For Research Use Only. Not for use in diagnostic procedures.
September 2016
Document # 11319113 v01
ILLUMINA PROPRIETARY
GenomeStudio
®
Genotyping
Module v2.0
Software Guide
ii
Document # 11319113 v01
This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the
contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This
document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed,
or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license
under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order
to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read
and understood prior to using such product(s).
FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN
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ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S)
DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE).
© 2016 Illumina, Inc. All rights reserved.
Illumina, GenomeStudio, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its
affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective
owners.
Revision History
Document
Date
Description of Change
Document #
11371113 v01
September
2016
Supported GenomeStudio Genotyping Module v2.0
Document #
11371113 rev.A
November
2008
• Changed the name of BeadStudio Genotyping Module to
GenomeStudio Genotyping Module
• Supported GenomeStudio Genotyping Module v1.0
Document #
11284301 rev.A
December
2007
Supported BeadStudio Genotyping Module v3.2
Document #
11207066 rev.C
February
2007
Supported BeadStudio Genotyping Module
Document #
11207066 rev.B
March
2006
Supported BeadStudio Genotyping Module
Document #
11207066 rev.A
December
2005
Supported BeadStudio Genotyping Module
GenomeStudio Genotyping Module v2.0
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Document # 11319113 v01
Table of Contents
Revision History iii
Table of Contents v
Chapter 1 Overview 1
Introduction 2
Install the GenomeStudio Software 3
Start the GenomeStudio Software 4
Chapter 2 Getting Started 5
Introduction 6
Create a Project From LIMS 7
Create a Project From a Sample Sheet 8
Create a Project From Directories 9
Import Cluster Positions 10
Chapter 3 Viewing Data 11
Introduction 12
Full Data Table 13
SNP Table 15
Samples Table 18
Paired Sample Table 21
Errors Table 22
Chapter 4 Editing Data 23
Introduction 24
Main Window Menus 25
SNP Graph Toolbar 29
Data Table Toolbar 30
Context Menus 31
Chapter 5 Common Tasks 35
Select Samples in the SNPGraph 36
Display Marked Samples 37
Customize the SNP Table 38
View Samples in the Controls Dashboard 39
Update SNP Statistics 40
Change the No-Call Threshold 41
Chapter 6 Generating Clusters 43
Introduction 44
Cluster SNPs 45
Edit Clusters 46
Export a Cluster File 47
Chapter 7 Analyzing Data 49
Import Phenotype Information 50
Estimate the Gender of Selected Samples 51
Edit the Sample Properties 52
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Analyze Paired Sample Data 53
View Concordance Calculations 54
Export Allele Calls 55
Import Allele Calls 56
GenomeStudio Plug-ins 57
Chapter 8 Generating Reports 59
Introduction 60
Generate a Final Report 61
DNA Report 62
Locus Summary Report 63
Locus x DNA Report 65
Generate a Reproducibility and Heritability Report 66
Technical Assistance 69
Chapter 1
GenomeStudio Genotyping Module v2.0
1
Chapter 1 Overview
Overview
Introduction 2
Install the GenomeStudio Software 3
Start the GenomeStudio Software 4
Overview
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Document # 11319113 v01
Introduction
The Illumina
®
GenomeStudio Genotyping Module™ Genotyping Module Software v2.0
analyzes Illumina genotyping data to optimize call rates.
Before installing the Genotyping Module, you must have access to the Internet and a
MyIllumina account. If you do not have access to the Internet, see Technical Assistance on
page 69.
Features
You can perform the following tasks with the Genotyping Module:
} Identify poorly performing samples.
} Manually adjust cluster positions.
} Set genotyping and clustering intensity thresholds.
} Analyze genotyping data and create cluster files.
} Import and export cluster positions.
Install the GenomeStudio Software
GenomeStudio Genotyping Module v2.0
3
Install the GenomeStudio Software
1 Navigate to the GenomeStudio support page, and then select Downloads.
2 Select GenomeStudio Software 2.0, and then select GenomeStudio Genotyping
Module 2.0 Installer.
3 Accept the software terms and license agreement, and then click Install.
Overview
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Start the GenomeStudio Software
1 From your desktop, double-click the GenomeStudio icon.
2 In the Platform Login Form dialog box, enter your email and password from your
MyIllumina account.
3 Click Log In.
Chapter 2
GenomeStudio Genotyping Module v2.0
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Chapter 2 Getting Started
Getting Started
Introduction 6
Create a Project From LIMS 7
Create a Project From a Sample Sheet 8
Create a Project From Directories 9
Import Cluster Positions 10
Getting Started
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Introduction
You can create a Genotyping Module project from one of the following sources of sample
data:
} An Illumina LIMS database
} A sample sheet
} Directories containing intensity data files
Create a Project From LIMS
GenomeStudio Genotyping Module v2.0
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Create a Project From LIMS
1 From your desktop, double-click the GenomeStudio icon.
2 In the new project pane, click Genotyping.
3 Click Next.
4 Click Select from LIMS, and then click Next.
5 Click Login, and then enter your LIMS user name and password.
6 Click OK.
7 At the Institute field, select your institution.
8 At the Investigator field, select your investigator.
9 At the Project field, select your project.
10 At the Product field, select your product.
If your product is multi-species, expand the product to select an individual species.
11 Click Finish.
12 [Optional] Click Use StartDate and select a start date from the calendar.
13 [Optional] Click Use End Date and select an end date from the calendar.
14 Click OK.
15 [Optional] Click Yes to calculate the heritability and reproducibility errors.
16 Click OK.
Getting Started
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Create a Project From a Sample Sheet
1 In the new project pane, click Genotyping, and then click Next.
2 In the Create field, enter the project name, and then click Next.
3 Click Use sample sheet to load sample intensities, and then click Next.
4 In the Sample Sheet field, browse to your sample sheet (*.csv) file.
5 In the Data Repository field, browse to the directory that contains your raw intensity
(*.idat) files.
6 In the Manifest Repository field, browse to the directory that contains your
SNPmanifest (*.bpm) file.
The software uses this directory to locate the names of the SNPmanifests.
7 Click Next.
8 [Optional] Click the Import cluster positions from a cluster file checkbox. See Import
Cluster Positions on page 10.
a Select Browse, highlight the cluster file, and select Open.
9 Click Finish.
Genotyping Module loads the files from the sample sheet and displays the data.
Create a Project From Directories
GenomeStudio Genotyping Module v2.0
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Create a Project From Directories
1 In the new project pane, click Genotyping, and then click Next.
2 In the Create field, enter the project name, and then click Next.
3 Click Load sample intensities by selecting directories with intensity files, and then
click Next.
4 At the Manifest Repository field, browse to the file that contains your SNPmanifest
(*.bpm) file.
5 At the Data Repository field, browse to the directory that contains your raw intensity
(*.idat) files.
