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MGI DNBSEQ-G400 User Manual

Genetic sequencer
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Part No.: H-020-000093-00
Address:
Building 24, Stage 3.1, BioLake Accelerator, No.388, 2nd Gaoxin Road, East Lake
High-Tech Development Zone, 430075, Wuhan, P.R.China
E-mail:
MGI-service@mgi-tech.com
Website:
www.mgi-tech.com
Genetic Sequencer
DNBSEQ-G400
W u h a n M G I T e c h C o . , L t d .
Version: 5.0

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  • Page 1 Part No.: H-020-000093-00 Genetic Sequencer DNBSEQ-G400 Version: 5.0 Address: Building 24, Stage 3.1, BioLake Accelerator, No.388, 2nd Gaoxin Road, East Lake High-Tech Development Zone, 430075, Wuhan, P.R.China E-mail: MGI-service@mgi-tech.com W u h a n M G I T e c h C o . , L t d .
  • Page 2 MGI. Any unauthorized person should not use this manual. MGI does not make any promise of this manual, including (but not limited to) any commercial of special purpose and any reasonable implied guarantee. MGI has taken measures to guarantee the correctness of this manual.

  • Page 3: Revision History

    Revision history 版本 版本 Date Version June 1, 2022 March 5, 2021 Revision Revision March 17, 2020 August 23, 2019 Initial release Initial release October 30, 2018...

  • Page 4: Table Of Contents

    Contents Safety Conventions General safety Electrical safety Mechanical safety Components safety Biological safety Symbols Device Label Packaging Device overview Intended use Working principle Structural composition Basic components Front view Rear view Left view Right view Flow cell compartment Reagent compartment Control software Self-test Main interface...
  • Page 5 Shutdown or restart interface About interface Getting started Preparing the laboratory Site requirements Operating environment requirements Network requirements Operating environments of the computer Software security Inspecting the device Preparing the power supply Preparing peripheral devices Preparing DNBs Preparing the reagent cartridge and flow cell Reagent cartridge and sequencing flow cell Cleaning cartridge and washing flow cell Installing the device...
  • Page 6 Sequencing interface Disposing of reagent cartridge and flow cell Performing a wash Performing a regular wash Performing a maintenance wash Maintaining the device Maintaining the main unit Maintaining the power supply Maintaining the flow cell stage Overview of flow cell stage Cleaning the flow cell stage Replacing the sealing gasket Maintaining the waste container...
  • Page 7 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

  • Page 8: Safety

    Safety This chapter describes basic safety information about the device. Carefully read and understand the information before use to ensure correct operations, best performance and personnel safety. Keep this manual at hand for consultation at any time.

  • Page 9: Conventions

    Conventions The following table describes conventions that are used in this manual: Item Description Indicates that the operator should operate the device by following the instructions. Otherwise, it might result in personal injury. Indicates that the operator should operate the device by following the instructions.

  • Page 10: Electrical Safety

    Maintain the device by following the instructions in Maintaining the device on Page 53 to ensure best performance. Otherwise, it might result in device malfunction or even personal injury. Only the technical support authorized by the manufacturer or the qualified, trained personnel can unpack, install, move, and maintain the device.

  • Page 11: Mechanical Safety

    Do not use the device in close proximity to the sources of strong electromagnetic fields, such as unshielded sources of radiated emissions. Radiated signals can reduce the accuracy of the results. Ensure that the device is properly grounded, and the grounding resistance is less than 4 Ω.

  • Page 12: Biological Safety

    Biological safety Chemicals in reagents and waste might cause personal injury through contact with the skin, eyes, and mucosa. Follow the safety standards of your laboratory and wear protective equipment (such as laboratory coat, protective glasses, mask, and gloves) when performing a sequencing run. If you accidentally splash the reagent on the skin or into eyes, immediately flush the affected area with large amounts of water, and get medical aid immediately.

  • Page 13: Label

    Symbol Name Description Warning; Indicates hazards arising from dangerous dangerous voltages. voltage Indicates the terminal of a Protective earth protective earth (ground) electrode. Warns of a hazard from laser Warning; laser beam beam. Indicates the fuse F10AL250V Fuse specification specification. USB 2.0 port USB connection.

  • Page 14: Packaging

    Symbol Name Description Indicates that this device m e e t s t h e re q u i re m e n t s of Directive 2011/65/EU on RoHS mark the restriction of the use of certain hazardous substances in electrical and electronic equipment.
  • Page 15 Symbol Name Description Indicates a medical device F r a g i l e , h a n d l e t h a t c a n b e b r o k e n o r with care d a m a g e d i f n o t h a n d l e d carefully.

  • Page 16: Device Overview

    Device overview This chapter describes the intended use, working principle, structural composition, and basic components of the device.

  • Page 17: Intended Use

    Intended use The device is a sequencing instrument that measures optical and electronic signals of the reporting molecules to decode the sequence information of a piece of DNA or RNA fragment through the use of instrument specific reagents and flow cells imaging hardware, and data analysis software.

  • Page 18: Structural Composition

    The following figure demonstrates how to load DNBs: DNBs Flow cell Decorated sites evenly spread on the flow cell Each site contains a single DNB Figure 2 Loading DNBs The DNB and sequencing reagent are pumped into the sequencing flow cell through the device’s liquid system. Each DNB combines with the fluorescence group.

  • Page 19: Basic Components

    Component Description Gas-liquid Provides the gas-liquid support that is required for the system biochemical reaction. Electric control Controls the electric system. system Reagent storage Provides the reagent storage environment. system Power supply Provides the power supply for the device. system Display system Provides the human-computer interaction interface.
  • Page 20 Name Description Displays the current status of the device: z Green: the device is running. z Blue: the device is in standby status. Status indicator z Red: an error occurs. z Yellow: a warning appears, but the device keeps running. Supporting feet Supports the main unit to ensure stability.

  • Page 21: Rear View

    Rear view Figure 4 Rear view Name Description V e n t i l a t i o n Ventilates the device. outlet Wheel Used for moving the device. Connects to USB devices such as the keyboard, USB 2.0 port mouse, and scanner.

  • Page 22: Left View

    Left view Figure 5 Left view Name Description Flow cell Holds flow cells and controls the temperature compartment for biochemical reactions. You can observe the status of the fluidics Window system and negative pressure gauge through the window. Ventilation inlet Ventilates the device.

  • Page 23: Right View

    Name Description Button of the flow Press to open the flow cell compartment cell compartment door. door Keyboard drawer Holds the keyboard and mouse. Right view Figure 6 Right view...
  • Page 24 Name Description Powers on or off the device. z Switch to the position to power on the Power switch device. z Switch to the position to power off the device. Connects the power cord. Fuses are installed in Power port the port.

  • Page 25: Flow Cell Compartment

    Flow cell compartment Figure 7 Flow cell compartment Name Description Flow cell Press the button of the flow cell compartment door compartment door to open the door. Holds the flow cell B and controls the Flow cell stage B temperature that is required for biochemical reaction.

  • Page 26: Reagent Compartment

    Name Description Holds the flow cell A and controls the Flow cell stage A temperature that is required for biochemical reaction. Flow cell attachment Press to activate the vacuum for attachment button A or release of the flow cell A. Flow cell attachment Press to activate the vacuum for attachment button B...

  • Page 27: Control Software

    Name Description H o l d s t h e re a g e n t c a r t r i d g e a t appropriate temperatures. z Reagent cartridge A is placed on the left. It provides the required reaction components for flow cell Reagent container z Reagent cartridge B is placed on...

  • Page 28: Self-Test

    Self-test After you power on the device and log in to the computer, self-test starts. If the self-test succeeds, the main interface appears. If the self-test fails, perform the following steps: 1. In the main interface, tap , and select Log to check the detailed self-test results that are recorded in the log.
  • Page 29 The following table describes the function of each area or button in the main interface: Name Description Notification area Indicates the warnings, errors, date, and time. Flow cell A Indicates the status of flow cell A and provides operation area wash and sequence options.
  • Page 30 Item Description Temperature of the flow cell stage is outside the normal range. Negative pressure is normal. Negative pressure is outside the normal range. Basecalling is connected. Errors occur in the basecalling connection. Images are being uploaded to the basecalling. This icon is dynamic.

  • Page 31: Log Interface

    Item Description Sufficient space of the waste container. Insufficient space of the waste container. The system runs independently, without being connected to the server on which the ZLIMS software is installed. The system is connected normally to the server on which the ZLIMS software is installed.

  • Page 32: System Settings Interface

    System settings interface You can change system settings in this interface. To open the system settings interface, perform the following steps: 1. Log in to your account. 2. Tap and select Settings. The following table describes the function of controls in the interface: Item Description...

  • Page 33: Shutdown Or Restart Interface

    Item Description Tap to discharge the residual liquid in all fluidics lines to the waste container. Empty fluidics line The fluidics line that is being emptied is highlighted. T a p t o p e r fo r m a s e l f - t e s t fo r t h e Device hardware of the device.

  • Page 34: Getting Started

    Getting started This chapter describes laboratory preparations and sequencing preparations.

