Design Markers | Process BeadChip | Analyze Data®

GenomeStudio 2.0 Data Analysis Software
A comprehensive data analysis tool supporting microarray genotyping experiments.
HighlightslBroad Compatibility
Analyze data from any Illumina array-based genotyping assaylVersatile Analysis for Any Genome
Genotype both diploid and polyploid organismslIntuitive Project Creation
Create and manage genotyping projects with an intuitive
interfacelCustomizable Data Visualization
Examine data from a genome-wide view to single-baseresolution with various display tools

Introduction®

Illumina offers a broad spectrum of innovative and powerful Infinium
array-based genotyping assays. GenomeStudio 2.0 Data Analysis
Software supports these diverse assays with an integrated DNA-todata workflow for all Illumina arrays. GenomeStudio Software features
performance-optimized tools and a user-friendly graphical interface
that enable researchers to convert microarray data into meaningful
results quickly and easily.

Figure 1: GenomeStudio 2.0 Data Analysis Software—GenomeStudio Software
supports automated analysis of data generated using any Illumina array-based
genotyping assay and features diploid and polyploid genotyping and CNVdetection.

Versatile Analysis for Any Genome
GenomeStudio Software supports the spectrum of Illumina arraybased genotyping applications, enabling analysis of both diploid andpolyploid organisms (Figure 1).

Diploid Genotyping
Genotyping data for diploid organisms generated using Infinium assays®
on the iScan System are analyzed in the default GenomeStudio
Genotyping Module. This module uses trusted algorithms to normalize,
cluster, and call genotypes. Data quality is monitored in real time withinternal controls and other QC functions. Individual single nucleotide
polymorphisms (SNPs) can be viewed as SNP Graphs (Figure 2). Users
interested in deeper investigation of individual SNPs, particularly with
nonstandard samples (samples with low input or whole-genomeamplified samples) can edit SNP Graphs. Genotype summary statistics
and results are automatically reported and exportable in acustomizable format for use in third-party downstream analysis
software.

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Structural variation is identified using genotyping probes to measure
relative intensity shifts to detect breakpoints in copy number variations(CNVs) and loss of heterozygosity (LOH) along chromosomal
segments. CNV and LOH are reflected through analysis of a moving
window in log R ratio and B allele frequency that is displayed relative tomarker position along chromosomal segments.

Polyploid Genotyping
Analyzing data obtained from genotyping polyploid organisms requires
special considerations that depend on the level and type of ploidy ofthe organism. Polyploid genotyping is also dependent on theexpectations of segregation in the included samples. For example, inapplications involving polyploid plants, genotyping is often performed
for lines that are fixed for alternate alleles at a particular SNP locus.
Handling of these sample sets is integrated into the GenomeStudio
Polyploid Genotyping Module by allowing the investigator to allocate
the expected sample sets. By reducing the expectation of seeing
heterozygotes, genotypes are called seamlessly. With the Polyploid
Genotyping Module, analyzing genotypes of polyploid organisms isperformed in a streamlined fashion with automated genotype calling.

Design Markers | Process BeadChip | Analyze DataIntuitive Project Creation Interface
GenomeStudio Software makes it easy to create projects and identify
input data locations with an intuitive wizard interface. After a project iscreated, users can view and display all data associated with eachexperiment type easily.
Users with the optional Illumina Laboratory Information Management
System (LIMS), sample tracking, and robotic automation control cantake advantage of GenomeStudio Software integration for increased
efficiency in overall project management for all Infinium genotyping
assays. These platforms, custom designed for Illumina workflows, allow
labs to maximize their throughput.

Simple Graphical User Interface

Figure 2: Genotyping Module SNP Graph—The graphical display of results in theGenomeStudio Genotyping Module is a SNP Graph with data points color codedfor the call (red = AA, purple = AB, blue = BB). Genotypes are called for eachsample (dots) by their signal intensity (Norm R, Y-axis) and Allele Frequency (NormTheta, X-axis) relative to canonical cluster positions (dark shading) for a given SNPmarker.

The Polyploid Genotyping Module implements the density-based
spatial clustering of applications with noise (DBSCAN) algorithm andthe new PolyGenTrain algorithm to call as many clusters as expected
for up to octoploid organisms. After generating clusters, genotypes canbe called in a fully automated fashion. Similar to the Genotyping
Module for diploid organisms, individual SNPs can be graphicallydisplayed (Figure 3), and genotype summary reports are exportable forfurther downstream analysis.

GenomeStudio Software provides a set of intuitive graphical userinterfaces (GUI) and data visualization features for the control anddisplay of genotyping and clustering results (Figure 4). GenomeStudioSoftware enables thorough understanding of the large data sets
generated by Illumina genotyping assays by providing multimodal
examination from a broad, genome-wide view down to a fine-grained
single-base view. GenomeStudio Software displays results at all scales
to enable researches to examine high-resolution genome-wide data
effectively.

Versatile Data Visualization
Displaying data in the Illumina Genome Viewer (IGV) quickly reveals
genome-wide orientation and broad trends. Chromosome or regionlevel trends of array data are visualized in the Illumina Chromosome
Browser (ICB). To find trends across samples, markers, or different
assays, the GenomeStudio framework provides a wide range ofgraphical plotting and display tools (Table 1).
When trends or interesting regions are identified with graphical analysis
tools, looking at individual data points becomes essential.
GenomeStudio Software supports this single-base level of analysis ofindividual SNP genotypes with table displays (Table 1). Table views arecustomizable for sorting and to show or hide various data categories.
Table data is exportable in formats compatible with other downstream
analysis tools.

Figure 3: Polyploid Clustering Module SNP Graph—The graphical display ofresults in the GenomeStudio Polyploid Module is a SNP Graph with data points
color coded per cluster for the call. The number of clusters expected depends onuser-defined parameters for the level of ploidy (eg, tetraploidy, hexaploidy,octoploidy) and type of ploidy (eg, alloploidy vs. autoploidy).

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Design Markers | Process BeadChip | Analyze Data

Figure 4: GenomeStudio Software Interface—GenomeStudio Software features a user-friendly graphical interface for the control and display of genotyping and clusteringresults.

For R esearch Use On ly. Not f or u se in diagn ost ic procedu res.

Design Markers | Process BeadChip | Analyze Data

Table 1: GenomeStudio Software Display Options

Summary

Global Visualization
Illumina Genome Viewer (IGV)
Illumina Chromosome Browser (ICB)
GraphsHeat Maps
Scatter Plots
Histograms

GenomeStudio Software provides an integrated platform for data
analysis of all Illumina array-based genotyping assays. The graphicaldisplay of results generated from data analysis supports high-level andin-depth views of whole-genome variation. GenomeStudio Software
enables analysis of genotyping data from both diploid and polyploidorganisms to drive biological insights more efficiently.

Line Graphs

Ordering Information

Box Plots
Frequency Plots

GenomeStudio Software is available at no charge and can be
downloaded from the GenomeStudio Support Page on the Illumina
website.

Pie Charts
TablesSamples Table
SNP Table
Full Data Table

Learn More

Integrated Controls Dashboard

To learn more about GenomeStudio 2.0 Software and third-party
analysis tools, visit www.illumina.com/genomestudio.

Illumina array-based assays contain internal sample-dependent andsample-independent controls so researchers can have confidence
that they are producing high-quality data. Researchers can use theControls Dashboard, integrated into GenomeStudio Software, tomonitor the performance of all controls easily.

To learn more about analysis workflows for microarray data, read theMicroarray Data Analysis Workflows technical note.

Table 2: Minimum GenomeStudio Software System
Requirements
Parameter

Microarray Data Analysis

CPU Speed

2.0 GHz or greater

Processor

64-bitMemory8 Gb or moreHard Drive

250 Gb or largerOperating System

Windows 7 or higher

Illumina, Inc. • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
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© 2016 Illumina, Inc. All rights reserved. Illumina, GenomeStudio, Infinium, iScan, and the pumpkin orange color are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. Pub. No. 970-2008-038. Current as of 13 October 2016