Illumina Lab Automation Software Solution (iLASS) Infinium Genotyping v1.0 consists of two workflows:

• iLASS Infinium Genotyping Assay v1.0

• iLASS Infinium Genotyping Assay with PGx v1.0

Each workflow includes a preconfigured protocol with the following functionality:

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step of the protocol.

• Automatic step transition when required.

• Automatic placement of samples when required.

• Automated assignment of QC Pass/Fail based on the user-selected threshold values.

• A routing script that allows library sequencing with any Illumina instrument.

Illumina Lab Automation Software Solution (iLASS) Infinium Genotyping v1.1 consists of three workflows:

• iLASS Infinium Genotyping Assay v1.1

• iLASS Infinium Genotyping Assay with PGx v1.1

• iLASS Infinium Batch DNA v1.1

The iLASS Infinium Batch DNA v1.1 workflow is a single-step protocol that supports preparation of automated cherry-picking of samples.

iLASS Infinium Genotyping Assay v1.1 and iLASS Infinium Genotyping Assay with PGx v1.1 workflows, each includes a preconfigured protocol with the following functionality:

• Automated calculation of sample and buffer volumes.

• Automated calculation or display of reagents at every step of the protocol.

• Automatic step transition when required.

• Automatic placement of samples when required.

• Automated assignment of QC Pass/Fail based on the user-selected threshold values.

• A routing script that allows library sequencing with any Illumina instrument.

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

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)
• 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)
• 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

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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Container

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)
• 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

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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

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

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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

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)
• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

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)
• 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)
• 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

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)
• 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

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)
• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

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)
• 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

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)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table (Global Step Fields)

  • Derived Sample

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

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)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table (Global Step Fields)

  • Derived Sample

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

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Make WGA and PGx (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name: Make WGA and PGx (ILASS Infinium Genotyping Assay v1.1)

• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Container

Step 2: Amplify WGA (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Amplify WGA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 3: Amplify PGx (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Amplify PGx (ILASS Infinium Genotyping Assay with PGx v1.1)

• Step Type = No Outputs

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 4: Recombine and Fragment DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Recombine and Fragment DNA (ILASS Infinium Genotyping Assay v1.1)

• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Container

Step 5: Precipitate DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • PM1-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 6: Resuspend DNA (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • IHX-Infinium

    • Supplier = Illumina

  • RA1-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Protocol 2: BeadChip Processing (ILASS Infinium Genotyping Assay with PGx v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Prepare Hyb Chamber (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB2-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 2: Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)

• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 3: Wash BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 4: Extend and Stain BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)

• 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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 5: Wash and Coat BeadChips (ILASS Infinium Genotyping Assay with PGx v1.1)

• Master Step Name = Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

  • XC4-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay with PGx v1.1)

Protocol Type = Other

Next Steps Configuration

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

• Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.1)

• Step Type = Analysis

• Derived Sample Generation = Fixed, 1

• Instrument Types

  • iScan

    • Vendor = Illumina

Record Details

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

  • Scan Log - Manually uploaded

  • Run Metrics File - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample
  • Measurement

Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay with PGx v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

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

• Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)

• Step Type = Analysis

• Derived Sample Generation = Fixed, 1

Automations

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)
• Step File Placeholders

  • Log - Automatically attached

  • Analysis Report - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Protocol 1: Target Prep (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Make WGA (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Make WGA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Instrument Types

  • Hamilton Star

    • Vendor = Hamilton

• Reagent Kits

  • AAX-Infinium

    • Supplier = Illumina

  • MA1-Infinium

    • Supplier = Illumina

  • MA2-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)
• Step File Placeholders

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Container

Step 2: Amplify WGA (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Amplify WGA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 3: Fragment DNA (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Fragment DNA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • FMS-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 4: Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • PM1-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 5: Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • IHX-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Protocol 2: BeadChip Processing (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB2-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 2: Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)

• 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 Array EX-24

  • Infinium Genotyping Array EX-48

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 3: Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Step 4: Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Instrument Types

  • Tecan EVO

    • Vendor = Tecan

• Reagent Kits

  • ATX-Infinium

    • Supplier = Illumina

  • EML-Infinium

    • Supplier = Illumina

  • LX1-Infinium

    • Supplier = Illumina

  • LX2-Infinium

    • Supplier = Illumina

  • PB1-Infinium

    • Supplier = Illumina

  • STX-Infinium

    • Supplier = Illumina

  • XC3-Infinium

    • Supplier = Illumina

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Step 5: Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Master Step Name = Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

  • XC4-Infinium

    • Supplier = Illumina

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}"

Record Details

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

  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Other

Next Steps Configuration

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

• Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.1)

• Step Type = Analysis

• Derived Sample Generation = Fixed, 1

• Instrument Types

  • iScan

    • Vendor = Illumina

Record Details

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

  • Scan Log - Manually uploaded

  • Run Metrics File - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample
  • Measurement

Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

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

• Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)

• Step Type = Analysis

• Derived Sample Generation = Fixed, 1

Automations

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)
• Step File Placeholders

  • Log - Automatically attached

  • Analysis Report - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample