# iLASS Infinium Genotyping Assay v1.0 ## Protocol 1: Automated Target Prep (iLASS Infinium Genotyping Assay v1.0) Protocol Type = Sample Prep **Next Steps Configuration**

### Step 1: Select First Workflow Step (ILASS Infinium Genotyping Assay v1.0) * Master Step Name = Select First Workflow Step (ILASS Infinium Genotyping Assay v1.0) * Step Type = No Outputs #### Automations

Select First Step 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:validateSampleCount -min 1 -max 1" ``` {% endcode %}

#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | --------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------- | | First Workflow Step Options | Text Dropdown | Required Field |

Presets

Run Make WGA Step Manually
Run Batch DNA Step on Hamilton
Run Make WGA Step on Hamilton

| * Step File Placeholders * Log - Automatically attached * AssayRunLog - Manually uploaded ### Step 2: Batch DNA Automated (ILASS Infinium Genotyping Assay 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 Automated (ILASS Infinium Genotyping Assay v1.0) * Master Step Name: Make WGA (ILASS Infinium Genotyping Assay v1.0) * 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) | **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 WGA Container | Text | | | ### Step 4: Make WGA Manual (ILASS Infinium Genotyping Assay v1.0) * Master Step Name = Make WGA (ILASS Infinium Genotyping Assay v1.0) * 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) | **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 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 %}

#### 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 6: Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0) * Master Step Name = Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0) * Step Type = No Outputs * Instrument Types * Tecan EVO * Vendor = Tecan * Reagent Kits * FMS-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 | | | Plate Transfer Plan | Multiline Text | Read Only | | * Step File Placeholders * Log - Automatically attached * AssayRunLog - Manually uploaded ### Step 7: Precipitate DNA Automated (ILASS Infinium Genotyping Assay 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 * 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 8: Resuspend DNA Automated (ILASS Infinium Genotyping Assay 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 #### 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 (ILASS Infinium Genotyping Assay v1.0) Protocol Type = Sample Prep **Next Steps Configuration**

### Step 1: Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay 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 Array EX-24

* Infinium Genotyping 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 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 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 * 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) | **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 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 v1.0) Protocol Type = Other **Next Steps Configuration**

### Step 1: Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay 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

#### 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 | | | 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 | | | Imaging Result | Text | | | ## Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay v1.0) Protocol Type = Sample Prep **Next Steps Configuration**

### Step 1: Invoke Infinium Analysis (ILASS Infinium Genotyping Assay 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 | |