6 Select one or more directories, and click Add, and then click Next.
7 [Optional] Click the Import cluster positions from a cluster file checkbox. See Import
Cluster Positions on page 10.
a Select Browse, highlight the cluster file, and select Open.
8 [Optional] In the Project Settings area, select the following options:
} Pre-Calculate
} Cluster SNPs
} Calculate Sample and SNP Statistics
} Calculate Heritability
} Gen Call Threshold
9 Click Finish.
Getting Started
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Import Cluster Positions
You can import a cluster (*.egt) file when creating a project in the Genotyping Module.
1 In the GenomeStudio Project Wizard, click the Import cluster positions from a cluster
file checkbox.
2 At the Cluster File field, browse to the cluster file you want to use.
3 [Optional] Click Pre-Calculate to optimize your project speed based on your computer
memory capabilities.
4 [Optional] In the Project Creation Actions settings, select from the following options:
} Cluster SNPs
} Calculate Sample and SNP Statistics
} Calculate Heritability
5 At the GenCall Threshold field, specify the score cutoff for this project.
We recommend the 0.15 GenCall score cutoff for Infinium products.
6 Click Finish.
Chapter 3
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Chapter 3 Viewing Data
Viewing Data
Introduction 12
Full Data Table 13
SNP Table 15
Samples Table 18
Paired Sample Table 21
Errors Table 22
Viewing Data
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Introduction
The Genotyping Module has many views, such as graphs, tables, and project information.
The views are detachable docking windows. Click and drag the windows to where you
want to dock them on the main window. The views show the following data:
View Description
Sample Graph
All SNPs for the selected sample.
SNP Graph
All samples for the selected SNP in the SNP table and Full Data
table.
SNP Graph Alt
All samples for the selected SNP in the SNP table and Full Data
table. (Use to compare 2 different views of the samples.)
Full Data Table
Data for all samples.
SNPTable
Statistics for each SNP.
Samples Table
Data for each sample.
Paired Sample Table
Statistics for paired samples.
Errors Table
Discrepancies between replicate or related samples
Log Window
A list of the activities that are created by the software.
Project Window
Manifests and sample barcodes loaded in the project.
Table 1 Views in Genotyping Module
Full Data Table
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Full Data Table
The Full Data table contains data for all the samples.
Column Heading Description
Index
SNP index row.
Name
SNP name.
Address
Bead type identifier.
Chr
SNP chromosome.
Manifest
Manifest name of the SNP.
Position
Chromosomal position of the SNP.
GenTrain Score
Score for a SNP from the GenTrain clustering algorithm.
FRAC A
Fraction of the A nucleotide in the top genomic sequence.
FRAC C
Fraction of the C nucleotide in the top genomic sequence.
FRAC G
Fraction of the G nucleotide in the top genomic sequence.
FRAC T
Fraction of the T nucleotide in the top genomic sequence.
Table 2 Full Data Table Columns
Column Heading Description
GType
Genotype for the sample.
Score
SNP call score for the sample.
Theta
Normalized Theta-value for the sample.
R
Normalized R-value for the sample.
X Raw
Raw intensity of the A allele.
Y Raw
Raw intensity of the B allele.
X
Normalized intensity of the A allele.
Y
Normalized intensity of the B allele.
B Allele Freq
B allele frequency for this sample as interpolated from known B
allele frequencies of 3 canonical clusters: 0, 0.5 and 1 if it is equal
to or greater than the theta mean of the BB cluster.
B Allele Freq is between 0 and 1, or set to NaN for loci
categorized as intensity only.
Table 3 Full Data Table Subcolumns
Viewing Data
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Column Heading Description
Log R Ratio
Base-2 log of the normalized R value over the expected R value
for the theta value (interpolated from the R-values of
theclusters).
For loci categorized as intensity only; the value is adjusted so
that the expected R value is the mean of the cluster.
Top Alleles
Illumina-designated top strand genotype.
Import Calls
Genotype calls for an imported sample.
Concordance
Numeric correlation between the top allele call for a SNP in the
project and the imported allele call of a SNP from another
project.
Orig Call
Genotype call of SNP and sample at the time the project was
originally clustered.
CNV Value
Copy number estimate at each locus.
CNV Confidence
Level of confidence that the Copy Number Value (CNV) is
correct based on the algorithm used.
Plus/Minus Alleles
Genotype for the sample, as related to the nucleotide alleles on
the plus strand.
SNP Table
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SNP Table
The SNP Table shows the statistics for each SNP.
Column Heading Description
Index
SNPindex row.
Name
SNP name.
Chr
SNP chromosome.
Position
SNP chromosomal position.
ChiTest 100
Normalized Hardy-Weinberg p value calculated using genotype
frequency. The value is calculated with 1 degree of freedom and
normalized to 100 individuals.
Het Excess
Excess of heterozygotes measurement for the SNP based on
Hardy-Weinberg Equilibrium.
0—No excess of heterozygotes
(-) Negative values—A deficiency of heterozygotes
AA Freq
Frequency of AA calls.
AB Freq
Frequency of AB calls.
BB Freq
Frequency of BB calls.
Call Freq
Call frequency.
Minor Freq
Minor allele frequency.
Aux
User-defined auxiliary value for the SNP.
Rep Errors
The number of reproducibility errors for the SNP as allele
comparisons between replicates.
SNP
Nucleotide substitution for the SNP on the Illumina ILMN
strand.
ILMN Strand
Design strand designation.
Customer Strand
Customer strand designation.
Top Genomic Sequence
Sequence on the top strand around theSNP.
Comment
User-defined comment. Right-click in the column to set the
value.
Norm ID
Normalization ID for the SNP.
HW Equil
Hardy-Weinberg Equilibrium score for the SNP.
Concordance
Measurement between 2 genotypes from the same SNP locus.
Table 4 SNP Table Columns
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Column Heading Description
CNV Region
SNPs and nonpolymorphic probes falling in known CNV
regions.
This column populates information from the product manifest
and may not be current because the number of known CNV
regions is constantly changing.
Exp Clusters
Number of expected clusters for a locus:
1—Nonpolymorphic probes
2—Mitochondrial DNA and Y loci
3—Any other loci
This column populates information from the product manifest.
Intensity Only
Indicates locus information.
1—Locus with intensity information only that is not included in
GenomeStudio statistics such as Call Rate.
0—Locus with intensity and genotyping information that is
included in GenomeStudio statistics such as call rate.
The column populates information from the product manifest
and can be edited.
Column Heading Description
Address
The SNPindex row.
GenTrain Score
The SNP cluster quality.
Orig Score
The original GenTrain score for the SNP before edits.
Edited
The SNP was edited after identifying clustering positions.
1—Edited
0—Unedited
Cluster Sep
The cluster separation measurement for theSNP that ranges
between 0 and 1.
AA T Mean
The theta value of the AA cluster center in normalized polar
coordinates.
AA T Dev
The standard deviation in theta of the AA cluster in normalized
polar coordinates.
