iLASS Infinium Genotyping with PGx Assay v1.1

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)

  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 Run History	Multiline Text
    Experiment Name	Text	Read Only
    Product Type	Text	Read Only
    Last Run Datetime	Text	Read Only
    IsInProgress	Toggle Switch	Read Only	Default = No

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

Set Next Step - Advance 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 '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 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

Set Next Step - Advance 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 '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 = 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 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)

  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 Input Containers	Text	Read Only

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)

  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 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)

  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: 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

Set Next Step - Advance 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 '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 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)

  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 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

Set Next Step - Advance 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 '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 (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)

  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 (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

Set Next Step - Advance 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 '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 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

• Sample Table (Global Step Fields)

  • Derived Sample

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Array Instrument	Text		Default = iScan

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)

  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
  Comment	Multiline Text
  Log	Multiline Text	Read Only
• Step File Placeholders

  • Scan Log - Manually uploaded

  • Run Metrics File - Manually uploaded

• 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
  • Measurement

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

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

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

  • Analysis Report - Manually uploaded

• 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