TruSight Oncology 500 ctDNA v1.1

Overview

TruSight Oncology 500 ctDNA v1.1 includes the following functionality:

• Preconfigured TruSight Oncology 500 ctDNA v1.1 protocol that supports the preparation of 48 libraries from cfDNA.

• 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: TruSight Oncology 500 ctDNA v1.1

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 2

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 3

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 '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 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-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 true \
-h false \
-exp 'output.::Sample Volume (uL):: = (step.::Desired Input (ng):: / output.::Concentration:: ) ; \
output.::Buffer Volume (uL):: = step.::Final Volume (uL):: - output.::Sample Volume (uL):: ' \
-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}"

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 = Column

• Destination Containers

  • 96 well plate

Record Details

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

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 2: Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)

• Step Type = No Outputs

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 1

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 2

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 3: Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 3

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 4: Index PCR (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Index PCR (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Add Labels

• 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)

Add Labels

• Label Groups

  • TruSight Oncology 500 ctDNA NovaSeq

Record Details

• Step Data (Master Step Fields)
• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 5: Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 5

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 6

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 7

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 6: Capture Target One (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 5

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 6

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 '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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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}"

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 File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 7: Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)

• Step Type = No Outputs

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 5

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 6

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 7

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 8: Capture Target Two (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 3

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 5

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • Website = www.illumina.com

  • TruSight Oncology 500 ctDNA, Box 6

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 '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.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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}"

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 File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 9: Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

• Step Type = No Outputs

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 6

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 10: Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

• Master Step Name = Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSight Oncology 500 ctDNA, Box 3

    • Supplier = Illumina

    • Catalog Number = 20039252; 20039253; 20039254

    • 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 Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields