iLASS Infinium Genotyping with PGx Assay v1.0

Prerequisites

The following global fields are used by the workflow. If these fields are already defined, they do not need to be added again.

1. From Configuration, select the Custom Fields tab.

2. Under Global Fields, select Container.

3. Select Product Type.

4. Under Field Type, select Text.

5. Under Field Options, make the following selections:

   • Required Field — No

   • Read Only — Yes

6. Select Step Run History.

7. Under Field Type, select Multiline Text.

8. Under Field Options, make the following selections:

   • Required Field — No

   • Read Only — No

Protocol 1: Automated Target Prep with PGx (ILASS Infinium Genotyping Assay with PGx v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select First Workflow Step (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Select First Workflow Step with PGx (ILASS Infinium Genotyping Assay with PGx v1.0)

• Step Type = No Outputs

Automations

Select First Step with PGx v1.0

• 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 false -h false -exp 'if (step.::First Workflow Step Options with PGx:: == ::Run Make WGA and PGx Step on Hamilton::) {nextStep = ::Make WGA and PGx Automated (ILASS Infinium Genotyping Assay with PGx v1.0)::} ; if (step.::First Workflow Step Options with PGx:: == ::Run Make WGA and PGx Step Manually::) {nextStep = ::Make WGA and PGx Manual (ILASS Infinium Genotyping Assay with PGx v1.0)::} ; if (step.::First Workflow Step Options with PGx:: == ::Run Batch DNA Step on Hamilton::) {nextStep = ::Batch DNA Automated (ILASS Infinium Genotyping Assay with PGx v1.0)::}' -log {compoundOutputFileLuid0}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  First Workflow Step Options with PGx	Text Dropdown	Required Field	Presets Run Make WGA and PGx Step Manually Run Batch DNA Step on Hamilton Run Make WGA and PGx Step on Hamilton
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 2: Batch DNA Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name: Batch DNA Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = Standards

• Derived Sample Generation = Fixed, 1

• Instrument Types

  • Hamilton Star

    • Vendor = Hamilton

Placement = Enabled

• Sample Grouping = Group by Containers

• Well Sort Order = Column

• Placement Pattern = Same Shape

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
• Step File Placeholders

  • Plate Manifest - Manually uploaded

  • Log - Automatically attached

  • Plate Transfer Plan - Manually uploaded

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Plating Source Barcode	Text
    Plating Source Well	Text

Step 3: Make WGA and PGx Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Make WGA and PGx (ILASS Infinium Genotyping Assay with PGx v1.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 2

• Instrument Types

  • Hamilton Star

    • Vendor = Hamilton

• Reagent Kits

  • AAX-Infinium

    • Supplier = Illumina

  • MA1-Infinium

    • Supplier = Illumina

  • MA2-Infinium

    • Supplier = Illumina

  • MSM-Infinium

    • Supplier = Illumina

  • PGM-Infinium

    • Supplier = Illumina

  • PGP-Infinium

    • Supplier = Illumina

  • RPM-Infinium

    • Supplier = Illumina

Placement = Enabled

• Sample Grouping = Group by Containers

• Well Sort Order = Column

• Placement Pattern = Same Shape

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Plate Transfer Plan	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Container

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Related Source Container	Text
    Related PGX Container	Text
    Related WGA Container	Text

Step 4: Make WGA and PGx Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Make WGA and PGx (ILASS Infinium Genotyping Assay with PGx v1.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 2

• Instrument Types

  • Hamilton Star

    • Vendor = Hamilton

• Reagent Kits

  • AAX-Infinium

    • Supplier = Illumina

  • MA1-Infinium

    • Supplier = Illumina

  • MA2-Infinium

    • Supplier = Illumina

  • MSM-Infinium

    • Supplier = Illumina

  • PGM-Infinium

    • Supplier = Illumina

  • PGP-Infinium

    • Supplier = Illumina

  • RPM-Infinium

    • Supplier = Illumina

Placement = Enabled

• Sample Grouping = Group by Containers

• Well Sort Order = Column

• Placement Pattern = Same Shape

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Plate Transfer Plan	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 5: Amplify WGA Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Amplify WGA Manual (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

Automations

Set Next Step - Advance v1.0

• 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}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Incubate the WGA plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Source DNA Plate Barcode	Text

Step 6: Amplify PGx Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Amplify PGx Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Step Type = No Outputs

Automations

Set Next Step - Advance v1.0

• 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}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Thermocycler Start Time	Text
  Thermocycler End Time	Text
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Place the PGx plate in the thermal cycler and start the cycling program
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Source DNA Plate Barcode	Text

Step 7: Recombine and Fragment DNA Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Recombine and Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = Pooling

