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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