GenomeStudio Genotyping Module V2.0 User Guide (11319113) V2

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GenomeStudio® Genotyping
Module v2.0
Software Guide

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

ILLUMINA PROPRIETARY

Document # 11319113 v01
September 2016

This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the
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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
MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND
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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.

Document # 11319113 v01

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
Table of Contents

Chapter 1 Overview
Introduction
Install the GenomeStudio Software
Start the GenomeStudio Software

Chapter 2 Getting Started
Introduction
Create a Project From LIMS
Create a Project From a Sample Sheet
Create a Project From Directories
Import Cluster Positions

Chapter 3 Viewing Data
Introduction
Full Data Table
SNP Table
Samples Table
Paired Sample Table
Errors Table

Chapter 4 Editing Data
Introduction
Main Window Menus
SNP Graph Toolbar
Data Table Toolbar
Context Menus

Chapter 5 Common Tasks
Select Samples in the SNP Graph
Display Marked Samples
Customize the SNP Table
View Samples in the Controls Dashboard
Update SNP Statistics
Change the No-Call Threshold

Chapter 6 Generating Clusters
Introduction
Cluster SNPs
Edit Clusters
Export a Cluster File

Chapter 7 Analyzing Data
Import Phenotype Information
Estimate the Gender of Selected Samples
Edit the Sample Properties

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Analyze Paired Sample Data
View Concordance Calculations
Export Allele Calls
Import Allele Calls
GenomeStudio Plug-ins

Chapter 8 Generating Reports
Introduction
Generate a Final Report
DNA Report
Locus Summary Report
Locus x DNA Report
Generate a Reproducibility and Heritability Report

Technical Assistance

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Document # 11319113 v01

Chapter 1 Overview

Introduction
Install the GenomeStudio Software
Start the GenomeStudio Software

GenomeStudio Genotyping Module v2.0

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Chapter 1

Overview

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.

Document # 11319113 v01

Install the GenomeStudio Software

Install the GenomeStudio Software
1

Navigate to the GenomeStudio support page, and then select Downloads.

Select GenomeStudio Software 2.0, and then select GenomeStudio Genotyping
Module 2.0 Installer.

Accept the software terms and license agreement, and then click Install.

GenomeStudio Genotyping Module v2.0

Overview

Start the GenomeStudio Software

From your desktop, double-click the GenomeStudio

icon.

In the Platform Login Form dialog box, enter your email and password from your
MyIllumina account.

Click Log In.

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Chapter 2 Getting Started

Introduction
Create a Project From LIMS
Create a Project From a Sample Sheet
Create a Project From Directories
Import Cluster Positions

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Chapter 2

Getting Started

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

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Create a Project From LIMS

Create a Project From LIMS
1

From your desktop, double-click the GenomeStudio

icon.

In the new project pane, click Genotyping.

Click Next.

Click Select from LIMS, and then click Next.

Click Login, and then enter your LIMS user name and password.

Click OK.

At the Institute field, select your institution.

At the Investigator field, select your investigator.

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 Start Date 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.

GenomeStudio Genotyping Module v2.0

Getting Started

Create a Project From a Sample Sheet
1

In the new project pane, click Genotyping, and then click Next.

In the Create field, enter the project name, and then click Next.

Click Use sample sheet to load sample intensities, and then click Next.

In the Sample Sheet field, browse to your sample sheet (*.csv) file.

In the Data Repository field, browse to the directory that contains your raw intensity
(*.idat) files.

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.

Click Next.

[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.

Click Finish.
Genotyping Module loads the files from the sample sheet and displays the data.

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In the new project pane, click Genotyping, and then click Next.

In the Create field, enter the project name, and then click Next.

Click Load sample intensities by selecting directories with intensity files, and then
click Next.

At the Manifest Repository field, browse to the file that contains your SNP manifest
(*.bpm) file.

At the Data Repository field, browse to the directory that contains your raw intensity
(*.idat) files.

Select one or more directories, and click Add, and then click Next.

[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.

[Optional] In the Project Settings area, select the following options:
} Pre-Calculate
} Cluster SNPs
} Calculate Sample and SNP Statistics
} Calculate Heritability
} Gen Call Threshold

Click Finish.

GenomeStudio Genotyping Module v2.0

Create a Project From Directories

Getting Started

Import Cluster Positions
You can import a cluster (*.egt) file when creating a project in the Genotyping Module.

In the GenomeStudio Project Wizard, click the Import cluster positions from a cluster
file checkbox.

At the Cluster File field, browse to the cluster file you want to use.

[Optional] Click Pre-Calculate to optimize your project speed based on your computer
memory capabilities.

[Optional] In the Project Creation Actions settings, select from the following options:
} Cluster SNPs
} Calculate Sample and SNP Statistics
} Calculate Heritability

At the GenCall Threshold field, specify the score cutoff for this project.
We recommend the 0.15 GenCall score cutoff for Infinium products.

Click Finish.

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Chapter 3 Viewing Data

Introduction
Full Data Table
SNP Table
Samples Table
Paired Sample Table
Errors Table

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Chapter 3

Viewing Data

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:
Table 1 Views in Genotyping Module

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.

SNP Table

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.

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Full Data Table

Full Data Table
The Full Data table contains data for all the samples.
Table 2 Full Data Table Columns
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 3 Full Data Table Subcolumns
Column Heading

Description

GType

Genotype for the sample.

Score

SNP call score for the sample.

Theta

Normalized Theta-value for the sample.

Normalized R-value for the sample.

X Raw

Raw intensity of the A allele.

Y Raw

Raw intensity of the B allele.

Normalized intensity of the A allele.

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.

GenomeStudio Genotyping Module v2.0

Viewing Data

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.

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SNP Table

SNP Table
The SNP Table shows the statistics for each SNP.
Table 4 SNP Table Columns
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.

GenomeStudio Genotyping Module v2.0

Viewing Data

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.

Table 5 SNP Table Subcolumns

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.

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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.

GenomeStudio Genotyping Module v2.0

SNP Table

Column Heading

Viewing Data

Samples Table
The Samples Table shows the statistics for each sample.
Table 6 Samples Table Columns

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.

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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.

GenomeStudio Genotyping Module v2.0

Samples Table

Column Heading

Viewing Data

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

Table 7 Samples Table Per-Manifest Subcolumns

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.

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Paired Sample Table

Paired Sample Table
The Paired Sample table shows statistics for paired samples.
Table 8 Paired Sample Table Columns
Column

Description

Index

SNP index row.

Name

SNP name.

SNP

SNP.

Address

Bead type identifier.

Chr

SNP chromosome.

Position

SNP chromosomal position.

Table 9 Per-Pair Sample Subcolumns
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.

GenomeStudio Genotyping Module v2.0

Viewing Data

Errors Table
The Errors table shows reproducibility errors or parent-child heritability errors.
Table 10 Errors Table Columns

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.

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Chapter 4 Editing Data

Introduction
Main Window Menus
SNP Graph Toolbar
Data Table Toolbar
Context Menus

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Chapter 4

Editing Data

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.

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Main Window Menus

Main Window Menus
File Menu
Table 11 File Menu Functions
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.

Sets up printing options.

Recent Project

Selects a recent project to open.

Exit

Closes GenomeStudio Genotyping Module Genotyping
Module.

Edit Menu
Table 12 Edit Menu Functions
Function

Description

Cut

Cuts the selected content.

Copy

Copies the selected content.

GenomeStudio Genotyping Module v2.0

Editing Data

Function

Description

Paste

Pastes the selected content.

Select All

Selects all data in the table.

View Menu
Table 13 View Menu Functions
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.

Analysis Menu
Table 14 Analysis Menu Functions
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

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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
Table 15 Tools Menu Functions
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).

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

GenomeStudio Genotyping Module v2.0

Main Window Menus

Function

Editing Data

Help Menu
Table 16 Help Menu Functions
Function

Description

About GenomeStudio

Shows the GenomeStudio version and the software copyright
information.

Help

Opens the GenomeStudio support page.

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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
Polar Coordinates

Make Dots Larger

Description
Displays the plot in polar coordinates.
X-axis represents normalized theta.
Y-axis represents the distance of the point to the origin.
Displays the plot in Cartesian coordinates.
X-axis represents the intensity of the A allele.
Y-axis represents the intensity of the B allele.
Views samples in raw format. This option toggles
between raw and normalized values.
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.
Draws a rectangle area that includes the samples you
want to analyze.
Drags the graph in the direction you want to analyze.

Cartesian Coordinates

Plot Normalization Values

Default Mode
Pan Mode
Lasso Mode

Auto Scale X-Axis

Draws a region that includes the samples you want to
analyze.
Zooms in or out by scrolling your mouse wheel up and
down.
Scales SNPs to the X-axis.

Auto Scale Y-Axis

Scales SNPs to the Y-axis.

Zoom Mode

GenomeStudio Genotyping Module v2.0

SNP Graph Toolbar

Editing Data

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
Calculate
Select all
Copy selected rows to the
clipboard
Export displayed data to a
file
Import columns into the
table
Sort column (Ascending)

Copies selected rows or columns to the clipboard.
Exports selected rows or columns to a file.
Imports sample or loci data from a tab-delimited file.

Sort by multiple columns

Sorts the data table in ascending order by the selected
column.
Sorts the data table in descending order by the selected
column.
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.
Removes filter settings.

Sort column (Descending)

Clear filter
Lock selected columns
Unlock selected columns

Description
Updates all statistics in the table. The button is active
when statistics are out of sync.
Highlights all the rows in the data table.

Locks the selected column so it cannot scroll with other
columns.
Unlocks the selected column so that it scrolls with other
columns.

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Context Menus

Context Menus
Right-click in the graph or table to view the context menus.
Table 17 Graph Window Context Menu
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

Creates a new mark.

Clear Marks -

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

GenomeStudio Genotyping Module v2.0

Editing Data

Table 18 Full Data Table Context Menu
Function

Description

Show Only Selected
Rows

Shows your SNPs of interest.

Configure Marks

Configures marks.

Mark Selected Rows |

Creates a mark and marks selected rows.

Select Marked Rows

Selects marked rows.

Clear Marks |

Clears all marks.

Table 19 SNP 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 |

Creates a mark and mark selected rows.

Select Marked Rows

Selects marked rows.

Clear Marks |

Clears all marks.

Table 20 Samples Table Context Menu

Function

Description

Exclude Selected
Sample

Excludes the selected sample.

Include Selected
Sample

Includes the selected sample.

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Context Menus

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 |

Creates a mark and mark selected rows.

Select Marked Rows

Selects marked rows.

Clear Marks |

Clears all marks.

Table 21 Error Table Context Menu
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 |

Configures marks.

Select Marked Rows

Selects marked rows.

Clear Marks |

Clears all marks.

GenomeStudio Genotyping Module v2.0

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Chapter 5 Common Tasks

Select Samples in the SNP Graph
Display Marked Samples
Customize the SNP Table
View Samples in the Controls Dashboard
Update SNP Statistics
Change the No-Call Threshold

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Chapter 5

Common Tasks

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.

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.

To add additional samples without losing your original selection, press and hold the
Ctrl key and select additional samples.

[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.

[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.

Select Exclude Selected Samples.

Click Yes.

Plot Excluded Samples
After excluding one or more samples from your sample group, you can plot the excluded
samples in the genoplot.

In the main window, select Tools | Options | Project.

In Options, click the Plot excluded samples checkbox.

Click OK.

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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.

Select Configure Marks.

Click Add to create a mark.

Enter a name for your mark.

Select a color from the drop-down menu.

Click OK.

View Legend in Graph
1

In the main window, right-click in the graph.

Select Show Legend.

Click Yes.

GenomeStudio Genotyping Module v2.0

Display Marked Samples

Common Tasks

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.

In the SNP table, click the Column Chooser

tool.

Click the columns you want to display, and then click Show.

Click the columns you want to hide, and then click Hide.

[Optional] Select and drag a column back and forth between the Displayed and Hidden
Columns sections to customize your table.

[Optional] Select a column and drag the column header up or down in the order that
you want the columns to appear.

Click OK.

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View Samples in the Controls Dashboard

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.

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

GenomeStudio Genotyping Module v2.0

Common Tasks

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.

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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.

In the No-call Threshold field, enter your value.
We recommend the 0.15 GenCall cutoff score for Infinium products.

Click OK.

GenomeStudio Genotyping Module v2.0

Change the No-Call Threshold

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Chapter 6 Generating Clusters

Introduction
Cluster SNPs
Edit Clusters
Export a Cluster File

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Chapter 6

Generating Clusters

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.

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Cluster SNPs

Cluster SNPs
1

In the main window, select Analysis |

Cluster All SNPs.

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.

At the Clustering Intensity Threshold field, enter the value you want to use.

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.

In the Colors section, click the drop-down arrow to select the colors you want for the
specific genotype calls.

Click OK.

GenomeStudio Genotyping Module v2.0

Generating Clusters

Edit Clusters
Redefine the Cluster
1

Select the samples in the graph.

Right-click to display the context menu.

Select Define AB (or AA, or BB) cluster using selected samples.

Exclude Samples From Clustering
1

Select samples in the graph.

Right-click to display the context menu.

Select Cluster this SNP excluding selected samples.

Move the Cluster Location
1

In the graph, press and hold the Shift key.

Click at the center of the cluster. The

Drag the cluster to a new location.

move cursor appears.

Change the Cluster Height and Width

In the graph, press and hold the Shift key.

Click at the edge of an oval. The

Drag the edge of the oval to reshape the cluster.

resizing cursor appears.

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In the main window, select File | Export Cluster Positions.

Select 1 of the following options:
} For Selected SNPs
} For All SNPs

Browse to the location where you want to save your cluster file.

[Optional] Rename your cluster file.

Click Save.

GenomeStudio Genotyping Module v2.0

Export a Cluster File

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Chapter 7 Analyzing Data

Import Phenotype Information
Estimate the Gender of Selected Samples
Edit the Sample Properties
Analyze Paired Sample Data
View Concordance Calculations
Export Allele Calls
Import Allele Calls
GenomeStudio Plug-ins

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Chapter 7

Analyzing Data

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

In the main window, select File | Import Phenotype Information From File.

In the File name field, browse to the phenotype information file you want to use.

Click Open to import the file.

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In the Samples table, select the samples you want to analyze.

Right-click on the selected samples.

Select Estimate Gender for Selected Samples.

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.

GenomeStudio Genotyping Module v2.0

Estimate the Gender of Selected Samples

Analyzing Data

Edit the Sample Properties

In the Samples table, select the samples you want to analyze.

Right-click anywhere on the selected samples.

Select Sample Properties.

Enter the information in the appropriate column.

Click OK.

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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 reference sample.
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.

After you designate paired samples, the Paired Sample table shows the paired sample
data.

In the Paired Sample table, select the samples you want to analyze.

Analyze the paired sample with the following options:
a
b
c

[Optional] Select Analysis | Calculate Paired Sample LOH/CN Scores.
[Optional] View paired samples in the SNP graph.
[Optional] View paired samples in the Integrative Genomics Viewer (IGV).

GenomeStudio Genotyping Module v2.0

Analyze Paired Sample Data

Analyzing Data

View Concordance Calculations
The Genotyping Module can show the concordance calculations when you import allele
calls for the same sample from another project.

In the Samples table or in the Full Data table, click the Column Chooser

Select Concordance, and then click Show.

Click OK.

tool.

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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.

Browse to the location where you want to save the allele calls.

Click OK.

GenomeStudio Genotyping Module v2.0

Export Allele Calls

Analyzing Data

Import Allele Calls
You can import allele calls from another project to analyze in your project.

In the main window, select Analysis | Import Allele Calls.

Click Browse and navigate to the location of the allele calls you want to import.

Select the file you want from the Files Found in the Import Directory area.

Click OK.

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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.

In the column plugins table, select a row from the list of available column plugins.

[Optional] At the New Subcolumn Name field, enter a name for the subcolumn.

[Optional] In the Column Plug-In Properties table, right-click in the column to enter
new values.

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.

Click the Create New CNV Analysis drop-down menu, and then, select a CNV
algorithm.

