# 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 {% 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 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 {% 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 | | | 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 {% 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 = 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 {% 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 = 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 {% 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 = 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 {% 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 * 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 | | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.claritylims.illumina.com/ilass-and-infinium-arrays/ilass/ilass-infinium-genotyping-v1.1.0/ilass-infinium-genotyping-assay-pgx-v1.1.0.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.