Illumina BeadStudio Data Analysis Software Modules

Data Sheet: Software

Highlights of Illumina Beadstudio Software

• Cutting Edge:

powerful data manipulation, heat map and cluster analysis

• See Your Data in a New Way:

graphical analysis using the Illumina Genome Viewer (IGV) and

Illumina Chromosome Browser (ICB)

• High Performance:

sophisticated algorithms to support of genomic investigation

• Integrative:

common framework that supports multiple application

modules

• Freedom for Downstream Analysis:

export data for use in downstream applications (e.g.,

SpotFire

or GeneSpring

)

Introduction

As high-throughput systems enable increasingly complex bioinfor-

matics data to be generated, researchers turn towards managing,

processing, and analyzing their data. Thus, there is a need for a state-

of-the-art software package that combines ease-of-use with powerful

visualization tools to streamline the analysis process. Illumina is proud

to introduce its leading-edge analytical software platform, BeadStudio,

and its associated analytical modules (GT, GX, LOH Plus).

BeadStudio’s modular design allows Illumina to respond to evolving

customer needs by releasing add-on software modules that integrate

seamlessly into the BeadStudio Framework.

As new assays or applications are developed, the BeadStudio product

family will continue to support scientists’ most current needs. This

modular approach also enables users to rely on a familiar common

graphical user interface, minimizing the need for new software training

as additional modules are released. In addition, the BeadStudio archi-

tecture is designed to support the ow of information for downstream

data compatibility with other applications (e.g., SpotFire or Gene-

Spring).

Illumina

BeadStudio Data Analysis Software

Modules

Illumina’s BeadStudio delivers high-quality software for cutting-edge data analysis and advanced

visualization tools for the following applications: Genotyping, Gene Expression, and Loss of

Heterozygosity (LOH).

Genotyping (GT) Module

The BeadStudio GT Module provides automated genotype calling

and sample clustering. Powerful visualization tools and quality-control

features enable graphical output of data and reports on reproducibility

and Mendelian consistency. Bead Studio Framework features such

as heat maps, scatter plots, the Illumina Genome Viewer (IGV), the

Illumina Chromosome Browser (ICB), the Illumina Sequence Viewer

(ISV) and Innium Laboratory Information Management System (LIMS)

integration add additional functionality to this module.

Gene Expression (GX) Module

The BeadStudio GX Module is designed for analysis of Whole-

Genome Gene Expression BeadChips and Focused Arrays for the

Direct Hyb and DASL

Assays. Advanced analytical features include

gene-level analysis, statistical tools for differential expression analysis,

sample controls, heat maps (Figure 3), bar plots and clustering tools.

Enhanced data management enables hierarchical organization of

samples, groups, groupsets and associated project analysis.

Figure 1: Genoplot Generated Using Beadstudio

Genotyping Module

0.50

0.70

0.60

0.40

0.20

-0.10

0.30

0.10

0.00

Normalized R

0 0.20 0.40 0.800.60 1

Normalized Theta

rs872381

21 45 29

The BeadStudio Genotyping Module clusters genotype calls into AA, AB

and BB clusters for easy viewing and data analysis.

Data Sheet: Software

Loss of Heterozygosity Plus (LOH Plus) Module

The BeadStudio LOH Plus Module is designed to address chro-

mosomal aberrations and allelic imbalance in paired samples (e.g.,

matched normal/tumor pair). Key features of this module include: au-

tomated detection of chromosomal aberrations, custom bookmarking

of genomic regions of interest and a chromosomal heat map to reect

LOH/Copy Number-related intensity differences along chromosomes.

The Bookmarked Samples Report also allows the user to create a

summary of various aberrations.

Beadstudio Framework Features

The BeadStudio Framework is the basis of BeadStudio and includes

many customizable features and formats for powerful data analysis.

Project Wizard

The BeadStudio Project Wizard helps the user initiate and organize

projects with ease. Using the Project Wizard simplies decision-mak-

ing so less time is required for setup, allowing more time for analysis.

Illumina Genome Viewer (IGV)

The IGV allows visualization of sample-related data on a genome-wide

scale or at the chromosomal level. The IGV can display up to four

plots at a time (a single data series each) over a chosen chromosome

(Figure 2).

Illumina Chromosome Browser (ICB)

Using the ICB, the user can browse imported SNPs within the context

of a chromosome (e.g., SNPs relative to exons). Both the IGV and ICB

offer a wide range of visualization options for data analysis.

Data Tables

Advanced data table features allow the user to customize data viewing

for efcient and effective data analysis. Options include:

• importing columns

• adding derived columns

• sorting

• selecting and marking rows

• advanced data ltering

• exporting data

Reports

Custom or standard reports can be created for various types of analy-

sis. Implementing consistent report formats can streamline analysis

and discovery.

Figure 2: LOH Plus Module

log (subject sample

/reference sample)

intensities

heterozygote

allele frequency

difference between

paired samples

subject sample

allele frequency

reference sample

allele frequency

The Illumina Genome Viewer enables classic LOH analysis by comparing

reference and subject sample data from the same donor.

Table 1: Beadstudio Tools

Feature Highlight

BeadStudio Project Wizard Easy project set-up and organization

Illumina Genome Viewer View data patterns across the genome

Illumina Chromosome Browser Browse data at the chromosome and gene level

Illumina Sequence Viewer Browse data at the sequence level

Table Filters Congure with easy-to-use, rule-based options

Import Data Import cluster les, import columns into tables

Export Data Export cluster les, export table data

Generate Reports Create standard or custom reports

Scatter Plots For graphical viewing of data

Heat Map For graphical viewing of data

LOH/Copy Number Analyze Loss of Heterozygosity/Copy Number

Auto Detection Search for chromosomal aberrations (in addition to manual curation)

Data Integration Customize reports for integration into other downstream applications

Data Sheet: Software

Graphs

BeadStudio graphic display options allow the user to plot table data in

a number of ways, including the following formats:

• Histograms

• Line Graphs

• Scatter Plots

• Heat Maps

• Cluster Plots

• Many More Module-Specic

• Capabilities

Figure 3: Gene Expression Module

The heat map dendrogram clusters rows (Target ID) and columns (Differen-

tial Scores). Using the Heat Map tools within the Gene Expression Module

allows the investigator to easily visualize and analyze large amounts of data.

Data Integration

Customizable reports and data export options simplify integration with

other downstream analytical applications.

Summary

BeadStudio is designed to be leading-edge, modular and integrative.

BeadStudio consists of individual software modules specic to vari-

ous product applications. Users can rely on the familiar BeadStudio

Framework while minimizing additional product training as they expand

their analytical capabilities from a single module to multiple modules.

BeadStudio is designed for downstream data compatibility with other

applications. This modular architecture enhances the ow of informa-

tion from data analysis to downstream scientic discovery.

Additional Information

Visit www.illumina.com or contact us at the address below to learn

more about BeadStudio or other solutions from Illumina.

Table2: Hardware and Software Requirements

Feature Highlights

CPU Speed Intel

Pentium

2.0 GHz

or above

Memory Size ≥ 2 GB

Hard Drive ≥ 100 GB

Video Display 1280 x 1024 recommended,

1024 x 768 required

Monitor Display LCD or CRT 17” recommended

Operating System Windows XP - SP2 (32bit) or

Windows XP - SP2 (64 bit)

Specic OS Requirements Requires Microsoft .NET

framework 1.1 or above

Illumina, Inc. • 9885 Towne Centre Drive, San Diego, CA 92121 USA • 1.800.809.4566 toll-free • 1.858.202.4566 tel • [email protected] • illumina.com

For research use only

Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray,

Array of Arrays, Innium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, GenomeStudio, Genetic Energy, HiSeq, and HiScan are

registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective

owners. Pub. No. 970-2006-007 Current as of 13 July 2006

Data Sheet: Software

Ordering Information

Catalog No. Product Description

SW-10-101

BeadStudio Genotyping (GT) Module (Single

Seat) - New License

New single-seat license for BeadStudio Geno-

typing (GT) Module provides advanced tools for

SNP data analysis.

SW-10-102

BeadStudio Genotyping (GT) Module (Five Seats)

- New License

New single-seat license for BeadStudio Geno-

typing (GT) Module provides advanced tools for

SNP data analysis.

SW-10-200

BeadStudio Genotyping (GT) Module (Single Site

w/ Warranty) - Upgrade

Single-site upgrade license for systems with

warranty coverage. BeadStudio Genotyping (GT)

Module provides advanced tools for SNP data

analysis.

SW-10-300

BeadStudio Genotyping (GT) Module (Enterprise

w/ Warranty) - Upgrade

Enterprise upgrade license for system with

warranty coverage. BeadStudio Genotyping (GT)

Module provides advanced tools for SNP data

analysis.

SW-10-400*

BeadStudio Genotyping (GT) Module (Five Seats

w/Warranty) - Upgrade

Complimentary ve-seat upgrade license for

system with warranty coverage. BeadStudio

Genotyping (GT) Module provides advanced

tools for SNP data analysis.

SW-20-101

BeadStudio Gene Expression (GX) Module (Single

Seat) - New License

New single-seat license for BeadStudio Gene

Expression (GX) Module provides advanced

tools for gene expression data analysis.

SW-20-400*

BeadStudio Gene Expression (GX) Module (Five

Seats w/Warranty) - Upgrade

Complimentary ve-seat upgrade license for sys-

tem with warranty coverage. BeadStudio Gene

Expression (GX) Module provides advanced

tools for Gene Expression data analysis.

SW-30-101

BeadStudio LOH Plus Module (Single Seat) - New

License

New single-seat license for BeadStudio Loss of

Heterozygosity Plus (LOH Plus) Module provides

advanced tools for LOH/Copy Number data

analysis.

SW-30-400*

BeadStudio LOH Plus Module (Five Seats w/War-

ranty) - Upgrade

Complimentary ve-seat upgrade license for

system with warranty coverage. BeadStudio

Loss of Heterozygosity Plus (LOH Plus) Module

provides advanced tools for LOH/Copy Number

data analysis.

*free upgrade for current customers

For a complete listing of BeadStudio Products, contact Customer Solutions at address below.