AB T Mean
The theta value of the AB cluster center in normalized polar
coordinates.
AB T Dev
The standard deviation in theta of the AB cluster in normalized
polar coordinates.
BB T Mean
The theta value of the BB cluster center in normalized polar
coordinates.
BB T Dev
The standard deviation in theta of the BB cluster in normalized
polar coordinates.
Table 5 SNP Table Subcolumns
SNP Table
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Column Heading Description
AA R Mean
R value of the center of the AA cluster, in normalized
polarcoordinates
AA R Dev
Standard deviation in R of the AA cluster, in normalized
polarcoordinates
AB R Mean
The R value of the AB cluster center in normalized
polarcoordinates.
AB R Dev
The standard deviation in R of the AB cluster in normalized
polarcoordinates.
BB R Mean
The R value of the BB cluster center in normalized
polarcoordinates
BB R Dev
The standard deviation in R of the BB cluster in normalized
polarcoordinates.
Intensity Threshold
The intensity threshold value.
ILMN Strand
The design strand designation.
Address 2
The bead type unidentified for the second allele. It is only used
for Infinium I.
Norm ID
The normalization ID for the SNP.
Manifest
The manifest name of the SNP.
Viewing Data
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Samples Table
The Samples Table shows the statistics for each sample.
Column Heading Description
Index
Sample index row.
Sample ID
Sample identifier.
Call Rate
Percentage of SNPs that have a GenCall score greater than the
specified threshold.
Gender
User-specified gender for the sample.
p05 Grn
5th percentile of B allele intensity.
p50 Grn
50th percentile of B allele intensity.
p95 Grn
95th percentile of B allele intensity.
p05 Red
5th percentile of A allele intensity.
p50 Red
50th percentile of A allele intensity.
p95 Red
95th percentile of A allele intensity.
p10 GC
10th percentile GenCall score for all SNPs.
p50 GC
50th percentile GenCall score for all SNPs.
Rep Error Rate
Reproducibility error rate is calculated as 1 - sqrt(1 -
errors/max_possible_errors). Errors and max_possible_errors
do not include genotype calls that fall below the no-call
threshold.
PC Error Rate
Parent-child heritability error rate.
PPC Error Rate
Parent-parent-child heritability error rate.
Call Rate
Percentage of SNPs that have a GenCall score greater than the
specified threshold.
Aux
Arbitrary number you can use to differentiate and sort samples.
Right-click in the Samples Table to set this value.
Subset
Grouping of samples into a subset.
Array Info
Position on the slide for this sample in terms of the sentrix ID
and sentrix position.
Genotype
Genotype for this sample for the SNP currently selected in the
SNP Table.
Score
GenCall score for this sample for the SNP currently selected in
the SNP Table.
Table 6 Samples Table Columns
Samples Table
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Column Heading Description
Sample Name
Sample name.
Sample Group
User-entered sample group.
Sample Plate
Sample plate identifier.
Sample Well
Well within the sample plate.
Gender Est
Estimated gender.
Requeue Status
Sample requeue status in LIMS. Blank status indicates that the
sample does not need requeuing.
Concordance
Concordance across all SNPs for thissample. The value is
populated when alleles calls are imported for the same sample
from another project.
Ethnicity
Ethnicity of the individual from the acquired sample.
Age
Age of the individual from the acquired sample.
Weight
Weight in kg of the individual from the acquired sample.
Height
Height in meters of the individual from the acquired sample.
Blood Pressure Systolic
Systolic blood pressure of the individual from the acquired
sample.
Blood Pressure
Diastolic
Diastolic blood pressure of the individual from the acquired
sample.
Blood Type
Blood type of the individual from from the acquired sample.
Phenotype
Pos 1
Positive phenotype 1 of the individual from the acquired
sample.
Phenotype
Pos 2
Positive phenotype 2 of the individual from the acquired
sample.
Phenotype
Pos 3
Positive phenotype 3 of the individual from the acquired
sample.
Phenotype
Neg 1
Negative phenotype 1 of the individual from the acquired
sample.
Phenotype
Neg 2
Negative phenotype 2 of the individual from the acquired
sample.
Phenotype
Neg 3
Negative phenotype 3 of the individual from the acquired
sample.
Comment
User-entered comments.
Tissue Source
Tissue source of the individual from which this sample was
acquired.
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Column Heading Description
Calls
Number of loci called.
No Calls
Number of loci not called.
Excluded
Whether the sample is excluded.
1—Excluded
0—Included
Column Heading Description
Sentrix ID
Barcode number of the Universal Array Product to which this
sample was hybridized.
Sentrix Position
Section on the product.
Imaging Date
Imaging date.
Scanner ID
Name of the scanner.
PMT Green
Green PMT setting of the scanner.
PMT Red
Red PMT setting of the scanner.
Software Version
Version of the iScan software that scanned the sample.
User
User name of the individual that scanned the sample.
p05 Grn
5th percentile of B allele intensity.
p50 Grn
50th percentile of B allele intensity.
p95 Grn
95th percentile of B allele intensity.
p05 Red
5th percentile of A allele intensity.
p50 Red
50th percentile of A allele intensity.
p95 Red
95th percentile of A allele intensity.
p10 GC
10th percentile GenCall score over all SNPs.
p50 GC
50th percentile GenCall score over all SNPs.
Call Rate
Percentage of SNPs that have a GenCall score greater than the
specified threshold.
Table 7 Samples Table Per-Manifest Subcolumns
Paired Sample Table
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Paired Sample Table
The Paired Sample table shows statistics for pairedsamples.
Column Description
Index
SNP index row.
Name
SNP name.
SNP
SNP.
Address
Bead type identifier.
Chr
SNP chromosome.
Position
SNP chromosomal position.
Table 8 Paired Sample Table Columns
Columns Heading Description
Theta Ref.
Theta value for the reference sample.
Theta Sub.
Theta value for the subject sample.
|dTheta sub-ref|
Absolute value of the difference between subject and reference
theta values.
Allele Freq Ref.
Allele frequency of the reference sample.
Allele Freq Sub.
Allele frequency of the subject sample.
|dAlleleFreq sub-ref|
Absolute value of the difference between subject and reference
allele frequencyvalues.
R Ref.
R value for the reference sample.
R Sub.
R value for the subject sample.
Log2 (Rsub/Rref)
Log base 2 of the ratio of subject and reference R values.
GType Ref.
Genotype of the reference sample.
GType Sub.
Genotype of the subject sample.
LOH Score
Probability that there is loss of heterozygosity in a region of
interest.
CN Estimate
Estimate of the copy number at an individual locus.
CN Shift
Statistical confidence level between 0 and 1 indicating whether a
copy number change has occurred.
1— No copy number change.
0— Copy number change.
Table 9 Per-Pair Sample Subcolumns
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Errors Table
The Errors table shows reproducibility errors or parent-child heritability errors.
Column
Heading
Description
Error Index
Error index row.
