illumina iScan System Manual

Brand: illumina

Model: iScan

Category: Software

Type: System Manual

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August 2015

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ILLUMINA PROPRIETARY

iScan System Guide

ii Material # 20000396

Document # 11313539 v01

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Revision History

Document Date Description of Change

Material # 20000396

Document # 11313539

v01

August

2015

Added troubleshooting information for malfunctioning status

lights in the iScan Reader Issues section.

Document # 11313539

Rev. B

February

2011

Updated to reflect iScan Control Software (ICS) version 3.2,

including automated genotype calling functionality and other

features.

Document # 11313539

Rev. A

April

2008

Part number changed to 11313539.

Document # 11308663

Rev. A

April

2008

Initial release.

iScan System Guide iii

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Table of Contents

Revision History iii

Table of Contents v

Chapter 1 Overview 1

Introduction 2

Additional Resources 3

Instrument Components 4

Consumables Required 9

iScan System Requirements 10

Scanning Process Overview 11

Chapter 2 Starting the iScan System 13

Procedure Summary 14

Powering up the iScan System 15

Starting the iScan Control Software 16

Using LIMS with the iScan System 17

Chapter 3 Loading BeadChips 19

Procedure Summary 20

Cleaning a BeadChip 21

Loading BeadChips onto a Carrier 22

Loading a Carrier into the iScan Reader 24

Rescanning Barcodes 27

Chapter 4 Configuring iScan Control Software 29

Introduction 30

Omitting BeadChips from a Scan 31

Changing Scan Settings 32

Chapter 5 Scanning 35

Introduction 36

Starting a Scan 37

Monitoring the Scan Progress 38

Pausing, Resuming, and Stopping a Scan 39

Completing a Scan 40

Chapter 6 Viewing Scan Results 41

Introduction 42

Log Files 43

Scan Metrics 44

Images 45

Generated Files 49

Chapter 7 Shutting Down, Maintenance, and Service 51

Introduction 52

Shutting Down the iScan System 53

Maintenance 54

Service 55

iScan System Guide v

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Appendix 8 Troubleshooting 57

Handling Errors 58

Issue Types 59

Registration Issues 60

Auto-Alignment Issues 62

iScan Reader Issues 64

Image Quality Issues 67

iScan Control Software Display Issues 69

Index 71

Technical Assistance 73

Chapter 1

iScan System Guide 1

Chapter 1 Overview

Overview

Introduction 2

Additional Resources 3

Instrument Components 4

Consumables Required 9

iScan System Requirements 10

Scanning Process Overview 11

Overview

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Introduction

The iScan System is an easy-to-use, laser-based, high-resolution benchtop optical imaging

system that can rapidly scan and collect large volumes of data from Illumina DNA

analysis and RNA analysis high-density BeadChips.

With powerful scanning tools for gene expression and genotyping applications, the iScan

System supports the rapid, sensitive, and accurate imaging of Illumina BeadChip products.

Incorporating the highest performance optics and detection systems, the iScan System

delivers outstanding data quality and reproducibility with dramatically reduced scan time.

BeadChips are substrates used for multisample analysis in Illumina genotyping and gene

expression applications. Assay features are loaded into wells of a BeadChip to create an

organized array. The iScan System compiles a virtual representation of a BeadChip,

acquires images of the BeadChip features, records the information, and exports the data for

downstream analysis.

The iScan System can be integrated with Illumina LIMS (laboratory information

management software) and assay automation options, such as the AutoLoader

(AutoLoader2 or AutoLoader 2.x model), to maximize throughput to thousands of samples

per day. When used with Infinium® HD BeadChips and the AutoLoader, the iScan System

can report up to 225 million genotypes in a single day, offering the fastest path to

discovery.

Audience and Purpose

This guide describes the instrument components, software interface, consumables, and

operational procedures for scanning Illumina BeadChips on the iScan System.

This guide is for laboratory personnel and other individuals responsible for:

}Operating the iScan System

}Performing instrument and component maintenance

}Training personnel

WARNING

Using controls, making adjustments, or performing procedures other than the procedures

specified in this guide can result in hazardous laser light or radiation exposure.

Additional Resources

iScan System Guide 3

Additional Resources

The following documentation is available for download from the Illumina website.

Resource Description

iScan System Site Prep Guide

(document # 1000000000661)

Provides specifications for laboratory space, electrical

requirements, and environmental considerations.

iScan SystemQuickReference

Card (part # 11313555)

Provides instructions for starting up and shutting down the

iScan system.

iScan System Quick Reference

Guide (part #15020712)

Provides an overview of instrument components and

software, instructions for imaging data on BeadChips, and

instructions for starting up and shutting down the iScan

system.

iScan SystemSafety and

Compliance Guide (part #

15022905)

Provides safety information and product compliance

statements for the iScan system.

Visit the iScan System support page on the Illumina website for access to documentation,

software downloads, and online training.

Overview

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Instrument Components

The iScan consists of the following components:

}iScan Reader

}Instrument control computer

}BeadChip carrier or carriers

}Power cords and other accessories

}[Optional] AutoLoader System

In addition to these components, purchase BeadChips developed for your application.

iScan Reader

The iScan Reader is a laser-based, high-resolution optical imaging system that includes red

and green lasers for detecting fluorescence information on BeadChips. BeadChips are

placed into carriers and the carriers are loaded 1 at a time into the adapter plate in the

iScan Reader tray.

NOTE

The adapter plate is calibrated to each individual iScan Reader. Do not switch adapter plates

between iScan Readers.

Figure 1 iScan Reader with Loaded BeadChips

ABeadChip Carrier

BAdapter Plate

CiScan Reader Tray

iScan Reader Barcode Scanner

The barcode scanner is internal to the iScan Reader, and allows you to identify each

BeadChip accurately.

Instrument Components

iScan System Guide 5

Status Lights

The iScan Reader status indicator lights and scan bar on the front panel show the status of

the instrument.

Figure 2 Status Lights and Scan Bar

Status Light Description

Power (blue) Steady blue indicates that the instrument is on.

Ready (green

check)

Steady green indicates that the instrument has been initialized and is ready

to scan. The Ready light flashes during initialization.

Warning

(amber

triangle)

Solid amber indicates that an instrument error has occurred. Try cycling the

power.

Scan Bar

(vertical blue

bar)

Steady indicates that the instrument is scanning. The Scan Bar is the blue

LED pipe to the left of the tray.

iScan Reader Tray

The iScan Reader tray accepts up to 4 BeadChips loaded in a BeadChip carrier.

Instrument Control Computer

The iScan Control Software (ICS) installed on instrument control computer allows you to

control the iScan Reader during BeadChip scanning.

Hard Drive Configuration

The iScan System contains 2 permanent drives (C: and D:) on the computer and 1

removable drive (H:) within the iScan Reader.

Drives C: and D: are physically separate drives; they are not part of 1 large drive

partitioned into 2 drives.

Overview

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Drive Description

C: Drive C: is ~75GB in size and is installed with all the generic scanner software

required to run the iScan System. It has 2 partitions, 1 for the Windows operating

system and 1 for the BIOS. This drive contains at least 30GB in free disk space on

this drive to keep the scanner from slowing down or timing out during a scan.

D: The scanner uses drive D: to hold the temporary images and scan data before

*.idat files are created for a sample. Drive D: is about 500GB and is intended to

store scan data locally. It has a single partition for the entire drive.

H: The iScan Reader houses a removable drive H: that contains a reader-specific

configuration file. This file keeps reader-specific information with the iScan Reader,

in case the computer fails.

WARNING

Do not disconnect or format the H: drive. Doing so removes all reader-specific

information, requiring an Illumina Field Service Engineer to reinstall and reconfigure

the iScan System.

iScan Control Software

The iScan Control Software (ICS) allows you to control the iScan Reader when scanning

BeadChips. iScan Control Software includes a graphical user interface for:

}Loading BeadChips

}Acquiring images

}Automatically registering and extracting images

}Organizing and viewing the acquired images

Instrument Components

iScan System Guide 7

BeadChip Carriers

The iScan System comes with 1 BeadChip carrier. The carrier holds up to 4 BeadChips for

scanning at 1 time.

The BeadChip carriers consist of the following components.

Figure 3 BeadChip Carrier

ALatches (closed)

BRaised Stops

CBeadChip Slots

DLift Button

ERecessed Pin

Carrier and BeadChip Barcodes

BeadChip carrier barcodes are used to identify the individual BeadChip carriers and

determine when a BeadChip position is occupied or empty.

These barcodes are necessary when performing automated scanning. During automated

scanning, the barcodes enable problem BeadChips to be quickly located in the output or

error stacks. They also tell the scanner when to retry scanning a BeadChip position when it

does not successfully read a BeadChip barcode on the first attempt.

