Protocol 1: Batch DNA (ILASS Infinium Batch DNA v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Batch DNA (ILASS Infinium Batch DNA v1.1)

• Master Step Name = Batch DNA (ILASS Infinium Batch DNA v1.1)

• Step Type = Standard

• 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

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

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

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

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

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

Record Details

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

  • Log - Automatically attached

  • Analysis Report - Manually uploaded

• Sample Table (Global Step Fields)

  • Derived Sample

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.

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