TruSight Oncology 500 ctDNA v1.1

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Last updated 1 month ago

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

Count Samples and Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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}"

Calculate Normalization

Trigger Location = Record Details
Trigger Style = Manual button

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}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Count Samples and Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Count Samples and Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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