Overview

The Equalizer Workflow AmpliSeq for Illumina BRCA Panel is part of the preconfigured AmpliSeq for Illumina BRCA Panel protocols supporting the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

This protocol includes the following:

• Preconfigured AmpliSeq for Illumina BRCA Panel protocol that supports the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step in the protocol.

• Automatic step transition when required.

• Automatic placement of samples when necessary.

• Automated assignment of QC Pass/Fail, based on user-selected threshold values.

• A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: Equalizer Workflow (AmpliSeq for Illumina BRCA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

• Reagent Kits

  • Agencourt AMPure XP Beads

    • Supplier = Thermo

    • Catalog Number = NC9959336; NC9933872

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 2: Amplify Library (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
      -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
      -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

Group of Defaults

• Step Data

  • Group of Defaults = Equalizer Workflow

  • Master Step Fields
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Perform Capture and Clean Up (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library Equalizer for Illumina

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 4: Elute Library (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Elute Library (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Overview

The Standard Workflow AmpliSeq for Illumina BRCA Panel is part of the preconfigured AmpliSeq for Illumina BRCA Panel protocols supporting the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

This protocol includes the following:

• Preconfigured AmpliSeq for Illumina BRCA Panel protocol that supports the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step in the protocol.

• Automatic step transition when required.

• Automatic placement of samples when necessary.

• Automated assignment of QC Pass/Fail, based on user-selected threshold values.

• A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: Standard Workflow (AmpliSeq for Illumina BRCA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

• Reagent Kits

  • Agencourt AMPure XP Beads

    • Supplier = Thermo

    • Catalog Number = NC9959336; NC9933872

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 2: Amplify Library (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

• Reagent Kits

  • Agencourt AMPure XP Beads

    • Supplier = Thermo

    • Catalog Number = NC9959336; NC9933872

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

Group of Defaults

• Step Data

  • Group of Defaults = Standard Workflow

  • Master Step Fields
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 3: Perform Second Clean Up (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • Agencourt AMPure XP Beads

    • Supplier = Thermo

    • Catalog Number = NC9959336; NC9933872

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Overview

The Library Prep AmpliSeq for Illumina BRCA Panel is part of the preconfigured AmpliSeq for Illumina BRCA Panel protocols supporting the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

This protocol includes the following:

• Preconfigured AmpliSeq for Illumina BRCA Panel protocol that supports the preparation of uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step in the protocol.

• Automatic step transition when required.

• Automatic placement of samples when necessary.

• Automated assignment of QC Pass/Fail, based on user-selected threshold values.

• A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: Library Prep (AmpliSeq for Illumina BRCA Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Dilute DNA (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 2: Qubit (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Qubit (AmpliSeq for Illumina v1.1)

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName}

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

  • QC Log File - Automatically attached

  • QC Result File - Automatically attached

  • Upload File - Manually uploaded

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 4: Amplify Targets (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Amplify Targets (AmpliSeq for Illumina v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq BRCA Panel for Illumina

    • Supplier = Illumina

    • Catalog Number = 20019168
  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

Group of Defaults

• Step Data

  • Group of Defaults = BRCA

  • Master Step Fields
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 5: Partially Digested Amplicons (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina v1.1)

• Step Type = No Outputs

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 6: Ligate Indexes (AmpliSeq for Illumina BRCA Panel v1.1)

• Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • AmpliSeq Library PLUS for Illumina

    • Supplier = Illumina

    • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

Automations

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Add Labels

• Label Groups

  • AmpliSeq CD Indexes Set A for Illumina

  • AmpliSeq CD Indexes Set B for Illumina

  • AmpliSeq CD Indexes Set C for Illumina

  • AmpliSeq CD Indexes Set D for Illumina

  • AmpliSeq UD Indexes for Illumina (24 Indexes)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields