iLASS Infinium Genotyping Assay v1.0

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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

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"

Record Details

Step Data (Master Step Fields)
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)
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

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)
Step File Placeholders
- Log - Automatically attached
- AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
- Container

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)
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

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)
Step File Placeholders
- Log - Automatically attached
- AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
- Derived Sample

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)
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)
Step File Placeholders
- Log - Automatically attached
- AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
- Derived Sample

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)
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)
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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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)
Step File Placeholders
- Log - Automatically attached
- AssayRunLog - Manually uploaded

Step 3: Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

Master Step Name = Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Reagent Kits
- PB1-Infinium
  - Supplier = Illumina

Automations

Set Next Step - Advance v1.0

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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)
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)
Step File Placeholders
- Log - Automatically attached
- AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
- Derived Sample

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)
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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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)
Step File Placeholders
- Log - Automatically attached
Sample Table (Global Step Fields)
- Derived Sample

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

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)
Step File Placeholders
- Log - Automatically attached
Sample Table (Global Step Fields)
- Derived Sample