  • Page 35: Preparing The Laboratory

    Preparing the laboratory Site requirements z Ensure that the laboratory floor is level and with a gradient of less than 1/200, and the laboratory bench has a weight capacity of over 300 kg (661.4 lb). z Ensure that the laboratory is free of dust, corrosive and flammable gas, heat and wind sources, and vibrations.

  • Page 36: Network Requirements

    z Maximum altitude: 3000 m (9843 ft) z Pollution level: 2 Because the temperature and humidity fluctuations influence the accuracy of the sequencing results, we recommend that you install an air conditioning system and a dehumidifier in the laboratory to maintain appropriate temperature and humidity.

  • Page 37: Inspecting The Device

    z Four USB ports: connect to external USB devices, such as the keyboard, mouse and the quick response (QR) code scanner, or reserved for future use. Access control User account types of the control software include the guest account, standard user account, and advanced user account. For detailed access authorization, contact the technical support.

  • Page 38: Preparing The Power Supply

    Preparing the power supply z To ensure a steady and uninterrupted power supply for the device during operation, we recommend the use of a separate UPS. For details about the UPS installation protocol, consult the UPS supplier. z We recommend that the required power supply of the UPS be no less than 3 kVA (including the power supply of the server).

  • Page 39: Preparing The Reagent Cartridge And Flow Cell

    Preparing the reagent cartridge and flow cell Chemicals in reagents and waste might cause personal injury through contact with the skin, eyes, and mucosa. Follow the safety standards of your laboratory and wear protective equipment (such as laboratory coat, protective glasses, mask, and gloves) when performing a sequencing run. Reagent cartridge and sequencing flow cell Use only the reagent cartridge and flow cell of the manufacturer for the sequencing process.

  • Page 40: Powering On Or Off The Device

    Powering on or off the device z Ensure that the power switch is in the position before connecting to the power supply. z The mains supply socket should be a standard three-prong socket and its protective grounding terminal should be connected to the protective grounding cable of the power supply system.
  • Page 41 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

  • Page 42: Sequencing

    Sequencing This chapter describes the sequencing workflow and washing procedures. Read and follow the instructions to ensure correct operations.

  • Page 43: Sequencing Workflow

    Sequencing workflow The sequencing workflow is as below: Log in Perform a pre-run wash Load the DNB, reagent cartridge, and flow cell Review parameters Start sequencing Perform a wash z Chemicals in reagents and waste might cause personal injury through contact with the skin, eyes, and mucosa.

  • Page 44: Performing A Pre-Run Wash

    4. Log in to the control software with the user name and password that are provided by the manufacturer. Performing a pre-run wash Before each sequencing run, perform a regular wash to flush impurities out and to empty the fluidics line. For details, refer to Performing a regular wash on Page 47 Loading DNBs 20.0°C...
  • Page 45 If there is no QR code on the tube, type the serial number of the tube with the on-screen keyboard or the physical keyboard. 4. Select a barcode range from the list on the right of DNB ID box. to add or remove a line of DNB ID if needed. 5.

  • Page 46: Loading The Reagent Cartridge

    Loading the reagent cartridge 20.0°C Status: Preparing Sequencing cartridge XXXXXXXXXX Step1 Step2 Previous Next Figure 13 Reagent cartridge loading interface Perform the following steps: 1. Place the prepared reagent cartridge close to the device. For details on preparing the reagent cartridge, refer to the relevant reagent kit user manual.

  • Page 47: Loading The Flow Cell

    4. Push the reagent cartridge in the direction of the arrow shown on the cartridge into the reagent compartment until it stops. Figure 14 Loading the reagent cartridge 5. Close the reagent compartment door. 6. Tap Next. Loading the flow cell 20.0°C Status: Preparing Flow cell ID:...
  • Page 48 Perform the following steps: 1. Press the button of the flow cell compartment door to open the door. 2. Wipe the surface of the aluminum chuck of the flow cell stage with a clean cloth moistened with 75% ethanol, and then let it air- dry.
  • Page 49 After the flow cell is securely seated, do not move it again. Moving the flow cell might cause the sealing gaskets to misalign with holes of the fluidics line. Figure 17 Loading the flow cell If the flow cell is not absorbed properly, wipe the flow cell stage and the back of the flow cell with a clean cloth moistened with 75% ethanol, and then let it air-dry.

  • Page 50: Reviewing Parameters

    Reviewing parameters 20.0°C Status: Preparing Review Item Content User name xxxx DNB ID xxxxxxxx Sequencing cartridge ID xxxxxxxxxx Flow cell ID xxxxxxxxxx Recipe xxxx Start phase Previous Start Figure 18 Parameter review interface Carefully check each item in the review interface, and do one of the following: z If you find errors, tap Previous to return to the previous interface and reset parameters.

