Prime Instrument.

5.4 Performing Maintenance Routines

Simple system maintenance routines to keep the system in check.

5.4.1 About this task

When the droplet reader is powered on and connected to QXDx Acquisition Software. The software provides some maintenance options. Use the following options for routine maintenance and calibration:

5.4.2 Procedure

• Click Maintenance > Prime Instrument to prime the syringes, ﬂuid lines, etc. with droplet reader oil and remove air from the system, for example, perform this after replacing droplet reader oil.

Maintenance

• Click Maintenance > Flush Instrument — to clear the syringes and ﬂuid lines if a clog is suspected

• The other options are used mainly by ﬁeld service technicians when setting up or troubleshooting the system:

a. Click Maintenance > Color Calibration to calibrate the system or new set of probes using

a color calibration plate setup. The Droplet Reader calibration is performed using a droplet standard plate with known size droplets containing FAM and VIC standard dyes. These premade droplets are used in photomultiplier adjustments, color calibration, and veriﬁcation of proper ﬂuidics performance.

5.5 Quality Control

5.5.1 Well Aggregation

• Each plate contains Calibrators, Controls along with Samples and are measured in two replicate wells

• Each well must individually produce sufﬁcient number of detected droplets in order to be used for further processing

• The measurement for replicate wells are compared for consistency, if the results fall outside of acceptable imprecision, no valid result is reported. See the exceptions below.

5.5.2 Calibrators

• Both calibrators (0.1%IS and 10%IS) must produce results within the specs.

• If a Calibrator fails, then the entire plate will fail, rendering the results invalid and no. In which case, the sample results are not reported.

• In the event of failed calibration, repeat the run starting with the RT reaction step.

5.5.3 Controls

• All control samples must produce data values within specs

□ H-CTRL and L-CTRL must be within speciﬁed range

□ Negative Control must produce a negative result

If any of the control samples fail – the entire plate will fail, rendering the results invalid and no.

• No sample results are reported.

• In the event a control fails, repeat the run starting with the RT reaction step

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Maintenance

6 Troubleshooting

Understand and troubleshoot possible system and analysis errors.

The system may indicate possible instrument, and mechanical errors in the software interface through pop-up

messages and analysis errors in the Errors section of the well and table review in the QXDx Analysis software.

The AutoDG also provides onscreen troubleshooting should an error occur. Steps to resolve such errors displays on the instrument screen, or message to contact Bio-Rad Technical Support displays in case of errors that do not have a clear workaround.

Consult each subsections below to understand the different types of errors and how to remedy them.

6.1 Restarting a Run on AutoDG after an Error

6.1.1 About this task

If the AutoDG encounters an obstruction during the run, it will stop the run and display an error message indicating the area of the deck that needs your immediate attention.

6.1.2 Procedure

1. Open the door and remove the obstruction and/or replace the consumable indicated in the onscreen error message.

2. Close the door and touch OK on the error display.

3. Touch the Conﬁgure Sample Plate icon on the home screen; the AutoDG Instrument remembers the status of all consumables so long as it remains connected to a power supply.

4. On the screen, select the columns of samples remaining to be processed and touch OK. Example of error message displayed when the lid is left on the box of tips placed in the left tip box holder. The run stops and an error message indicating the position of the error displays on the touch screen.

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Troubleshooting

5. Touch the Start Droplet Generation icon to resume the run.

Figure 9: AutoDG Example Error Message

6.2 Restarting a Run on AutoDG After a System Error

6.2.1 About this task

If the AutoDG encounters a system error during the run, it will stop the run and display an error message indicating that the instrument requires power cycling. If this error occurs do the following.

Figure 10: System Error Message Example

Troubleshooting

6.2.2 Procedure

1. Unplug the AutoDG Instrument from the power supply.

2. Wait 30 sec and plug it back in.

3. The AutoDG Instrument will not be able to recall the status of all consumables and will require manual conﬁrmation.

4. Reset the unused consumables and touch the Configure Sample Plate icon on the home screen.

5. Select the columns of samples remaining to be processed on the screen and touch OK.

6. Touch the Start Droplet Generation icon to restart the run.

6.3 Instrument and Mechanical Errors

Possible instrument and mechanical errors that can occur during a run.

6.3.1 QXDx Automated Droplet Generator System Errors

Consult the following table for information on instrument or mechanical errors and suggested actions to remedy them. These errors show in the code series 1xx-9xx.

Issue Description/Possible cause Suggested Action

No screen display

No response when you power on

the instrument

Screen display is missing characters, illegible, or not responsive to touch

Door won’t open or is hard to open

Light under a consumable

The instrument is disconnected from

the power source.

There was an LCD screen failure. Request service

The instrument is running.

The instrument is disconnected from

the power source.

Consumable is not inserted all of the way or is in the incorrect orientation.

