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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

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