TruSight Tumor 170 v2.0

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

Set Next Step - Remove

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Route DNA/RNA samples

• Trigger Location = Step
• Trigger Style = Automatic upon exit

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

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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 >= <= = != Default = >=
  Criteria 2 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - Automatically attached
  • Qubit Result File - Manually uploaded
• Sample Table

  • Enable QC Flags = Yes
  • Sample Display Default = Expand
  • Well Sort Order = Column
  • File Column Options

    • File Column Display = Hide
    • File Attachment Method = Auto
  • 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	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: Denature and Anneal RNA (TruSight Tumor 170 v2.0)

• Master Step Name = Denature and Anneal RNA (TruSight Tumor 170 v2.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • TruSight Tumor 170, Box 1

    • Supplier = Illumina
    • Catalog Number = OP-101-1004

The version of Denature and Anneal RNA master step name may be different depending on the version of IPP installed.

Automations

RNA Sample Dilution

• Trigger Location = Record Details
• Trigger Style = Manual button

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    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
  Dilution Concentration (ng/ul)	Numeric	Required Field	Range = 4.7 To 10 Decimal Places Displayed = 1
  FSM (ul)	Text Dropdown	Custom Entries	Presets 27 72 144 216
  RVT (ul)	Text Dropdown	Custom Entries	Presets 3 8 16 24
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets LQ-RNA HQ-RNA

• Step File Placeholders

  • Calculation Log File - Automatically attached
  • NextStep 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	Buffer Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 3: First Strand cDNA Synthesis (TruSight Tumor 170 v2.0)

• Master Step Name = First Strand cDNA Synthesis v2.0
• Step Type = No Outputs

The version of First Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets Synthesize 1st Strand 1stSS

• Step File Placeholders

  • Log File - Automatically attached
• Sample Table

  • Sample Display Default = Collapse
  • 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
    Project	Project Name	Built-in

Step 4: Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0)

• Master Step Name = Second Strand cDNA Synthesis (TruSight Tumor 170 v2.0.10)
• Step Type = No Outputs
• Reagent Kits

  • TruSight Tumor 170, Box 1

    • Supplier = Illumina
    • Catalog Number = OP-101-1004

The version of Second Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Thermal Cycler Program	Text	Read Only	Default = 2ndSS

• Step File Placeholders

  • Log File - Automatically attached
• Sample Table

  • Sample Display Default = Collapse
  • 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
    Project	Project Name	Built-in

Step 5: cDNA Clean Up (TruSight Tumor 170 v2.0)

• Master Step Name = cDNA Clean Up (TruSight Tumor 170 v2.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}_cDNA
• Reagent Kits

  • TruSight Tumor 170, Box 3

    • Supplier = Illumina
    • Catalog Number = OP-101-1004

The version of cDNA Clean Up master step name may be different depending on the version of IPP installed.

Automations

Assign Sample Type

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Remove

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Routing cDNA samples

• Trigger Location = Step
• Trigger Style = Automatic upon exit

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
  BIND1 Plate Barcode	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 3: DNA QC and Fragmentation (TruSight Tumor 170 v2.0)

Protocol Type = Library Prep