Check the power cord. Make sure that it is securely plugged in and the system is switched on.

Wait for droplet generation to complete or touch the Abort button on the screen to terminate the run early. Once movement has stopped inside the instrument, the door will unlock and can be opened easily.

Connect the instrument to a power supply and wait for initialization to complete; the door will unlock and can be opened easily.

Try positioning the consumable in a different orientation.

Red Oil Level icon

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AutoDG Oil bottle contains less than a full plate’s worth of oil and will require additional oil to complete the next run.

Be prepared to insert a new bottle of oil during the setup process for the next plate.

Troubleshooting

6.3.2 QXDx Droplet Reader System Errors

Consult the following table for information on instrument or mechanical errors and suggested actions to remedy

them. These errors show in the code series 1xx-9xx.

Code (Decimal) Name

101 CommReinitFailed

102 CommSPTIFailure

103 CommInvalidDetResponse

Description/Possible

cause

This error occurs after a low level SPTI command fails and reinitializing the SPTI interface fails as well.

Occurs when a low level instrument command fails. This indicates a possible communication failure between the software and instrument.

The instrument detector board echoes the command it receives from the software. If the echoed command, sequence, parameter number, or value does not match the sent values, this error occurs.

Suggested Action

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

Power cycle the instrument.

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

• Power cycle the instrument.

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

• Power cycle the instrument.

104 CommDetError

105 CommInvalidFluResponse

The instrument detector board reported that an error has occurred while running the command it received from the software.

The response was received after the ﬂuidics board command was issued with invalid value. Some data that was acquired during the run, before the failure occurred, may be usable.

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

• Power cycle the instrument.

Before performing a new run, power cycle the instrument.

Troubleshooting

Code (Decimal) Name

106 CommInvalidMotRespons

110 NotConnected

111 InvalidState

Description/Possible

cause

The response was received after the motor board command was issued with invalid value. Some data that was acquired during the run, before the failure occurred, may be usable.

A connection to the instrument could not be established or was lost.

A command was issued from an instrument state that did not support it. This could be due to a communication loss between the instrument and software.

Suggested Action

Before performing a new run, power cycle the instrument.

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

• Power cycle the instrument.

Before performing a new run, you should

• Disconnect and reconnect the USB cable.

• Power cycle the instrument.

201 MotNotEnabled

202, 203, 204 MotAtLimit (X, Y, Z)

Due to some mechanical errors the motors were disabled. The motor failed to reach the home position correctly, thus prohibiting it from being enabled.

The X, Y, Z motor has been at one of its limit switches for 5 consecutive polls of the motor position

Before performing a new run, you should

• reseat the plate/plate lid.

• check for incorrect or multiple plate heat seal foil layers.

• check for strain on all motor axes.

• power cycle the instrument.

Before performing a new run, you should

• Check X, Y, Z motor for obstructions.

• Power cycle the instrument.

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Troubleshooting

Code (Decimal) Name

205 XMotMoveTimeout

206 YMotMoveTimeout

Description/Possible

cause

A mechanical error has occurred as the X-axis was unable to reach the target position within the alloted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the Y-axis was unable to reach the target position within the alloted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

Suggested Action

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

207 ZMotMoveTimeout

210 XHomeTimeout

A mechanical error has occurred as the Z-axis was unable to reach the target position within the allotted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the X-axis was unable to reach the home position within the allotted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

Troubleshooting

Code (Decimal) Name

211 YHomeTimeout

212 ZHomeTimeout

Description/Possible

cause

A mechanical error has occurred as the Y-axis was unable to reach the home position within the allotted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the Z-axis was unable to reach the home position within the allotted time of 10 seconds. You may be able to use some data that was acquired during the run, before the failure occurred.

Suggested Action

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

213 MotAtLimit

214 MissingMotor

218 FailedToSetMotorState

219 MotorWhileDoorOpen

This indicates that one of the motors is at its limit.

This indicates a motor component of the instrument is not function correctly or missing.

A communication error has occurred as the motor failed to transition to the next state. You may be able to use some data that was acquired during the run, before the failure occurred.

A motor command was executed when door was still left open or is moving but not fully closed.

Before performing a new run

• Check for motor obstructions.

• Power cycle the instrument.

Before performing a run, Power cycle the instrument. Call Tech Support if the problem persists.

Before performing a new run, power cycle the instrument.

• Check the door position

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Troubleshooting

Code (Decimal) Name

301 PumpInvalidResponse

302 PumpInvalidValue

303 PumpNotInitialized

Description/Possible

cause

A mechanical error has occurred as the pump was not properly. You may be able to use some data that was acquired during the run, before the failure occurred.

A communication error has occurred as the pump received an invalid value that was sent as part of a command. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the pump has been unable to initialize. You may be able to use some data that was acquired during the run, before the failure occurred.

Suggested Action

Before performing a new run, power cycle the instrument.

304 PumpStalled

305 PumpValveStalled

A mechanical error has occurred as the pump has stalled. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the pump showed that its valve has stalled. You may be able to use some data that was acquired during the run, before the failure occurred.

Before performing a new run, power cycle the instrument.

Troubleshooting

Code (Decimal) Name

306 PumpError

307 PumpTimeout

308 PumpResponseGarbled

Description/Possible

cause

A mechanical error has occurred as the pump showed an irrecoverable error. You may be able to use some data that was acquired during the run, before the failure occurred.

A mechanical error has occurred as the pump was unable to become ready within 8 seconds, which is the default allotted time for the pump to be ready. Some data that was acquired during the run, before the failure occurred, may be usable.

Upon connecting to the instrument, the command to retrieve the pump revision received an incorrectly formatted response. Some data that was acquired during the run, before the failure occurred, may be usable.

Suggested Action

Before performing a new run, power cycle the instrument.

312 PumpHomeTimeout

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Before performing a new run, power cycle the instrument.

Troubleshooting

Code (Decimal) Name

316 PumpInvalidVelocity

317 PumpInvalidVolume

Description/Possible

cause

A mechanical error has occurred when trying to issue the move command to a pump that contained an invalid ﬂow rate. Some data that was acquired during the run, before the failure occurred, may be usable.

A mechanical error has occurred when trying to issue the move command to a pump that contained an invalid volume. Some data that was acquired during the run, before the failure occurred, may be usable.

Suggested Action

Before performing a new run, power cycle the instrument.

330 UnhandledFluidStatus

331 OilLevelCritical

332 WasteLevelCritical

An unknown ﬂuid status has occurred causing a ﬂuid error. Some data that was acquired during the run, before the failure occurred, may be usable.

The oil indicator is at a critical level causing a ﬂuid error and must be cleared before the data from the well is acquired. Some data that was acquired during the run, before the failure occurred, may be usable.

The waste indicator is at a critical level causing a ﬂuid error and must be cleared before the data from the well is acquired. Some data that was acquired during the run, before the failure occurred, may be usable.

Before performing a new run -

• Check all bottle levels.

• Close the bottle door.

Before performing a new run -

• Remove and replace the oil bottle

• Close the bottle door.

Before performing a new run

• Remove and replace the waste bottle.

• Close the bottle door.

Troubleshooting

Code (Decimal) Name

403 DAQStopFailed

406 InvalidLEDPower

502 SettingsChecksumError

Description/Possible

cause

The data acquisition mode could not be completed successfully due to a possible communication loss. Some data that was acquired during the run, before the failure occurred, may be usable.

Setting the LED power to an invalid value caused an electrical error. Some data that was acquired during the run, before the failure occurred, may be usable.

The checksum of the persistent storage was incorrect. This could be due a communication loss or an invalid checksum value.

Suggested Action

Before performing a new run, power cycle the instrument.

900 CommandNotImplemented

The instrument does not support the command. This could be due a communication loss or an invalid command.

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Troubleshooting

6.4 User Actions During Run

List of user actions and system actions during a system run.

Table 9: QXDx Droplet Reader actions

User Action

Open the plate lid NO. The lid cannot be opened N/A

Open the bottle door YES

Open the bottle door and replace the oil bottle with an empty bottle

Disconnect the USB cable YES

Is this action possible during a

run?

YES

Waits till the second well acquisition begins, then opens the door. Processes the second well. Pauses the run and warns user with the message Door is open. Fix the problem or abort the run. User can retry after closing the door or can abort the run.

Pauses the run and warns user with the message Door is open. Fix the problem or abort the run. User can retry after replenishing the oil bottle and closing the door or can abort the run.

Waits for 10 mins to reconnect to the instrument. If the cable is reconnected before timeout then the run resumes automatically. If the cable remains disconnected after the retry time limit, then the system pauses the run and warns user with the message 102 CommSPTIFailure error. The user can retry after reconnecting the USB cable and click Continue to restart the run.

System Action

Disconnect the power to the instrument

Bump the plate door YES

YES

Troubleshooting

6.5 Analysis Errors

The possible analysis error that can occur during a run and suggested user actions to ﬁx these analysis errors. The

analysis errors show 2xxx code series.

Code Message Text

2000 Droplet Quality

2001 Assay Phenotype

2002 Not Enough Reference

2003 Replicate Similarity

Description/Possible

Cause

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• Poor sample quality.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• Poor sample quality.

The range did not fall within the set threshold due to the sample concentration being too high or due to poor mixing.

The replicates did not meet the set concentration and limits for variability due to one or more of the following:

• Equal volume were not pipetted into replicate wells.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• Microﬂuidics issue occurred on the AutoDG

Suggested Action

Rerun the sample after thoroughly mixing. If the error persists, call technical support.