Error Type
Types of errors:
• Rep—Reproducibility
• P-C—Parent-Child heritability
• P-P-C—Parent-Parent-Child heritability
Child/Rep
Index
Sample index of the child sample involved in the
error.
Child/Rep
Sample ID of the child sample involved in the
error.
Child/Rep
GType
For a parental relationship error, the genotype of
the child.
Parent1/Rep
Index
Sample index of the Parent1 sample involved in
the error.
Parent1/Rep
Sample ID of the Parent1 sample involved in the
error.
Parent1/Rep
GType
For a parental relationship error, the genotype of
Parent1. For a replicate error, the genotype of
replicate 1.
Parent2
Index
Sample index of the Parent2 sample involved in
the error.
Parent2
Sample ID of the Parent2 sample involved in the
error.
Parent2
GType
For a parental relationship error, the genotype of
Parent2. For a replicate error, the genotype of
replicate 2.
SNP Index
SNP index number where the error occurred.
SNP Name
SNPname where the erroroccurred.
Table 10 Errors Table Columns
Chapter 4
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Chapter 4 Editing Data
Editing Data
Introduction 24
Main Window Menus 25
SNP Graph Toolbar 29
Data Table Toolbar 30
Context Menus 31
Editing Data
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Introduction
You can edit the data in the tables and graphs with the following tools:
Tools Description
Main Window Menus
The main window contains the following menus:
• File
• Edit
• Analysis
• Tools
• Window
• Help
SNP Graph Toolbar
Edits SNPs in the SNP, SNPAlt, and Sample graphs.
Data Table Toolbar
Selects, copies, filters, and sorts data in tables.
Context Menus
Right-click in graphs and tables to select additional functions.
Main Window Menus
GenomeStudio Genotyping Module v2.0
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Main Window Menus
File Menu
Function Description
New Project
Creates a new project.
Open Project
Opens a previously saved project.
Save Project
Saves all information in this project.
Save Project Copy As
Saves a copy of the current project.
Close Project
Closes the current project.
Load Additional
Samples
Opens the GenomeStudio Project Wizard. You can specify a
sample sheet or directories to load intensity files.
Import Cluster
Positions
Imports cluster positions from an *.egt file.
Export Cluster
Positions
Exports selected SNPs or all SNPs to an *.egt file.
Export Manifest
Exports a manifest (*.csv)file.
Update Project from
LIMS
Updates the project fromLIMS.
Import Phenotype
Information from File
Imports phenotype information for the samples from a file.
Page Setup
Sets up page properties.
Print Preview
Opens the Print Preview window.
Print
Sets up printing options.
Recent Project
Selects a recent project to open.
Exit
Closes GenomeStudio Genotyping Module Genotyping
Module.
Table 11 File Menu Functions
Edit Menu
Function Description
Cut
Cuts the selected content.
Copy
Copies the selected content.
Table 12 Edit Menu Functions
Editing Data
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Function Description
Paste
Pastes the selected content.
Select All
Selects all data in the table.
View Menu
Function Description
Save Current View
Saves the current window configuration.
Restore Default View
Restores the default window configuration.
Save Custom View
Saves a custom windowconfiguration.
Load Custom View
Loads a saved window configuration.
Log
Shows or hides the Log window.
Project
Shows or hides the Project window.
Table 13 View Menu Functions
Analysis Menu
Function Description
Exclude Samples by Best
Run
Includes the sample with the highest GC10 or GC50 score
for each sample ID. Excludes all the other samples.
Cluster All SNPs
Clusters all SNPs based on the samples in a project and
determine the genotype score for each locus. The clustering
function overrides cluster files that are clustered at project
creation.
Update SNP statistics
Updates SNP statistics.
Edit Replicates
Edits, includes, or excludes replicates for a sample.
Edit Parental Relationships
Edits, includes, or excludes P-C and P-P-C relationships for
a sample.
Update
Heritability/Reproducibility
Errors
Updates replicate P-C, and P-P-C heritability information in
columns andreports.
Reports
Generates the following reports:
• Reproducibility and Heritability Report
• Final Report
• DNA Report
• Locus Summary Report
• Locus x DNA Report
Table 14 Analysis Menu Functions
Main Window Menus
GenomeStudio Genotyping Module v2.0
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Function Description
View Controls Dashboard
Allows you to view intensity data associated with various
control probes.
Paired Sample Editor
Edits the list of paired samples.
Calculate Paired Sample
LOH/CN
Calculates LOH and copy number-related scores for paired
samples.
Show Genome Viewer
Shows the Illumina Genome Viewer (IGV).
Import Allele Calls
Imports allele calls.
Export Allele Calls
Exports allele calls.
Remove Imported Allele
Calls
Removes imported allele calls from theproject.
Create Plug-in Column
Selects an algorithm-based column plug-in. Use the column
plug-in to create asubcolumn.
Tools Menu
Function Description
Options
• Project—Changes the projectsettings.
• GenomeStudio—Modifies settings and attributes.
• Module—Modifies module properties for either Genotyping
or Polyploid Genotyping.
New Data Track Table
Adds a user-defined name for the new data track table.
Show Genome Viewer
Shows data in the Illumina Genome View (IGV).
Table 15 Tools Menu Functions
Window Menu
Click the checkbox to show or to hide the following windows:
} SNP Graph
} Heat Map
} SNPGraph Alt
} Samples Table
} Full Data Table
} SNP Table
} Paired Sample Table
} Errors Table
} Sample Graph
Editing Data
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Help Menu
Function Description
About GenomeStudio
Shows the GenomeStudio version and the software copyright
information.
Help
Opens the GenomeStudio support page.
Table 16 Help Menu Functions
SNP Graph Toolbar
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SNP Graph Toolbar
Use the buttons in the graph toolbar to change the way your data appears in the graphs.
These tools do not modify the data in your project.
Icon Tool Name Description
Polar Coordinates Displays the plot in polar coordinates.
X-axis represents normalized theta.
Y-axis represents the distance of the point to the origin.
Cartesian Coordinates Displays the plot in Cartesian coordinates.
X-axis represents the intensity of the A allele.
Y-axis represents the intensity of the B allele.
Plot Normalization Values Views samples in raw format. This option toggles
between raw and normalized values.
Make Dots Larger Enlarges the dot size.
Make Dots Smaller Reduces the dot size.
Copy Plot to Clipboard Copies the plot to the clipboard.
Shade Call Region Applies color to the gene plot calling regions.
The size of the shaded area defines the cutoff gene call
score.
Default Mode Draws a rectangle area that includes the samples you
want to analyze.
Pan Mode Drags the graph in the direction you want to analyze.
Lasso Mode Draws a region that includes the samples you want to
analyze.
Zoom Mode Zooms in or out by scrolling your mouse wheel up and
down.
Auto Scale X-Axis Scales SNPs to the X-axis.
Auto Scale Y-Axis Scales SNPs to the Y-axis.