[Optional] Click the Calculate Only Selected Samples checkbox.

[Optional] At the CNV Analysis Name field, enter a name.

[Optional] Modify parameters.

Click Calculate New CNV Analysis.
When analysis is complete, the CNV Region Display window opens.

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.

GenomeStudio Genotyping Module v2.0

GenomeStudio Plug-ins

Analyzing Data

In the main window, select Analysis | CNV Analysis.

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.

[Optional] Point the mouse over a region to view more information.

[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.

In the Full Data table, click the Column Chooser

button.

In the Hidden Subcolumns area, select CNV Value and CNV Confidence, and then,
click the Show button.

Click OK.

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Chapter 8 Generating Reports

Introduction
Generate a Final Report
DNA Report
Locus Summary Report
Locus x DNA Report
Generate a Reproducibility and Heritability Report

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Chapter 8

Generating Reports

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.

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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.

Click Next.

Select 1 of the following options:
} All samples
} Selected samples

Click Next.

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
target application for downstream analyses.

[Optional] Select Standard.
a
b
c

In the Available Fields area, select the fields you want to include in the report.
Press Ctrl to select multiple fields.
Click the Show button.
At the Group by field, select whether you want to group by sample or by SNP.

[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.

[Optional] Select Create map files.

[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.

GenomeStudio Genotyping Module v2.0

Generate a Final Report

Generating Reports

DNA Report
The Genotyping Module produces a DNA report in a comma-separated values (*.csv) file
format.
Table 22 DNA Report
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

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The Genotyping Module produces a locus summary report in a comma-separated values
(*.csv file) format.
Table 23 Locus Summary Report
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 fAB 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.

GenomeStudio Genotyping Module v2.0

Locus Summary Report

Generating Reports

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.

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The Genotyping Module produces a locus x DNA report in a comma-separated values
(*.csv) file format.
Table 24 Locus x DNA Report
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.

GenomeStudio Genotyping Module v2.0

Locus x DNA Report

Generating Reports

Generate a Reproducibility and Heritability Report
The Genotyping Module produces an error output report of the samples in a commaseparated values (*.csv file) format.
1

In the main window, select Analysis | Reports | Create Reproducibility and
Heritability Report.
} Without calculating errors
} With calculating errors

In the File Name field, enter a file name or accept the default name.

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 commaseparated values (*.csv file) format. The report contains the following sections:
}
}
}

Duplicate Reproducibility
Parent-Child Heritability
Parent-Parent-Child Heritability

Table 25 Duplicate Reproducibility
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 26 Parent-Child Heritability
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.

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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).

Table 27 Parent-Parent-Child Heritability
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 Parent2Child 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 nocall threshold.

P-P-C Heritability Freq

Heritability frequency calculated as (# Correct / Total).

GenomeStudio Genotyping Module v2.0

Generate a Reproducibility and Heritability

Statistic

Document # 11319113 v01

For technical assistance, contact Illumina Technical Support.
Table 28 Illumina General Contact Information
Website
Email

www.illumina.com
techsupport@illumina.com

Table 29 Illumina Customer Support Telephone Numbers
Region
Contact Number
Region
North America
1.800.809.4566
Japan
Australia
1.800.775.688
Netherlands
Austria
0800.296575
New Zealand
Belgium
0800.81102
Norway
China
400.635.9898
Singapore
Denmark
80882346
Spain
Finland
0800.918363
Sweden
France
0800.911850
Switzerland
Germany
0800.180.8994
Taiwan
Hong Kong
800960230
United Kingdom
Ireland
1.800.812949
Other countries
Italy
800.874909

Contact Number
0800.111.5011
0800.0223859
0800.451.650
800.16836
1.800.579.2745
900.812168
020790181
0800.563118
00806651752
0800.917.0041
+44.1799.534000

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.

GenomeStudio Genotyping Module v2.0

Technical Assistance

Illumina
San Diego, California 92122 U.S.A.
+1.800.809.ILMN (4566)
+1.858.202.4566 (outside North America)
techsupport@illumina.com
www.illumina.com

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GenomeStudio Genotyping Module V2.0 User Guide (11319113) V2

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