Dilute and rerun the sample after thoroughly mixing. If the error persists, call technical support.

Rerun the sample after thoroughly mixing. If the error persists, call technical support.

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Troubleshooting

Code Message Text

2004

2005 ABL Count per sample

Sample Validity (At least one well ok)

Description/Possible

Cause

Both sample wells did not meet the validation parameters due to one or more of the following:

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• An instrument error occurred.

Sample did not meet the minimum ABL copies count due to one or more of the following:

• Poor sample quality.

• Possibly degraded reagents.

Suggested Action

Rerun the sample after thoroughly mixing. If the error persists, call technical support.

• Rerun the sample after thoroughly mixing.

• Request for a new patient sample and rerun tests with the new sample.

• Check the expiration date and storage conditions of the kit lots used for the sample run.

• If the error persists, call technical support.

2006 Thresholding Well Quality

Sample well did not meet the quantitative threshold in ddPCR due to one or more of the following:

• Poor sample quality.

• Possibly degraded reagents.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• An instrument error occurred.

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• Check the expiration date and storage conditions of the kit lots used for the sample run.

• If the error persists, call technical support.

Troubleshooting

Code Message Text

2007 Plate Thresholding

2008

High Positive Control Quality

Description/Possible

Cause

Sample well did not meet the thresholding quality due to one or more of the following:

• Poor sample quality.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

The High Positive Control did not meet concentration limits due to one or more of the following:

• Incorrect sample placement.

• Possibly degraded high positive control.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

Suggested Action

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• If the error persists, call technical support.

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• Check the expiration date and storage conditions of the control sample.

• If the error persists, call technical support.

2009

Low Positive Control Quality

The Low Positive Control did not meet concentration limits due to one or more of the following:

• Incorrect sample placement.

• Possibly degraded low positive control.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• Check the expiration date and storage conditions of the control sample.

• If the error persists, call technical support.

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Troubleshooting

Code Message Text

2010 ~10%IS Calibrator Quality

2011 ~0.1% IS Calibrator Quality

Description/Possible

Cause

The ~10% IS Calibrator did not meet required ratio within range due to one or more of the following:

• Incorrect sample placement.

• Possibly degraded calibrator.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

The ~0.1% IS Calibrator did not meet required ratio within range due to one or more of the following:

• Incorrect sample placement.

• Possibly degraded calibrator.

• Poor mixing - you may not have pipetted thoroughly during sample preparation.

Suggested Action

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• Check the expiration date and storage conditions of the calibrator.

• If the error persists, call technical support.

• Rerun the sample after thoroughly mixing.

• Check for the sample quality.

• Check the expiration date and storage conditions of the calibrator.

• If the error persists, call technical support.

2012 NTC Quality

2013 Negative Control Quality

The sample copy count is greater than maximum copies (1) allowed due to possible contamination.

If the plate failed, decontaminate working area, instruments, and pipettes with bleach and ethanol. Then rerun the plate. If the error persists, call technical support

7 Speciﬁcations

7.1 QXDx AutoDG Speciﬁcations

Consult the table below for the optimal system speciﬁcations of AutoDG.

Figure 11: Instrument Dimensions

Table 10: System Speciﬁcations

Weight 100 lb (45.4 kg)

Size (W x D x H) 26 x 22 x 26” (66 x 56 x 66 cm)

Electrical requirements 100–240 V, 50/60 Hz, 90 W; voltage ﬂuctuations not to exceed +10%

of ratings (for external power supply provided)

Fuse 4 A, 24 V internal (not user serviceable)

Temperature 18–30ºC

Altitude 0–6,560 ft (0–2,000 m)

Humidity 50% max (noncondensing)

Pollution degree 2 (indoor use)

Installation category II (external power supply plugs into standard AC receptacle)

Ventilation requirements 5” (13 cm) left and right of machine and 2” (5 cm) behind should be

unobstructed for proper ventilation

7.2 QXDx Droplet Reader Speciﬁcations

Consult the table below for the optimal system speciﬁcations for QXDx Droplet Reader.

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Speciﬁcations

Figure 12: Instrument Dimensions

Table 11: System Speciﬁcations

Weight 56.6lb. (26 kg)

Size (W x D x H) 26 x 20.5 x 11.5” (660 x 521 x 292 cm)

Electrical requirements 100–240 V, 50/60 Hz, 1 A; voltage ﬂuctuations not to exceed

+10% of ratings (for external power supply provided); fuse: T5AV, 250 V

Temperature 18–30ºC

Altitude 0–6,560 ft (0–2,000 m)

Humidity 85% max(noncondensing)

Pollution degree 2(indoor use)

Installation category II(external power supply plugs into standard AC receptacle)

Ventilation requirements 5” (12 cm) left and right of machine and 10” (25 cm) behind

should be unobstructed for proper ventilation

Table 12: Performance Speciﬁcations

Starting sample size 25 μl

QXDx Automated Droplet Generator, IVD capacity

QXDx Droplet Reader, IVD capacity 1–96 samples

Sample illumination Light-emitting diodes

Sample detection Multi-pixel photon counter

1–8 samples/cartridge 20,000 Droplets per 20μl sample

Detection channels FAM (EvaGreen), HEX (VIC)

Linear dynamic range 5 orders of magnitude

Precision ±10%

Droplets per 96-well plate, million ~1.5

8 Advanced Administration

The Manage Users and Configure System modules are only available to the system administrator. These modules

enable the system administrator to manage users and conﬁgure system settings.

8.1 Changing the Password

Change an existing password for the current user.

8.1.1 Procedure

1. Open and login to the QXDx software using the administrator credentials.

2. Click User > Change Password

3. Enter the Old Password.

4. Enter the New Password and reenter to conﬁrm.

5. Click OK to save the new password or click Cancel to quit without saving.

8.2 Adding, Editing and Deleting Users

As an administrator, you can manage users of the system.

8.2.1 Procedure

1. Open and login to the QXDx software using the administrator credentials.

2. Click User > Manage Users

3. Do one of more of the following:

• Click on a new row to add a new user. Enter User Name, Full Name, Password, and Role.

• For an existing user, click a cell to edit and replace with new value.

• To delete a user, in that user row, click the Remove checkbox to select it.

4. Click OK to exit the screen and save changes made.

5. Enter User Name, Full Name, Password, and Role.

8.3 Managing Assays

As an administrator, you can manage assays on the system. Managing assays allows user to upload new ‘.APF’ – assay protocol ﬁle.

8.3.1 Procedure

1. Open and login to the QXDx software using the administrator credentials.

2. Click Conﬁgure System > Manage Assays.

3. Click Add Assay to import a new APF into the software

a. Find the APF ﬁle in your ﬁle system on the computer.

b. Click open to import the ﬁle

4. Click Remove Assay by clicking on the list of Assays in the software

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Advanced Administration

8.4 Conﬁguring Database Connection

8.4.1 Procedure

1. Open and login to the QXDx software using the administrator credentials.

2. Click Conﬁgure System > Database Conﬁguration

3. Enter the hostname or IP address in the Acquisition Machine Name ﬁeld.

4. Enter the Port Number.

5. Click Test Connection to check if the conﬁguration works correctly.

6. Click Save to save changes and close the window. Otherwise click Restore to cancel changes.

8.5 Backing Up and Restoring Data

As a system administrator, you may back-up and restore from back-up.

8.5.1 About this task

Always make sure to backup before restoring from another backup. Restoring will replace the current database with the restored backup.

8.5.2 Procedure

1. Open and login to the QXDx software using the administrator credentials.

2. Click Conﬁgure System > Backup Now

3. Browse to the location you wish to save the backup and click OK. The backup ﬁle is saved to the selected location.

4. To restore from a saved backup, Click Configure System > Restore Backup.

5. Click Yes on the dialog that opens to conﬁrm that you wish to replace the current database with the restored copy.

8.6 Lab Conﬁguration

As a system administrator, you may setup and customize your laboratory information, which will appear readily in reports.

8.6.1 About this task

Upon installation of instrument and software, remember to setup your laboratory details. They are editable by an administrator following initial setup.

8.6.2 Procedure

1. Open and login to the QXDx Analysis software using the administrator credentials.

2. Click Conﬁgure System > Lab Conﬁguration

3. Input following details: Lab Name, Lab Address

4. Select Test/Assay (i.e. BCR-ABL), Enter generic testing comments made visible in the report.

Advanced Administration

8.7 Event Log

As a system administrator, you may generate an event log report for your audit.

8.7.1 About this task

Event Log report maybe valuable information while troubleshooting or audit of changes actions/ comments added to any run by any user.

8.7.2 Procedure

1. Open and login to the QXDx Analysis software using the administrator credentials.

2. Click Reports > Event Log

3. Selects and Time for audit of activities/actions performed.

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Advanced Administration

NOTES:

Index

Symbols

96-well PCR plate

loading .................................................................. 2-8

placing into the plate holder ................................. 3-1

Aborting a run ............................................................ 2-12

Adding lot information ................................................. 4-2

Administration, advanced ............................................ 8-1

Analysis Errors .......................................................... 6-13

Applied Well Settings................................................... 4-4

Assays, Managing ....................................................... 8-1

AutoDG ........................................................................1-2

about ..................................................................... 2-1

AutoDG Pipet Tips, loading ......................................... 2-7

Automated Droplet Generation Oil

bottle loading ........................................................ 2-2

loading .................................................................. 2-9

Automated Droplet Generator ..................................... 1-2

Backing up and restoring data .................................... 8-2

Bottle of Oil, loading .................................................... 2-2

Droplet Plate assembly, loading .................................. 2-9

Droplet plate, creating ................................................. 2-5

Droplet Reader ............................................................ 1-2

Droplet Reader Oil, replacing ...................................... 5-4

Editing lot information .................................................. 4-2

Errors

analysis ............................................................... 6-13

Droplet Reader System ........................................ 6-4

Instrument and Mechanical .................................. 6-3

restarting run after ................................................ 6-1

System, restarting a run after ............................... 6-2

Event Log .................................................................... 8-3

Exporting Run Logs .................................................. 2-16

Firmware, updating ..................................................... 5-2

Flush Instrument ......................................................... 5-4

Indication for Use ........................................................1-1

Instrument deck lighting .............................................. 2-4

Instrument errors ......................................................... 6-3

Intended Use ............................................................... 1-1

Calibrators ................................................................... 5-5

Components, System .................................................. 1-3

Conﬁguration, lab ........................................................ 8-2

Conﬁguring database connection ............................... 8-2

Consumables, disposition after power loss ................. 2-3

Controls ....................................................................... 5-5

D-10, general description ............................................ 1-1

Data, backing up and restoring ................................... 8-2

Database Connection, conﬁguring .............................. 8-2

DG32™ AutoDG Cartridges, loading .......................... 2-7

Droplet Digital PCR Workﬂow ..................................... 1-1

Lab Conﬁguration ........................................................ 8-2

Light Indicators ............................................................ 3-3

96-well PCR plate ................................................. 2-8

AutoDG Pipet Tips ................................................ 2-7

Automated Droplet Generation Oil .......................2-9

DG32™ AutoDG Cartridges ................................. 2-7

Droplet Plate assembly ......................................... 2-9

Log

Event ..................................................................... 8-3

maintenance ......................................................... 5-2

Lot Information, adding or editing ................................ 4-2

Index

Maintenance ................................................................ 5-1

Flush Instrument ................................................... 5-4

Log 5-2

Prime Instrument .................................................. 5-4

routines, performing .............................................. 5-4

Mechanical errors ........................................................ 6-3

Oil Purge Reservoir, cleaning......................................5-3

Password, changing .................................................... 8-1

Performance Speciﬁcations......................................... 7-2

Plate (droplet), creating ............................................... 2-5

Plate Layout, sample ................................................... 2-1

Plate, sealing ............................................................. 2-13

Power loss ................................................................... 2-3

Prime Instrument ......................................................... 5-4

Quality Control ............................................................. 5-5

QXDx Droplet Reader Speciﬁcations .......................... 7-1

QXDx™ Acquisition software ...................................... 4-1

QXDx™ Analysis Software ......................................... 4-1

QXDx™ Automated Droplet Generator (AutoDG) ...... 1-2

about ..................................................................... 2-1

speciﬁcations ........................................................ 7-1

QXDx™ Droplet Reader .............................................. 1-2

System errors ....................................................... 6-4

using ..................................................................... 3-1

QXDx™ Droplet Reader System Errors...................... 6-4

QXDx™ Software, about ............................................. 4-1

viewing .................................................................. 4-5

Run

aborting ............................................................... 2-12

restarting after an error ......................................... 6-1

restarting after system error ................................. 6-2

starting .................................................................. 2-3

starting a new run ................................................. 4-4

user actions during ............................................. 6-12

Run Logs

accessing ............................................................ 2-14

exporting ............................................................. 2-16

Sample Plate Layout ...................................................2-1

Sealing the Plate ....................................................... 2-13

Setup and Operation ................................................... 1-2

Software ...................................................................... 4-1

QXDx™ Acquisition .............................................. 4-1

QXDx™ Analysis .................................................. 4-1

updating ................................................................ 5-2

Speciﬁcations

performance ......................................................... 7-2

QXDx AutoDG ......................................................7-1

QXDx Droplet Reader .......................................... 7-1

system .................................................................. 7-2

System .................................................................. 7-1

Starting a New Run ..................................................... 4-4

Starting a Run ............................................................. 2-3

System

components .......................................................... 1-3

setup and operation .............................................. 1-2

speciﬁcations ........................................................ 7-1

System Error, restarting a run after ............................. 6-2

Removing waste .......................................................... 5-4

Reports ........................................................................ 4-7

Results

printing .................................................................. 4-5

Technical Assistance ................................................... 1-4

Thermal cycler speciﬁcations ...................................... 1-2

Touch screen status indicators .................................... 2-4

Troubleshooting ........................................................... 6-1

Index

Universal Kit components ........................................... 1-4

User Actions During Run........................................... 6-12

Users, adding, editing, and deleting ............................ 8-1

Waste, removing.......................................................... 5-4

Well Editor, using ......................................................... 4-4

12010873revA QXDx AutoDG Droplet Digital PCR System Instruction Manual I-3I-2 QXDx AutoDG Droplet Digital PCR System Instruction Manual 12010873revA

Bio-Rad Laboratories, Inc.