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Data Table Toolbar
Use the buttons in the table toolbar to change the appearance of your data in the statistics
tables. These tools do not modify the data in your project.
Icon Name Description
Calculate Updates all statistics in the table. The button is active
when statistics are out of sync.
Select all Highlights all the rows in the data table.
Copy selected rows to the
clipboard
Copies selected rows or columns to the clipboard.
Export displayed data to a
file
Exports selected rows or columns to a file.
Import columns into the
table
Imports sample or loci data from a tab-delimited file.
Sort column (Ascending) Sorts the data table in ascending order by the selected
column.
Sort column (Descending) Sorts the data table in descending order by the selected
column.
Sort by multiple columns Sorts the data table by more than one column.
Line plot Displays a line plot of the sample or loci statistics.
Scatter plot Displays a scatter plot of the sample or loci statistics.
Histogram plot Displays a histogram of the sample or loci statistics.
Box plot Displays a box plot of the sample or loci statistics.
Frequency plot Displays a frequency plot of the sample or loci statistics.
Pie chart Displays a pie chart of the sample or loci statistics.
Calculate new column Calculates data for a new column.
Column chooser Adds, removes, or moves columns in the data tables.
Filter rows Hides or shows rows of data based on the criteria you
specify.
This feature does not remove samples or loci from your
data set. It is for viewing information in the data table
only.
Clear filter Removes filter settings.
Lock selected columns Locks the selected column so it cannot scroll with other
columns.
Unlock selected columns Unlocks the selected column so that it scrolls with other
columns.
Context Menus
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Context Menus
Right-click in the graph or table to view the context menus.
Function Description
Define AA cluster
using selected sample
Determines the size and position of the AA genotypecluster.
Define AB cluster
using selected sample
Determines the size and position of the AB genotypecluster.
Define BB cluster using
selected sample
Determines the size and position of the BB genotypecluster.
Cluster this SNP
Determines cluster locations and score for eachlocus.
Cluster this SNP
Excluding Selected
Samples
Determines the cluster locations for each locus except the
excluded locations.
Configure Mark
Marks selected samples in a color youchoose.
Mark Selected Points -
<Add New>
Creates a new mark.
Clear Marks - <All>
Clears all marks.
Exclude Selected
Samples
Excludes selected samples from thegenoplot.
Include Selected
Samples
Includes selected samples in the genoplot.
Show Legend
Displays the genoplot marks legend.
Show Excluded
Samples
Shows excluded samples.
Auto Scale Axes
Scales the axes.
Show Only Selected
Shows the selected samples.
Copy Image to File as
Copies an image to 1 of the following files:
• bitmap
• GPEG
• PNG
• GIFF
• TIFF
Table 17 Graph Window Context Menu
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Function Description
Show Only Selected
Rows
Shows your SNPs of interest.
Configure Marks
Configures marks.
Mark Selected Rows |
<Add New>
Creates a mark and marks selectedrows.
Select Marked Rows
Selects marked rows.
Clear Marks | <All>
Clears all marks.
Table 18 Full Data Table Context Menu
Function Description
Cluster Selected SNP
Clusters a selected SNP.
Zero Selected SNP
Zeroes a selected SNP.
Set Genotyping
Intensity Threshold for
Selected SNPs
Opens the Set Genotyping Intensity Threshold dialog box. You
can enter the threshold value.
Set Aux Value
Sets the aux value of a SNP.
Update Selected SNP
Statistics
Updates selected SNP statistics.
SNP Properties
Opens the SNP Properties dialog box. You can manually edit the
properties.
Show Only Selected
Rows
Shows only selected rows in the SNP Table.
Configure Marks
Configures marks.
Mark Selected Rows |
<Add New>
Creates a mark and mark selectedrows.
Select Marked Rows
Selects marked rows.
Clear Marks | <All>
Clears all marks.
Table 19 SNP Table Context Menu
Function Description
Exclude Selected
Sample
Excludes the selected sample.
Include Selected
Sample
Includes the selected sample.
Table 20 Samples Table Context Menu
Context Menus
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Function Description
Recalculate Statistics
for Selected Sample
Recalculates statistics for selected samples.
Recalculate Statistics
for All Samples
Recalculates statistics for all samples.
Estimate Gender for
Selected Samples
Estimates gender for the selected samples.
Display Image
Displays image when you have the *.idat file, the *.locs file, the
*.xml file, and the *.jpg or *.tif image file for the sample or
samplesection.
Set Aux Value
Sets the aux value of a sample.
Sample Properties
Changes values for sample data.
Upload Selected
Samples to Illumina
Controls Database
Uploads selected samples to the Illumina Controls Database.
Show Only Selected
Rows
Shows only selected rows.
Configure Marks
Configures marks.
Mark Selected Rows |
<Add New>
Creates a mark and mark selectedrows.
Select Marked Rows
Selects marked rows.
Clear Marks | <All>
Clears all marks.
Function Description
Show Only Selected
Rows
Configures the Samples table to show only selected rows.
Edit Replicates
Edits replicates.
Edit Parental
Relationships
Edits parental relationships.
Configure Marks
Allows you to configure marks.
Mark Selected Rows |
<Add New>
Configures marks.
Select Marked Rows
Selects marked rows.
Clear Marks | <All>
Clears all marks.
Table 21 Error Table Context Menu
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Chapter 5
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Chapter 5 Common Tasks
Common Tasks
Select Samples in the SNPGraph 36
Display Marked Samples 37
Customize the SNP Table 38
View Samples in the Controls Dashboard 39
Update SNP Statistics 40
Change the No-Call Threshold 41
Common Tasks
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Select Samples in the SNPGraph
For the SNP Graph, selected rows in the Samples Table correspond with the samples in the
SNP Graph.
1 In the main window, select the SNPGraph tab.
2 In the Default Mode, click-and-drag on the graph to draw a rectangle.
When you release the button, all points in the rectangle are selected.
3 To add additional samples without losing your original selection, press and hold the
Ctrl key and select additional samples.
4 [Optional] To change to (Pan Mode), position the cursor over an empty region of the
plot (not on a cluster), then press and hold the Shift key.
5 [Optional] To change to (Lasso Mode), press and hold the Z key.
Selected samples are highlighted in yellow by default.
Figure 1 SNP Graph
Exclude Samples
You can exclude poor quality samples from clustering.
1 In the main window, right-click in the SNPGraph.
2 Select Exclude Selected Samples.
3 Click Yes.
Plot Excluded Samples
After excluding one or more samples from your sample group, you can plot the excluded
samples in the genoplot.
1 In the main window, select Tools | Options | Project.
2 In Options, click the Plot excluded samplescheckbox.
3 Click OK.
Display Marked Samples
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Display Marked Samples
You can customize the color of the selected samples. Marked samples overwrite the default
genotyping colors.
