# 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

#### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

Set Next Step - Advance v1.0

#### 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

Set Next Step - Advance v1.0

#### 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

### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

#### 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 | |