For further information, please contact the Bio-Rad office nearest you or visit our website at www.bio-rad.com/diagnostics

Clinical Diagnostics Group

4000 Alfred Nobel Drive Hercules, California 94547 Telephone (510) 724-7000 FAX (510) 741-6373 www.bio-rad.com/diagnostics

Australia, Bio-Rad Laboratories Pty. Ltd., Level 5, 446 Victoria Road, Gladesville NSW 2111 • Phone 61-2-9914-2800 • Telefax 61-2-9914-2888 Austria, Bio-Rad Laboratories Ges.m.b.H., Hummelgasse 88/3-6, A-1130 Vienna • Phone 43-1-877-8901 • Telefax 43-1-876-5629 Belgium, Bio-Rad Laboratories N.V., Winninglaan 3, BE-9140 Temse • Phone +32 (3)710-53-00 • Telefax +32 (3)710-53-01 Brazil, Bio-Rad Laboratórios Brasil Ltda, Rua Alfredo Albano da Costa, 100, Lagoa Santa - MG, CEP: 33400-000 • Phone +55 (31)3689-6600 • Telefax +55 (31)3689-6611 Canada, Bio-Rad Laboratories, Ltd., 2403 Guénette Street, Montréal, Québec H4R 2E9 • Phone 1-514-334-4372 • Telefax 1-514-334-4415 China, Bio-Rad Laboratories Shanghai Ltd., 3rd Floor, #18 Dong Fang Road, Bldg E, Poly Plaza, Pudong, Shanghai, PRC 200120 • Phone 86-21-61698500 • Telefax 86-21-61698599 Czech Republic, Bio-Rad spol. s r.o., Nad ostrovem 1119/7, 147 00 Prague 4 • Phone 420-241-430-532 • Telefax 420-241-431-642 Denmark, Bio-Rad Laboratories, Symbion Science Park, Fruebjergvej 3, DK-2100 Copenhagen East • Phone +45-4452-1000 • Telefax +45-4452-1001 Finland, Bio-Rad Laboratories, Linnanherrankuja 16, FIN-00950 Helsinki • Phone 358-9-804-22-00 • Telefax 358-9-7597-5010 France, Bio-Rad, 3 boulevard Raymond Poincaré, 92430 Marnes-la-Coquette • Phone 33-1-47-95-60-00 • Telefax 33-1-47-41-91-33 Germany, Bio-Rad Laboratories GmbH, Heidemannstrasse 164, D-80939 Munich • Phone +49 (0)89-318-840 • Telefax +49 (0)89-31884-100 Greece, Bio-Rad Laboratories M E.P.E, 2-4 Mesogeion Street, Fourth Floor 115 27 Athens • Phone 30-210-7774396 • Telefax 30-210-7774376 Hong Kong, Bio-Rad Pacific Ltd., Unit 1101, 11/F DCH Commercial Centre, 25 Westlands Road, Quarry Bay • Phone 852-2789-3300 • Telefax 852-2789-1290 Hungary, Bio-Rad Hungary Ltd., H-1082 Budapest, Futo Street 47-53, Hungary • Phone +36-1-459-6100 • Telefax +36-1-459-6101 India, Bio-Rad Laboratories (India) Pvt. Ltd., Bio-Rad House, 86-87, Udyog Vihar Phase IV, Gurgaon, Haryana 122 015 • Phone 1800-180-12 24 • Telefax 91-124-2398115 Israel, Bio-Rad Laboratories Ltd., 14 Homa Street, New Industrial Area, Rishon Le Zion 75655 • Phone 972-3-9636050 • Telefax 972-3-9514129 Italy, Bio-Rad Laboratories S.r.l., Via Cellini 18/A, 20090 Segrate, Milan • Phone +39-02-216091 • Telefax +39-02-21609553 Japan, Bio-Rad Laboratories K.K., Tennoz Central Tower 20F, 2-2-24 Higashi-Shinagawa, Shinagawa-ku, Tokyo 140-0002 • Phone 81-3-6361-7070 • Telefax 81-3-5463-8481 Korea, Bio-Rad Korea Ltd., 10th Floor, Hyunjuk Building, 832-41, Gangnam-gu, Seoul 135-080 • Phone 82-2-3473-4460 • Telefax 82-2-3472-7003 Mexico, Bio-Rad, S.A., Avenida Eugenia 197, Piso 10-A, Col. Nar varte, C.P. 03020 Mexico, D.F. • Phone +52 (55)5488-7670 • Telefax +52 (55)1107-7246 The Netherlands, Bio-Rad Laboratories B.V., Postbus 222, 3900 AE Veenendaal • Phone +31-318-540666 • Telefax +31-318-542216 New Zealand, Bio-Rad New Zealand, 189 Bush Road Unit B, Albany, Auckland • Phone 64-9-415-2280 • Telefax 64-9-415-2284 Norway, Bio-Rad Laboratories, Nydalsveien 33, 0484 Oslo • Phone +47-23-38-41-30 • Telefax +46(0)8-5551-2780 Poland, Bio-Rad Polska Sp. z o.o., Nakielska Str. 3, 01-106 Warsaw • Phone 48-22-3319999 • Telefax 48-22-3319988 Portugal, Bio-Rad Laboratories, Lda., Edificio Prime, Ave. Quinta Grande, 53 – Fracção 3B Alfragide 26114-521 Amadora • Phone 351-21-472-7700 • Telefax 351-21-472-7777 Russia, Bio-Rad Laboratorii, 117105, Russian Federation, Moscow, Varshavskoe sh., 9, Bldg., 1B • Phone +7-495-721-1404 • Telefax +7-495-721-1412 Singapore, Bio-Rad Laboratories (Singapore) Pte. Ltd., 27 International Business Park, #01-02 iQuest @IBP, Singapore 609924 • Phone 65-6415-317 0 • Telefax 65-6415-3189 South Africa, Bio-Rad Laboratories (Pty) Ltd., 34 Bolton Road, Parkwood, Johannesburg 2193 • Phone 27-11-442-85-08 • Telefax 27-11-442-85-25 Spain, Bio-Rad Laboratories, S.A., C/ Caléndula, 95, Edificio M. Miniparc II, El Soto de la Moraleja, 28109 Madrid • Phone 34-91-590-5200 • Telefax 34-91-590-5211 Sweden, Bio-Rad Laboratories A.B., Box 1097, Solna Strandväg 3, SE-171 54, Solna • Phone +46-8-555-127-00 • Telefax +46-8-555-127-80 Switzerland, Bio-Rad Laboratories AG, Pra Rond 23, CH-1785 Cressier • Phone +41 (0)26-67 4-55-05/06 • Telefax +41 (0)26-674-52-19 Taiwan, Bio-Rad Laboratories Taiwan Ltd., 14F-B, No. 126 Nan-King East Road, Sec. 4, Taipei, Taiwan 10546 R.O.C. • Phone 886-2-2578-7189 • Telefax 886-2-2578-6890 Thailand, Bio-Rad Laboratories Ltd., 1st & 2nd Floor, Lumpini I Bldg., 239/2 Rajdamri Road., Lumpini, Pathumwan, Bangkok 10330 • Phone 662-651-8311 • Telefax 662-651-8312 United Kingdom, Bio-Rad Laboratories Ltd., Bio-Rad House, Maxted Road, Hemel Hempstead, Herts HP2 7DX • Phone +44 (0)20-8328-2000 • Telefax +44 (0)20-8328-2550

Bio-Rad 12010873revA ATMOS C 051 Thorax Operating Instructions

Specifications and Main Features

Frequently Asked Questions

User Manual

Legal Notices

Safety and Regulatory Compliance

Instrument Safety Warnings

PPE (Personal Protective Equipment) Training

Transporting the Instrument

Electrostatic Discharge

Radiated Emissions

Sensitivity to Electromagnetic Fields

1.1 Introduction

1.2 Intended Use and Indication for Use

1.4 Setting Up and Operating the System

1.5 System Components

Technical Assistance

2.1 Sample Plate Layout

2.3 Starting a Run on AutoDG

2.4 Sealing the Plate after a Run on AutoDG

2.5 Accessing Run Logs

2.6 Exporting an AutoDG Run Log

3 Using the QXDx Droplet Reader

3.2 Light Indicators

4.1 Adding or Editing Lot Information

4.2 Starting a New Run

4.3 Using the Well Editor

4.4 Viewing and Printing of Results

4.5 Reports

5.1 Updating the Software and Firmware

5.2 Cleaning the Oil Purge Reservoir

5.3 Replacing Droplet Reader Oil and Removing Waste

5.4 Performing Maintenance Routines

5.5 Quality Control

6 Troubleshooting

6.1 Restarting a Run on AutoDG after an Error

6.2 Restarting a Run on AutoDG After a System Error

6.3 Instrument and Mechanical Errors

6.4 User Actions During Run

6.5 Analysis Errors

8 Advanced Administration

8.1 Changing the Password

8.2 Adding, Editing and Deleting Users

8.3 Managing Assays

8.5 Backing Up and Restoring Data

8.7 Event Log

Index