1 In the main window, right-click in the SNPGraph.
2 Select Configure Marks.
3 Click Add to create a mark.
4 Enter a name for your mark.
5 Select a color from the drop-down menu.
6 Click OK.
View Legend in Graph
1 In the main window, right-click in the graph.
2 Select Show Legend.
3 Click Yes.
Common Tasks
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Customize the SNP Table
Use the Column Chooser to select the columns you want to display in the SNP table and
arrange the columns in any order.
1 In the SNP table, click the Column Chooser tool.
2 Click the columns you want to display, and then click Show.
3 Click the columns you want to hide, and then click Hide.
4 [Optional] Select and drag a column back and forth between the Displayed and Hidden
Columns sections to customize your table.
5 [Optional] Select a column and drag the column header up or down in the order that
you want the columns to appear.
6 Click OK.
View Samples in the Controls Dashboard
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View Samples in the Controls Dashboard
View your samples in the Controls dashboard.
1 In the main window, select Analysis | View Controls Dashboard.
The Controls dashboard does not show excluded samples.
2 Click File, and select 1 of the following options:
} Export Data—Lets you save the data in a (*.csv) file.
} Page Setup
} Print Preview
} Print
} Close
Common Tasks
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Update SNP Statistics
When you adjust the loci or metrics, the SNP statistics require an update as indicated by
the red highlighted rows in the SNPtable.
The time to update increases with the size of the project. For best practices, make several
edits before updating the SNPs statistics.
1 In the main window, select Analysis | Update SNP Statistics.
Change the No-Call Threshold
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Change the No-Call Threshold
In the SNPgraph, samples are colored by their genotype call. Samples that are in black and
are located in the lighter shaded regions indicate that they fall below the user-defined
threshold value. As a result, these samples are assigned as no-call.
1 In the main window, select Tools | Options | Project.
2 In the No-call Threshold field, enter your value.
We recommend the 0.15 GenCall cutoff score for Infinium products.
3 Click OK.
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Chapter 6
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Chapter 6 Generating Clusters
Generating Clusters
Introduction 44
Cluster SNPs 45
Edit Clusters 46
Export a Cluster File 47
Generating Clusters
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Introduction
Genotype calls for genotyping assays are based on information from a standard or custom
cluster file that provides statistical data from a sample set. The clustering process can
generate the most accurate genotype for the data set loaded in the project because the
locations of the heterozygotes and homozygotes for each SNP can vary from SNP to SNP.
In the Genotyping Module, we use the Gentrain3 clustering algorithm to minimize
erroneously clustered loci and deliver accurate genotyping data.
The software can automatically determine the cluster positions of the genotypes and
estimate the missing clusterpositions for SNPs that have 1 or 2 clusters that lack
representation.
We recommend that you have a minimum of 100 or more diverse samples to achieve a
representation of all clusters. The most desirable number of samples to use for cluster file
generation varies depending on the minor allele frequency of your SNPs and the studied
population.
Cluster SNPs
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Cluster SNPs
1 In the main window, select Analysis | Cluster All SNPs.
2 Click Yes to update SNP statistics for all SNPs.
Change the Clustering Intensity Threshold
You can change the clustering intensity threshold before reclustering all SNPs.
1 In the main window, select Tools | Options | Project.
2 At the Clustering Intensity Threshold field, enter the value you want to use.
3 Click OK.
Change the Color of Cluster Calls
In the SNPgraph, the software assigns a color to samples based on their genotype call. You
can customize the colors.
1 In the main window, select Tools | Options | Project.
2 In the Colors section, click the drop-down arrow to select the colors you want for the
specific genotype calls.
3 Click OK.
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Edit Clusters
Redefine the Cluster
1 Select the samples in the graph.
2 Right-click to display the context menu.
3 Select Define AB (or AA, or BB) cluster using selectedsamples.
Exclude Samples From Clustering
1 Select samples in the graph.
2 Right-click to display the context menu.
3 Select Cluster this SNP excluding selected samples.
Move the Cluster Location
1 In the graph, press and hold the Shift key.
2 Click at the center of the cluster. The move cursor appears.
3 Drag the cluster to a new location.
Change the Cluster Height and Width
1 In the graph, press and hold the Shift key.
2 Click at the edge of an oval. The resizing cursor appears.
3 Drag the edge of the oval to reshape the cluster.
Export a Cluster File
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Export a Cluster File
1 In the main window, select File | Export Cluster Positions.
2 Select 1 of the following options:
} For Selected SNPs
} For All SNPs
3 Browse to the location where you want to save your cluster file.
4 [Optional] Rename your cluster file.
5 Click Save.
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Chapter 7
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Chapter 7 Analyzing Data
Analyzing Data
Import Phenotype Information 50
Estimate the Gender of Selected Samples 51
Edit the Sample Properties 52
Analyze Paired Sample Data 53
View Concordance Calculations 54
Export Allele Calls 55
Import Allele Calls 56
GenomeStudio Plug-ins 57
Analyzing Data
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Import Phenotype Information
You can import a phenotype information file (*.csv) into a project. The file must contain an
Index column that corresponds to the Index column in the Samples table.
You can import the following phenotypes in a Genotyping Module project:
} Gender
} Ethnicity
} Age
} Weight
} Blood Pressure Systolic
} Blood Pressure Diastolic
} Blood Type
} Phenotype Pos 1
} Phenotype Pos 2
} Phenotype Pos 3
} Phenotype Neg 1
} Phenotype Neg 2
} Phenotype Neg 3
1 In the main window, select File | Import Phenotype Information From File.
2 In the File name field, browse to the phenotype information file you want to use.
3 Click Open to import the file.
Estimate the Gender of Selected Samples
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Estimate the Gender of Selected Samples
1 In the Samples table, select the samples you want to analyze.
2 Right-click on the selected samples.
3 Select Estimate Gender for Selected Samples.
4 Select 1 of the following options:
} Yes—The Gender and Gender Est columns are populated with the estimated gender
for the selected samples.
} No—The Gender Est column is populated with the estimated gender for the selected
samples.
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Edit the Sample Properties
1 In the Samples table, select the samples you want to analyze.
2 Right-click anywhere on the selected samples.
3 Select Sample Properties.
4 Enter the information in the appropriate column.
5 Click OK.
Analyze Paired Sample Data
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Analyze Paired Sample Data
Paired sample data is useful for analyzing chromosomal aberrations. The Paired Sample
table shows the differences in statistical measurements for a pair of samples, such as a
subject sample and a referencesample.
Create paired samples by designating 1 of the following:
} Subject-and-reference pairs in the sample sheet used to create a project.
} Subject-and-reference samples using the paired samples editor.
1 In the main window, select Analysis | Paired Sample Editor.
2 After you designate paired samples, the Paired Sample table shows the paired sample
data.
3 In the Paired Sample table, select the samples you want to analyze.
4 Analyze the paired sample with the following options:
a [Optional] Select Analysis | Calculate Paired Sample LOH/CN Scores.
b [Optional] View paired samples in the SNP graph.
c [Optional] View paired samples in the Integrative Genomics Viewer (IGV).
