BioNano Genomics Saphyr 60325 Manual de usuario

For Research Use Only. Not for use in diagnostic procedures.

Saphyr® System User Guide

for Saphyr P/N 60325

Document Number: 30247

Document Revision: A

30247 Rev A, Saphyr System User Guide for Saphyr P/N 60325 Page 2 of 43

Table of Contents

Legal Notice ............................................................................................................................. 3

Revision History ...................................................................................................................... 4

Chapter 1: Overview................................................................................................................ 5

Introduction..............................................................................................................................5

Features...................................................................................................................................5

Workflow..................................................................................................................................5

Prepare Sample.......................................................................................................................5

Chapter 2: Getting Started...................................................................................................... 6

Start the Saphyr Instrument.....................................................................................................6

Laser Safety Light....................................................................................................................6

Instrument Status Light............................................................................................................7

ICS Home Screen Options.......................................................................................................7

Chapter 3: Configure Analysis Settings in Bionano Access ............................................... 8

Chapter 4: Prepare Chip.......................................................................................................... 9

Load Sample on Saphyr Chip..................................................................................................9

Saphyr Clip Care ...................................................................................................................12

Chapter 5: Perform Run........................................................................................................ 13

Insert Saphyr Chip.................................................................................................................13

Configure Run........................................................................................................................15

Chip and Flowcell States .......................................................................................................18

Pausing a Run to Insert a New Chip and/or Remove a Completed Chip...............................19

Pausing the Run to Rehydrate the Chip.................................................................................22

Stopping the Run...................................................................................................................23

Remove Chip(s).....................................................................................................................24

Chapter 6: Analyze Data........................................................................................................ 25

Data Transfer for Analysis .....................................................................................................25

Chapter 7: Maintenance........................................................................................................ 26

Clean Saphyr Clip Plugs........................................................................................................26

Clean the Objective Lens.......................................................................................................26

Replace Air Filter ...................................................................................................................27

Appendix A............................................................................................................................. 28

Appendix B............................................................................................................................. 31

Appendix C............................................................................................................................. 34

Appendix D............................................................................................................................. 36

Appendix E............................................................................................................................. 37

Appendix F............................................................................................................................. 39

Appendix G ............................................................................................................................ 40

Appendix H............................................................................................................................. 41

Additional Resources............................................................................................................ 42

Technical Assistance............................................................................................................ 43

30247 Rev A, Saphyr System User Guide for Saphyr P/N 60325 Page 3 of 43

Legal Notice

For Research Use Only. Not for use in diagnostic procedures.

This material is protected by United States Copyright Law and International Treaties. Unauthorized use of this

material is prohibited. No part of the publication may be copied, reproduced, distributed, translated, reverse-

engineered or transmitted in any form or by any media, or by any means, whether now known or unknown,

without the express prior permission in writing from Bionano Genomics. Copying, under the law, includes

translating into another language or format. The technical data contained herein is intended for ultimate

destinations permitted by U.S. law. Diversion contrary to U. S. law prohibited. This publication represents the

latest information available at the time of release. Due to continuous efforts to improve the product, technical

changes may occur that are not reflected in this document. Bionano Genomics reserves the right to make

changes in specifications and other information contained in this publication at any time and without prior notice.

Please contact Bionano Genomics Customer Support for the latest information.

BIONANO GENOMICS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED

OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A

PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL BIONANO

GENOMICS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON

ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL

DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED

TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT BIONANO

GENOMICS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

Patents

Products of Bionano Genomics may be covered by one or more U.S. or foreign patents.

Trademarks

The Bionano Genomics logo and names of Bionano Genomics products or services are registered trademarks or

trademarks owned by Bionano Genomics in the United States and certain other countries.

Bionano Genomics®, Saphyr®, Saphyr Chip®, and Bionano Access® are trademarks of Bionano Genomics, Inc.

All other trademarks are the sole property of their respective owners.

No license to use any trademarks of Bionano Genomics is given or implied. Users are not permitted to use these

trademarks without the prior written consent of Bionano Genomics. The use of these trademarks or any other

materials, except as permitted herein, is expressly prohibited and may be in violation of federal or other applicable

laws.

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Revision History

Revision

Notes

Initial Release

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Chapter 1: Overview

Introduction

CAUTION: Prior to operating the Saphyr®Instrument, please review the Saphyr System Safety Guide (P/N

30253) for all safety and compliance information.

The Saphyr System (Saphyr Instrument with Instrument Controller and Bionano Access®Server) together with the

Saphyr Compute and Bionano Compute provides rapid, high-throughput, long-range genome mapping for de

novo assembly of genome maps, hybrid scaffolding of NGS, and structural variation analysis. This User Guide is

for the Saphyr System with dual chip capability, P/N 60325. If you have Saphyr P/N 60239 with single chip

capability, please see User Guide P/N 30143.

Features

•Easy load-and-goworkflow – TheadaptiveloadingfeatureintheInstrumentControlSoftware (ICS) ensures

that the optimal conditions for DNAmoleculeloadingaremaintainedthroughoutthescanning.The initial

hands-on-time is approximately 5 minutes.

•Continuous running of the instrument – The dual chip capability of the instrument allows users to run the

instrument continuously. Two chips can be loaded onto the stage. When one chip has completed its run, the

instrument automatically moves on to the other chip. The completed chip can be removed and replaced with a

new chip at the user’s convenience while the other chip is running via the pause workflow.

•Convenient setup and flow – Bionano Access allows users to design experiments, track run performance,

perform downstream analysis, and sharedata.

•Real-time analysis – Bionano Access enables users to view real-time data andperformance metrics from

any internet browser with connection to your Access Server as the run progresses.

Workflow

To perform a run on the Saphyr, use the following workflow example as a guide:

1. Perform DNA isolation and labeling of samples.

2. Set up an experiment and specify run parameters on BionanoAccess.

3. Load the samples on a Saphyr Chip®and attach the Saphyr Clip to the chip.

4. Turn the Saphyr instrument on and sign in to the Instrument Control Software(ICS).

5. Insert the Saphyr Chip into the instrument.

6. Setup a run.

7. Track run performance and analyze data on Bionano Access.

8. Remove the chip from the instrument.

Prepare Sample

For details on DNA isolation and labeling of samples, visit the Bionano Support page.

Prepare

Sample

Prepare

Chip

Set Up

Experiment

Perform

Run

Analyze

Data

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Chapter 2: Getting Started

Start the Saphyr Instrument

1. Locate the power switch on the back of theinstrument.

2. Toggle the power switch to turn the instrument on.

3. Log into Windows. Use the username and password that were given to you by the Bionano Field Service

Engineer (FSE) or Field Application Scientist (FAS). If you forgot the username or password, please

contact Bionano Support.

Laser Safety Light

CAUTION: Before lifting the sample door to insert or remove the Saphyr chip, ensure the laser safety light is

blue (below, left). If the laser safety light is red (below, right), do not open the sample door and contact

Bionano Genomics Support for assistance; users may be at risk for laser radiation exposure if the sample

door isopened. For additional information, please refer to the Saphyr System Safety Guide (P/N 30253).

Important: If the laser safety light is red, do not use. Contact Bionano Genomics Support.

Laser Safety Light Instrument Status Light

30247 Rev A, Saphyr System User Guide for Saphyr P/N 60325 Page 7 of 43

Instrument Status Light

The instrument status light indicates the following:

Color

Description

Light off The instrument is powered off.

Flashing yellow The instrument is initializing.

Green The instrument is ready to use.

Flashing green The instrument is running or the workflow has been paused.

Red The instrument encountered an error. Note: This does not present a safety

issue to the user.

1. Launch the Instrument Control Software (ICS) using the shortcut icon on the desktop of the attached

Instrument Control computer. When the software is launched, the Saphyr instrument will initialize. This

can be seen by clicking on the status icon. A description of all icons can be found in Appendix C and a

description of the initialization screen can be found in Appendix D.

2. Enter the username and password. This is the username and password that has been set up on Bionano

Access. See Chapter 3 for instructions.

3. Click Logon.

ICS Home Screen Options

The following menu appears on the Home Screen. Not all options are available at all times, depending on the

state of the instrument.

Option

Description

Insert Chip Allows users to insert the Saphyr Chip into the Saphyr instrument.

Configure Run Allows users to set up a run. This option is only available if a chip is

loaded.