  • Page 51: Performing A Sequencing Run

    Performing a sequencing run z Ensure that all compartment doors are closed. Sequencing run cannot be started when the reagent compartment door is open. z Do not open any compartment door on the device during sequencing, to prevent damage to the device and adverse effects on sequencing results. z Do not open the reagent compartment door during sequencing, to avoid adverse effects on sequencing results.
  • Page 52 Item Description Shows the row of the flow cell lane that is being imaged, and the total rows. Shows the column of the flow cell lane that is being Column imaged, and the total columns. Tap it to pause, and tap it again to resume sequencing. Tap it and a confirmation dialog box appears.
  • Page 53 Performing a wash Chemicals in reagents and waste might cause personal injury through contact with the skin, eyes, and mucosa. Follow the safety standards of your laboratory and wear protective equipment (such as laboratory coat, protective glasses, mask, and gloves) when performing a sequencing run. z We do not recommend that you use other disinfectants or wash solutions except for those that are mentioned in this manual.
  • Page 54 Wash type Wash solution Frequency 1 M NaCL and 0.05% Tween-20 for well No.15, and 0.05% Tween-20 for other wells (First time: maintenance wash) 0.1 M NaOH z For SE sequencing: every week (Second time: Maintenance z For PE sequencing: after each maintenance wash) wash sequencing run...
  • Page 55 Or after sequencing, tap Wash in the sequencing completed interface. 20.0°C Status: Idle Sequencing Completed Click ’Wash’ and change to a cleaning cartridge Step1 Step2 Wash Figure 19 Sequencing completed interface...
  • Page 56 2. In the wash interface, select Regular from the Wash type list. 20.0°C Status: Preparing Wash type: Regular Step1 Step2 Step3 Back Wash Figure 20 Wash interface You can tap Back to return to the main interface. 3. Prepare the tube and cleaning cartridge. For details, contact the technical support.

  • Page 57: Performing A Maintenance Wash

    7. After wash, remove the washing flow cell, tube, and cleaning cartridge. 8. Tap Back to return to the main interface. 9. Store the washing flow cell at room temperature. The washing flow cell can be reused for only one month. Dispose of the flow cell according to local regulations and safety standards of your laboratory.
  • Page 58 6. After the wash starts, open the flow cell compartment door, and check whether the wash solution passes through the flow cell. 7. After wash, replace the cartridge and tube with new ones, and tap Wash. Repeat step 3-5 to perform the second time wash. 8.
  • Page 59 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

  • Page 60: Maintaining The Device

    Maintaining the device This chapter describes maintenance procedures of the device and its parts. Perform maintenance regularly to ensure that the device runs smoothly.

  • Page 61: Maintaining The Power Supply

    Maintaining the main unit Perform the following maintenance when the device is powered off: z Every month, clean the surface (including the touch screen) of the device with a 75% alcohol wipe. Ensure that the surface is free of DNBs, reagents, blood, and saliva. z We do not recommend that you use other disinfectants or wash solutions except for those that are mentioned in this manual.
  • Page 62 Maintaining the flow cell stage Overview of flow cell stage Figure 21 Flow cell stage Name Name Sealing gasket Vacuum inlet Aluminum chuck Vacuum adsorption slot Figure 22 Front view of the flow cell Name Alignment hole...
  • Page 63 Name Location of the QR code Figure 23 Rear view of the flow cell Name Silicon chip Cleaning the flow cell stage Perform cleaning and maintenance for the flow cell stage before each use. Failure to do so might affect the attachment of flow cell to the chuck.
  • Page 64 4. Use a dust remover to carefully blow particulate matter and dust from the surface of the silicon chip and aluminum chuck until they are clean. 5. Press the flow cell attachment button on the flow cell stage. 6. Place the flow cell on the flow cell stage. Ensure that the front side of flow cell is facing upward, and the QR code is on the right.
  • Page 65 Perform the following steps: 1. Remove the sealing gaskets both on the left and right with tweezers. Figure 24 Removing the sealing gaskets 2. Install new gaskets with tweezers. Ensure that the top of gasket is facing up as shown, and gaskets are seated securely and flatly. Maintaining the waste container The waste container is connected to the device through tubes.

  • Page 66: Troubleshooting

    3. Pour the waste into an appropriate waste container, and dispose of the waste according to local regulations and safety standards of your laboratory. 4. Add sufficient laboratory-grade water into the waste container, attach the lid back onto the container if necessary, and gently swirl it until all inner walls are cleaned.
  • Page 67 Problem Possible cause Recommended action 1. P e r fo r m a s e l f - t e s t i n t h e z The system maintenance interface. parameters C h e c k t h e r e c o r d o f t h e are not set hardware that fails the self-test.

  • Page 68: Storage And Transportation

    Problem Possible cause Recommended action z The flow cell is not attached 1. Install the washing flow cell properly. and perform wash procedures. z The flow cell C h e c k w h e t her a s t rin g o f is not securely bubbles pass through the flow After...

  • Page 69: Disposal Of The Device

    Disposal of the device The service life of this device is seven years, which is determined by the simulated service life evaluation method. For the date of manufacture, refer to the label on the device. Perform the maintenance according to the requirements mentioned in this manual.

  • Page 70: Specifications

    Specifications Item Description The device not in IVDD annex II and not for Category self-testing/performance evaluation Laser classification of the Class 1 laser product device 1086 mm × 756 mm × 710 mm Dimensions (42.8 inches × 29.8 inches × 28 inches) Net weight Approximately 193 kg (425.5 lb) z Type: LCD...
  • Page 71 Item Description z Temperature: -20 ℃ to 50 ℃ (-4 ℉ to 122 ℉ ) z Relative humidity: 15% RH to 90% RH, Transportation/Storage non-condensing environment requirements z Atmospheric pressure: 70 kPa to 106 z Maximum altitude: 3000 m (9843 ft)

  • Page 72: Compliance Information

    Compliance information The device complies with following standards: Item Standard z IEC 61326-1:2020 Electrical equipment for measurement, control and laboratory use – EMC requirements – Part 1: General requirements Electromagnetic Compatibility z IEC 61326-2-6:2020 (EMC) Electrical equipment for measurement, control and laboratory use –...
  • Page 73 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

  • Page 74: Performance Specifications

    Performance specifications To comprehensively evaluate the accuracy and reproducibility of the device for DNA sequencing of different DNBs and DNA sizes, the national DNA references from different sources of DNBs (human, bacteria and virus), different genome sizes and reference materials for GC content are sequenced in three times.
  • Page 75 Reference Concentration Repetition Accuracy rate GC-rich bacteria DNA 100 ng 99.74% GC-rich bacteria DNA 100 ng 99.75% GC-rich bacteria DNA 100 ng 99.74% GC-rich bacteria DNA precision 0.011% HPV11 DNA 2 μg 99.79% HPV11 DNA 2 μg 99.77% HPV11 DNA 2 μg 99.77% HPV11 DNA...
  • Page 76 The test results are as below: Table 4 Test results of “genetic sequencer precision manufacturer references” Experiment Accuracy rate Precision rate Accuracy: Based on the default operation and analysis process, obtain the number of mismatched bases by comparing the sequencing z Experiment 1: results with the 99.77%...
  • Page 77 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

  • Page 78: Manufacturer Information

    Manufacturer information Manufacturer Wuhan MGI Tech Co., Ltd. Building 24, Stage 3.1, BioLake Accelerator, No.388, 2nd Gaoxin Road, East Lake High- Address Tech Development Zone, 430075, Wuhan, P.R.China Technical support Wuhan MGI Tech Co., Ltd. Technical support E-mail MGI-service@mgi-tech.com...
  • Page 79 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...
  • Page 80 European representative information Name Shanghai International Holding Corp. GmbH (Europe) Address Eiffestrasse 80, 20537 Hamburg, Germany...
  • Page 81 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...
  • Page 82 Index About interface 26 anti-shock 30 anti-tilt labels 30 Barcode settings 26 Biological safety 5 Cleaning cartridge 32 combinatorial probe-anchor synthesis 10 computer 29 Disposal 62 electromagnetic environment 3 Flow cell compartment 15 laser 2 Laser classification 63 fluidics line 3...
  • Page 83 fuse 4 import barcode 25 import or export the data 25 in vitro diagnosis 3 library preparation reagent kit 31 LIMS software 24 Loading DNBs 37 Loading the flow cell 40 Loading the reagent cartridge 39 Log interface 24 Logging in 36 Main interface 21 Maintenance interface 25 maintenance wash 32...
  • Page 84 pre-run wash 37 reagent compartment 13 regular wash 32 sealing gasket 57 Shutdown or restart interface 26 Status area 22 storage space 43 Symbols 5 System settings interface 25 Troubleshooting 59 Upload 25 wash solutions and frequencies 46 waste container 58 ZLIMS 24...
  • Page 85 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

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