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View Concordance Calculations
The Genotyping Module can show the concordance calculations when you import allele
calls for the same sample from another project.
1 In the Samples table or in the Full Data table, click the Column Chooser tool.
2 Select Concordance, and then click Show.
3 Click OK.
Export Allele Calls
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Export Allele Calls
You can compare the allele calls in your project to the allele calls in another project. When
you export allele calls and import them into another project, the sample names in the
project must be the same. If the sample names do not match, the allele calls cannot be
compared.
1 In the main window, select Analysis | Export Allele Calls.
2 Browse to the location where you want to save the allele calls.
3 Click OK.
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Import Allele Calls
You can import allele calls from another project to analyze in your project.
1 In the main window, select Analysis | Import Allele Calls.
2 Click Browse and navigate to the location of the allele calls you want to import.
3 Select the file you want from the Files Found in the Import Directory area.
4 Click OK.
GenomeStudio Plug-ins
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GenomeStudio Plug-ins
The GenomeStudio Genotyping Module provides plug-ins for copy number (CN) analysis,
loss of heterozygosity (LOH) visualization, and other types of analysis. To download the
plug-ins, see GenomeStudio Plug-ins. You can install the plug-ins after installing the
Genotyping Module.
} Column plug-in—Creates subcolumns based on data in tables.
} CNV analysis plug-in—Creates a CNV analysis workflow in GenomeStudio,. See CNV
Analysis on page 57.
} Report plug-in—Creates custom reports.
Create a Custom Subcolumn
With the Column Plug-in option, you can create custom subcolumns in the Full Data table.
Install the column plug-in program to your desktop first, then copy the Dynamic Link
Libraries (DLL) file for the column plug-in to the directory: C:\Program
Files\Illumina\GenomeStudio 2.0
1 In the main window, select Analysis | Create Plug-In Column.
2 In the column plugins table, select a row from the list of available column plugins.
3 [Optional] At the New Subcolumn Name field, enter a name for the subcolumn.
4 [Optional] In the Column Plug-In Properties table, right-click in the column to enter
new values.
5 Click OK.
CNV Analysis
A CNV Analysis computes the estimated copy number (CNV Value) and the accuracy
score of the estimated copy number (CNV Confidence) for chromosomal regions in each
sample.
Create a CNV Analysis
Install one or more CNV analysis plug-ins before you can perform the task.
1 In the main window, select Analysis | CNV Analysis.
2 Click the Create New CNV Analysis drop-down menu, and then, select a CNV
algorithm.
3 [Optional] Click the Calculate Only Selected Samples checkbox.
4 [Optional] At the CNV Analysis Name field, enter a name.
5 [Optional] Modify parameters.
6 Click Calculate New CNV Analysis.
When analysis is complete, the CNV Region Display window opens.
7 Click OK to close the CNV Analysis dialog box.
Edit a CNV Analysis
You can activate or delete a CNV analysis. Also, you can use the CNV Analysis Region
Display and Full Data table to view the analysis.
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1 In the main window, select Analysis | CNV Analysis.
2 Edit the analysis in Current CNV Analyses list:
} Activate—Select the CNV analysis, and then, click OK.
} Delete—Right-click on the CNV analysis, and then, click Remove Analysis.
View CNV Analysis Region Display
The CNV Analysis Region Display is a heat map that shows the copy number values for
all samples. The heat map shows samples on the X-axis and chromosomal position on the
Y-axis.
1 In the main window, select Analysis | Show CNVRegion Display.
2 [Optional] Point the mouse over a region to view more information.
3 [Optional] Click the Zoom button to zoom in and out.
View CNV Analysis Data in the Full Data Table
You can view the CNV analysis that contains the estimated copy number and the
confidence score of the estimated copy number in the Full Data table.
1 In the Full Data table, click the Column Chooser button.
2 In the Hidden Subcolumns area, select CNV Value and CNV Confidence, and then,
click the Show button.
3 Click OK.
Chapter 8
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Chapter 8 Generating Reports
Generating Reports
Introduction 60
Generate a Final Report 61
DNA Report 62
Locus Summary Report 63
Locus x DNA Report 65
Generate a Reproducibility and Heritability Report 66
Generating Reports
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Introduction
You can generate the following reports using the Report Wizard:
} Final Report
} DNA Report
} Locus Summary Report
} Locus x DNA Report
Also, you can generate a Reproducibility and Heritability Report.
Generate a Final Report
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Generate a Final Report
The Genotyping Module produces a final report in a text (*.txt) or a comma-separated
values (*.csv) file format.
1 In the main window, select Analysis | Reports | Report Wizard.
By default, the final report option is selected.
2 Click Next.
3 Select 1 of the following options:
} All samples
} Selected samples
4 Click Next.
5 Select 1 of the following report formats:
} Standard—All data are presented in rows in the final report. You can choose the
statistics to include in the output.
} Matrix—Rows represent SNPs and columns represent samples. You can choose to
include the GenCall score or thegenotypes in the output.
} 3rd Party—You can specify the output style of the final report based on the
targetapplication for downstream analyses.
6 [Optional] Select Standard.
a In the Available Fields area, select the fields you want to include in the report.
Press Ctrl to select multiple fields.
b Click the Show button.
c At the Group by field, select whether you want to group by sample or bySNP.
7 [Optional] In the General Options area, select from the following:
} Tab —Generate the final report in a text (*.txt) file format.
} Comma—Generate the final report in a comma-separated values (*.csv) file format.
8 [Optional] Select Create map files.
9 [Optional] Specify the number of samples per file to include in the report.
10 Click Next.
11 At the Output Path field, browse to the directory you want to save the report or accept
the default directory.
12 At the Report Name field, enter a report name or accept the default name.
13 Click Finish.
The software generates the report and saves it in the specified directory.
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DNA Report
The Genotyping Module produces a DNA report in a comma-separated values (*.csv) file
format.
Statistic Description
Row
Row number.
DNA_Name
DNA name.
#No_Calls
Number of loci with GenCall scores below the call region
threshold.
#Calls
Number of loci with GenCall scores above the call region
threshold.
Call_Freq
Call frequency or call rate, calculated as
#Calls/(#No_Calls + #Calls).
A/A_Freq
Frequency of homozygous allele A calls.
A/B_Freq
Frequency of heterozygote calls.
B/B_Freq
Frequency of homozygous allele B calls.
Minor_Freq
Frequency of the minor allele.
50%_GC_Score
50th percentile GenCall score for all loci.
10%_GC_Score
10th percentile GenCall score for all loci.
0/1
An algorithm to determine whether to include or exclude
samples.
0—Exclude sample
1—Include sample
Table 22 DNA Report
Locus Summary Report
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Locus Summary Report
The Genotyping Module produces a locus summary report in a comma-separated values
(*.csv file) format.
Statistic Description
Row
Row number.
Locus_Name
Locus name from the manifest file.
IllumiCode_Name
Locus ID from the manifest file.
#No_Calls
Number of loci with GenCall scores below the call region
threshold.
#Calls
Number of loci with GenCall scores above the call region
threshold.
Call_Freq
Call frequency or call rate calculated as follows:
#Calls/(#No_Calls + #Calls)
A/A_Freq
Frequency of homozygote allele A calls.
A/B_Freq
Frequency of heterozygote calls.
B/B_Freq
Frequency of homozygote allele B calls.
Minor_Freq
Frequency of the minor allele.
GenTrain_Score
Quality score for samples clustered for this locus.
50%_GC_Score
50th percentile GenCall score for all samples.
10%_GC_Score
10th percentile GenCall score for all samples.
Het_Excess_Freq
Heterozygote excess frequency, calculated as (Observed -
Expected)/Expected for the heterozygote class. If f
AB
is the
heterozygote frequency observed at a locus, and p and q are the
major and minor allele frequencies, then het excess calculation is
the following:
ChiTest_P100
Hardy-Weinberg p-value estimate calculated using genotype
frequency. The value is calculated with 1 degree of freedom and
is normalized to 100 individuals.
Cluster_Sep
Cluster separation score.
AA_T_Mean
Normalized theta angles mean for the AAgenotype.
AA_T_Std
Normalized theta angles standard deviation for the
AAgenotype.
AB_T_Mean
Normalized theta angles mean for the ABgenotype.
Table 23 Locus Summary Report
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Statistic Description
AB_T_Std
Standard deviation of the normalized theta angles for the
ABgenotype.
BB_T_Mean
Normalized theta angles mean for the BBgenotypes.
BB_T_Std
Standard deviation of the normalized theta angles for the BB
genotypes.
AA_R_Mean
Normalized R value mean for the AAgenotypes.
AA_R_Std
Standard deviation of the normalized R value for the
AAgenotypes.
AB_R_Mean
Normalized R value mean for the ABgenotypes.
AB_R_Std
Standard deviation of the normalized R value for the
ABgenotypes.
BB_R_Mean
Normalized R value mean for the BBgenotypes.
BB_R_Std
Standard deviation of the normalized R value for the
BBgenotypes.
Locus x DNA Report
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Locus x DNA Report
The Genotyping Module produces a locus x DNA report in a comma-separated values
(*.csv) file format.
Statistic Description
instituteLabel
User-defined sample name for the DNA sample.
plateWell
Concatenation of the sample plate and sample well.
imageDate
Imaging date for the sample.
oligoPoolId
Manifest name.
bundleId
Bundle identifier.
status
Field is unused.
recordType
Record type shows 2 rows of data for each DNA sample.
• calls—A, B, or H
• Score_Call—GenCall score for the call.
data
Calls or scores for the DNA sample and locus.
Table 24 Locus x DNA Report
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Generate a Reproducibility and Heritability Report
The Genotyping Module produces an error output report of the samples in a comma-
separated values (*.csv file) format.
1 In the main window, select Analysis | Reports | Create Reproducibility and
Heritability Report.
} Without calculating errors
} With calculating errors
2 In the File Name field, enter a file name or accept the default name.
3 Click Save.
The software generates the report and saves it in the specified location.
Reproducibility and Heritability Statistics
The Genotyping Module produces a reproducibility and heritability report in a comma-
separated values (*.csv file) format. The report contains the following sections:
} Duplicate Reproducibility
} Parent-Child Heritability
} Parent-Parent-Child Heritability
Statistic Description
Rep1_DNA_Name
Sample name designated as replicate #1.
Rep2_DNA_Name
Sample name designated as replicate #2.
# Correct
Number of loci with consistent replicate
genotype comparisons.
# Errors
Number of loci with inconsistent replicate
genotype comparisons.
Total
Number of total genotype comparisons (1 genotype
comparison per locus per replicate pair). The report does not
include genotypes with intensities that fall below the no-call
threshold.
Repro_Freq
Reproducibility frequency. The error rate does not include
genotype calls that fall below the no-callthreshold.
Table 25 Duplicate Reproducibility
Statistic Description
Parent_DNA_Name
Sample name designated as parent in a
P-C relationship.
Child_DNA_Name
Sample name designated as child in a
P-C relationship.
Table 26 Parent-Child Heritability
Generate a Reproducibility and Heritability
GenomeStudio Genotyping Module v2.0
67
Statistic Description
# Correct
Number of loci with consistent parent-child genotype
comparisons.
# Errors
Number of loci with inconsistent parent-child
genotype comparisons.
Total
Number of total genotype comparisons (1 genotype
comparison per locus per parent-child pair). The report does not
include genotypes with intensities that fall below the no-call
threshold.
PC_Heritability_Freq
Heritability frequency calculated as (# Correct/Total).
Statistic Description
Parent1_DNA_Name
Sample name designated as parent #1 in a
P-P-C relationship.
Parent2_DNA_Name
Sample name designated as parent #2 in a
P-P-C relationship.
Child_DNA_Name
Sample name designated as child in a
P-P-C relationship.
# Correct
Number of loci with consistent Parent1-Child and Parent2-Child
genotype comparisons.
# Errors
Number of loci with inconsistent Parent1-Child or Parent2-
Child genotype comparisons.
Total
Total number of loci that contribute to the trio heritability
analysis. The report does not include loci for Parent1, Parent2,
or Child have genotypes with intensities that fall below the no-
call threshold.
P-P-C Heritability Freq
Heritability frequency calculated as (# Correct / Total).
Table 27 Parent-Parent-Child Heritability
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Document # 11319113 v01
Technical Assistance
GenomeStudio Genotyping Module v2.0
69
Technical Assistance
For technical assistance, contact Illumina Technical Support.
Website
www.illumina.com
Email
techsupport@illumina.com
Table 28 Illumina General Contact Information
Region Contact Number Region Contact Number
North America 1.800.809.4566 Japan 0800.111.5011
Australia 1.800.775.688 Netherlands 0800.0223859
Austria 0800.296575 New Zealand 0800.451.650
Belgium 0800.81102 Norway 800.16836
China 400.635.9898 Singapore 1.800.579.2745
Denmark 80882346 Spain 900.812168
Finland 0800.918363 Sweden 020790181
France 0800.911850 Switzerland 0800.563118
Germany 0800.180.8994 Taiwan 00806651752
Hong Kong 800960230 United Kingdom 0800.917.0041
Ireland 1.800.812949 Other countries +44.1799.534000
Italy 800.874909
Table 29 Illumina Customer Support Telephone Numbers
Safety data sheets (SDSs)—Available on the Illumina website at
support.illumina.com/sds.html.
Product documentation—Available for download in PDF from the Illumina website. Go
to support.illumina.com, select a product, then select Documentation & Literature.
Illumina
San Diego, California 92122 U.S.A.
+1.800.809.ILMN (4566)
+1.858.202.4566 (outside North America)
[email protected]
www.illumina.com