Overview

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Figure 4 Top View of BeadChip Carrier Barcode

ACarrier Barcode

BEmpty Barcode

Figure 5 Side View of BeadChip Carrier Barcode

If the carrier does not have a barcode number, the carrier barcode number is listed as the

barcode number for the first BeadChip in the carrier.

The format for the number is _1stBeadChipBarcode.

Power Cords and Other Accessories

The iScan System comes with power and connection cords that are connected for you by

authorized Illumina personnel as part of the system installation. Do not unplug or

disconnect any cords unless instructed by Illumina Technical Support.

Consumables Required

iScan System Guide 9

Consumables Required

This section lists the Illumina kits and user-supplied consumables required to scan

BeadChips using the iScan System.

Illumina BeadChip Kits

Before you begin scanning, complete the appropriate assay for your BeadChip and

application.

The iScan System is compatible with the following types of BeadChips:

}Infinium HD

}DirectHyb

}Universal BeadChips

The iScan System is not compatible with the following products:

}16-1 BeadChips

}Universal Array Matrix (UAM)

User-Supplied Consumables

Make sure that you have the following user-supplied consumables before you begin

scanning BeadChips.

Consumable Supplier Purpose

Alcohol wipes, 70% Isopropyl,

Medium

VWR, catalog#15648-981 Cleaning the back side of the

BeadChip.

Ethanol, 99.5%, ACS, absolute

(optional)

Fisher Scientific, catalog #

AC61509-5000

Lab tissue, low-lint VWR, catalog#21905-026

Overview

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iScan System Requirements

Lab Equipment Requirements

If you are a current Illumina customer and already have the correct hardware package for

the assay you plan to run, you do not need to purchase any additional lab equipment

besides the iScan System itself.

For example, if you already have the Infinium upgrade package for a BeadArray Reader,

you do not need to purchase any additional equipment to scan Infinium BeadChips on a

new iScan Reader.

Air Table Specifications

The iScan Reader instrument is sensitive to vibrations. Therefore, an air table is required to

help isolate the reader from vibrations produced by the surrounding environment. The air

table is placed between the reader and the laboratory benchtop and is hooked up to a

regulator connected to the house air line.

Set the air table pressure to a nominal value of 25psi. Do not allow the air table pressure

exceed 40psi. The maximum pressure from the house line to the air regulator is 80psi.

Viewing iScan System Information

To view iScan System information, perform the following steps.

1Open the iScan Control Software and click the menu button in the upper left corner

of the screen.

2Select About. The iScan Control Software About screen appears, showing the iScan

Control Software release version, hardware information, and contact information for

Illumina Technical Support.

Scanning Process Overview

iScan System Guide 11

Scanning Process Overview

This section provides an overview of the steps involved in scanning BeadChips with the

iScan System. See the referenced sections for detailed instructions.

NOTE

This process does not describe how to use the AutoLoader with the iScan System to

automate BeadChip loading. For more information, see the AutoLoader2 User Guide or the

AutoLoader 2.x User Guide.

1Make sure that you have downloaded the *.dmap files (decode data) for your

BeadChips. Use the Illumina Decode File Client to download *.dmap files from

Illumina for your BeadChips. Download the Decode File Client from your MyIllumina

account.

2Start the iScan System.

3Load the BeadChips onto a carrier, load the carrier into the iScan Reader tray, and scan

the BeadChip carrier barcodes. For more information, see Loading BeadChips on page 19.

4If necessary, select a different image format, scan settings, data normalization settings,

and input/output path. Make sure that input and output paths are correct. For more

information, see Configuring iScan Control Software on page 29.

5Scan BeadChips. For more information, see Scanning on page 35.

6View BeadChip images. For more information, see Viewing Scan Results on page 41.

7Remove BeadChips and shut down the iScan System. For more information, see

Shutting Down the iScan System on page 53.

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Chapter 2

iScan System Guide 13

Chapter 2 Starting the iScan System

Starting the iScan System

Procedure Summary 14

Powering up the iScan System 15

Starting the iScan Control Software 16

Using LIMS with the iScan System 17

Starting the iScan System

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Procedure Summary

Perform the following steps to start the iScan System.

1Power up the iScan Reader.

2Power up the iScan System computer.

3Start the iScan ControlSoftware.

These steps are described in the following sections, along with information on using LIMS

with the iScan System.

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