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TruSight Tumor 170 v2.0

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Last updated 17 days ago

Overview

TruSight Tumor 170 v2.0 includes the following functionality:

Preconfigured TruSight Tumor 170 v2.0 protocol that supports the preparation of samples for the detection of gene variants across 170 gene targets in nucleic acids extracted from FFPE cancer tissue samples.
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.
Routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0)

Master Step Name = DNA/RNA FFPE Extraction (TruSight Tumor 170 v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 2
Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
Reagent Kits
- QIAGEN AllPrep DNA/RNA FFPE Kit
  - Supplier = Qiagen
  - Catalog Number = 80234

The version of DNA/RNA FFPE Extraction master step name may be different depending on the version of IPP installed.

Automations

Set Sample Type

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 'if (output.name.endsWith(::_RNA::)) {output.::Sample Type:: = ::RNA::}; if (output.name.endsWith(::_DNA::)) {output.::Sample Type:: = ::DNA::}' -log {compoundOutputFileLuid0}"

Set Next Step - Remove

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 = ::REMOVE::' -log {compoundOutputFileLuid0}"

Route DNA/RNA samples

Trigger Location = Step
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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'RNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit RNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'DNA' \
--WORKFLOW 'TruSight Tumor 170 v2.0.10' \
--STEP 'Qubit DNA QC (TruSight Tumor 170 v2.0.10)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Type
  Text Dropdown
  Required Field
  Custom Entries
  Presets
  DNA
  RNA
  Project
  Project Name
  Built-in

Protocol 2: RNA QC and cDNA Synthesis (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit RNA QC (TruSight Tumor 170 v2.0)

Master Step Name = Qubit RNA QC (TruSight Tumor 170 v2.0.10)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

The version of Qubit RNA QC master step name may be different depending on the version of IPP installed.

Automations

Assign QC flags - RNA

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 {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid0} -qcResult {compoundOutputFileLuid2} && /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 'input.::Concentration (ng/ul):: = output.::Concentration (ng/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 = Column
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Type
  Text Dropdown
  Required Field
  Custom Entries
  Presets
  DNA
  RNA
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Criteria 1 - Operator
Text Dropdown
Custom Entries
Presets
>=
<=
=
!=
Default = >=
Criteria 1 - Source Data Field
Text
Default = Concentration (ng/ul)
Criteria 1 - Threshold Value
Numeric
Default = 4.7
Decimal Places Displayed = 2
Criteria 2 - Operator
Text Dropdown
Custom Entries
Presets