• Aliquot Generation = Fixed, 1

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • FMS-Infinium

    • Supplier = Illumina

Pooling

• Label Uniqueness = Off

• Sample Grouping = Group by Containers

• Well Sort Order = Row

Placement = Enabled

• Well Sort Order = Row

• Placement Pattern = Row

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Plate Transfer Plan	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 8: Precipitate DNA Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Precipitate DNA Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • PM1-Infinium

    • Supplier = Illumina

  • PMX-Infinium

    • Supplier = Illumina

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  100% 2-Propanol Prep Date	Date
  Batch ID	Text	Read Only
  Comment	Multiline Text
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    IsRecombined	Toggle Switch		Default = No
    Source DNA Plate Barcode	Text

Step 9: Resuspend DNA Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Resuspend DNA Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • IBX-Infinium

    • Supplier = Illumina

  • RA1-Infinium

    • Supplier = Illumina

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Protocol 2: Automated BeadChip Processing with PGx (ILASS Infinium Genotyping Assay with PGx v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

Placement = Enabled

• Sample Grouping = Group by Containers

• Well Sort Order = Row

• Placement Pattern = Row

• Destination Containers

  • Infinium Genotyping with PGx Array LCG-8

  

  • Infinium Genotyping with PGx Array EX-24

  

  • Infinium Genotyping with PGx Array EX-48

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Plate Transfer Plan	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 2: Prepare Hyb Chamber Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Prepare Hyb Chamber Manual (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Reagent Kits

  • PB2-Infinium

    • Supplier = Illumina

Automations

Set Next Step - Advance v1.0

• 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}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Add 400 µl PB2 to the top and bottom wells of each beadchip subchamber in the hybridization chamber.
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 3: Wash BeadChips Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

Automations

Set Next Step - Advance v1.0

• 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}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 4: Extend and Stain BeadChips Automated (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Extend and Stain BeadChips Automated (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • ATM-Infinium

    • Supplier = Illumina

  • ATX-Infinium

    • Supplier = Illumina

  • EML-Infinium

    • Supplier = Illumina

  • LX1-Infinium

    • Supplier = Illumina

  • LX2-Infinium

    • Supplier = Illumina

  • PB1-Infinium

    • Supplier = Illumina

  • RA1-Infinium

    • Supplier = Illumina

  • SML-Infinium

    • Supplier = Illumina

  • STX-Infinium

    • Supplier = Illumina

  • XC3-Infinium

    • Supplier = Illumina

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    IsRecombined	Toggle Switch		Default = No
    Source DNA Plate Barcode	Text

Step 5: Wash and Coat BeadChips Manual (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Wash and Coat BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

  • XC4-Infinium

    • Supplier = Illumina

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batch ID	Text	Read Only
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Add 310 ml PB1 to the PB1 wash dish. Add 310 ml XC4 to the XC4 wash dish.
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay with PGx v1.0)

Protocol Type = Other

Next Steps Configuration

Step 1: Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

• Instrument Types

  • iScan

    • Vendor = Illumina

Automations

Set Next Step - Advance v1.0

• 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}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  BeadChip Barcode	Text	Read Only
  Instrument Type	Text	Read Only
  Instrument	Text	Read Only
  Instrument Run ID	Text	Read Only
  Run Start Time	Text	Read Only
  Run Complete Time	Text	Read Only
  Run Status	Text	Read Only
  Failure Reason	Text	Read Only
  Log	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    BeadChip Name	Text	Read Only
    Sample Section	Text	Read Only
    Imaging Result	Text

Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay with PGx v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Invoke Infinium Analysis (ILASS Infinium Genotyping Assay with PGx v1.0)

• Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.0)

• Step Type = No Outputs

Automations

Start Analysis v1.0

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -c -l "/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 \
-exp 'if( step.::Analysis Run Name::.length()>255 ){ fail( ::Analysis Run Name exceeds maximum length of 255:: )}; if( !step.::Analysis Run Name::.matches(::^(?![wW][fF][rR]\\..*)(^[0-9a-zA-Z-_\\.]*$)::)) { fail( ::Analysis Run Name must consist of only alphanumeric, underscore, hyphen and period characters and cannot start with wfr.:: ) }; ' \
-log {compoundOutputFileLuid0} \
-t true \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/iscan-automation.jar \
script:start_process_analysis -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}"

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Analysis Configuration ID	Text	Required Field
  Analysis Run Name	Text	Required Field
  Analysis Start Time	Text	Read Only
  Analysis Complete Time	Text	Read Only
  Analysis Status	Text	Read Only
  Log	Multiline Text	Read Only
• Step File Placeholders

  • Log - Automatically attached

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    BeadChip Name	Text	Read Only
    Sample Section	Text	Read Only
    Analysis Result	Text	Read Only