Data

Administration Allows users to manage data on the Saphyr Instrument Controller, such

as managing disk space, and deleting runs. This option is only needed for

users who save their images during a run. See Appendix E for details.

Remove Chip Allows users to remove the chip from the Saphyr instrument. This option

is only available when a chip is loaded.

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Chapter 3: Configure Analysis Settings in Bionano Access

The Instrument Control Software and Bionano Access interact to allow users to track run progress and view

results in real time. Prior to performing the run on the Saphyr instrument, an experiment must be set up in

Bionano Access. For details on how to do this, as well as all Bionano Access analysis and visualization features,

see the Bionano Access Software User Guide (P/N 30142).

30247 Rev A, Saphyr System User Guide for Saphyr P/N 60325 Page 9 of 43

Chapter 4: Prepare Chip

Load Sample on Saphyr Chip

•Equilibrate the labeled samples and Saphyr chip (sealed in pouch) to room temperature for at least 30 minutes

prior to use.

Important: Do not open the pouch containing the Saphyr Chip when the chip is cold. Wait until the pouch

is at room temperature before removing the chip. Opening a chip while it is cold may damage the chip and

cause performance degradation.

•When loadingsample,ensure thereis no airflow around the chip to avoid sampleevaporation.

•Proceed through the following steps carefully, without interruption to minimize sampleevaporation.

•Use gloves (powder free) for this procedure.

•The instructions below are applicable for either two or three flowcell chips.

Important: Make sure that you load the samples in the same flowcells that you setup in Access in the step

above. Also, note the serial number of the chip so the chip can be associated with the correct experiment

in Chapter 5 below (chip tracking table provided below).

Chip SN - - - - - -

Flowcell 1 Sample :

Flowcell 2 Sample :

Flowcell 3 Sample :

Image: Saphyr Chip (left) and Saphyr Clip (right) with removable plugs (bottom right)

30247 Rev A, Saphyr System User Guide for Saphyr P/N 60325 Page 10 of 43

1. Open the pouch containing the SaphyrChip.

2. Place the chip on a clean and level lab bench.

3. With a 10 µl pipette, press the plunger down and hold at the first stop. Lower the pipettetip into the

sample and gently stir the sample with thetip.

4. Position the pipette tip near the middle or bottom of the sample and slowly aspirate 8.5 µl of thesample.

5. Begin loading the sample in the inlet well of flowcell 1.

Place the pipette tip into theflowcell1inletwellontherightofthechip,andthenslowlydispense the sample

until the bottom of the inlet well is coated with sample solution. Continue to dispense, adjusting the rate of

dispensing as the DNA travels slowly into the flowcell fingers, until the entire volume of 8.5 μl is in the

well.

The fluid level in the inlet well should be flat. If the sample overflows out of the well and onto the top of the

chip or onto the plastic, the flowcell is not usable. Always maintain positive pressure on the plunger to

avoid bubble formation.

6. Repeat steps 3 through 5 for flowcell 2 and flowcell 3 inletwells.

7. Set a timer for 2 minutes to allow the sample to wet through thenanochannels.

8. After two minutes, with a 20 µl pipette positioned near the middle or bottom of the sample, slowly aspirate

11 μl of the sample and slowly dispense the sample into the outlet well of flowcell 1. Repeat for flowcell2

and flowcell 3.

The fluid level in the outlet well should be flat. If the sample overflows out of the well and onto the top of

the chip or onto the plastic, the flowcell is not usable. Always maintain positive pressure on the plunger to

avoid bubble formation.

9. For flowcell 1, add 5 µl of nuclease-free water to the hydration reservoir on the outlet side of the chip (see

“OUTLET” on the chip label. Adding additional water or adding water to the reservoir on the inlet side of

the chip may lead to problems with the chip run.

10. Ensure that the fluid level in the inlet and outlet wells isflat relative to the top of the chip. Add the

necessary volume of nuclease-free water to the inlet and outlet wells of flowcell 1 toreplace sample

solution that hasevaporated.

Important: The inlet and outlet wells should be filled with sample solution during the initial load. Do

not compensate for lack of sample solution by adding nuclease-free water or buffer. Nuclease-free

water should only be added after all wells are loaded to replace volume lost by evaporation.

Outlet Hydration

Reservoir Inlet Hydration

Reservoir

Outlet Well Inlet Well

Fingers

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