Infinium XT Assay Manual v1.2

Overview

The Infinium XT Assay Manual workflow includes the following functionality.

• Preconfigured protocols to prepare 96 DNA samples for use with the 24x4 BeadChip.

• Support for custom content for XT format.

• Automated calculation of sample and buffer volumes.

• Automatic placement of samples when necessary.

• Automatic step transition when required.

• Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium XT Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Amplify DNA (Infinium XT Assay Manual v1.2)

• Master Step Name = Amplify DNA-Infinium XT v1.2

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • MA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • MA2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • NaOH

  • RAM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Validate MSA7 Plate Barcode and Set Sample Information

• Trigger Location = Placement

• 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 -exp 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA7:: ) ) {fail ( ::Invalid MSA7 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA7:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Set Infinium XT Kit Name and Next Step - Advance

• 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 'output.::Infinium Kit Name:: = step.::Infinium XT Kits:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Infinium XT Kits	Text	Required Field Read Only	Default = Infinium XT iSelect-96 Kit
  Instruction Notes	Multiline Text	Read Only	Default = Add 20 µl MA1 to each well of the plate. Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate. Add 4 µl 0.1N NaOH in to each sample well of the plate. Add 35 μl MA2 in to each sample well of the plate. Add 35 μl RAM in to each sample well of the plate.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 2: Incubate DNA (Infinium XT Assay Manual v1.2)

• Master Step Name = Incubate DNA-Infinium v1.2

• Step Type = No Outputs

Automations

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Step 3: Fragment DNA (Infinium XT Assay Manual v1.2)

• Master Step Name = Fragment DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • FMS-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes (HTS, XT)	Multiline Text	Read Only	Default = Add 25 μl FMS to each well of the plate.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Step 4: Precipitate DNA (Infinium XT Assay Manual v1.2)

• Master Step Name = Precipitate DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • 100% 2-propanol

  • PM1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  100% 2-propanol Prep Date	Date
  Blue Pellet Presence	Toggle Switch		Default = None Set
  Comment	Multiline Text
  Instruction Notes (HTS, XT)	Multiline Text	Read Only	Default = Add 50 μl PM1 to each well of the plate Add 155 μl 100% 2-propanol to each sample well

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Step 5: Resuspend DNA (Infinium XT Assay Manual v1.2)

• Master Step Name = Resuspend DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • RA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Protocol 2: BeadChip Processing (Infinium XT Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to XT BeadChip (Infinium XT Assay Manual v1.2)

• Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • PB2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

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 'output.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 24x4 XT BeadChip

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  XT Instruction Notes	Multiline Text	Read Only	Default = Using a 20 μl, 8-channel precision pipette, dispense 15 μl DNA sample into the appropriate BeadChip sections.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Step 2: Wash BeadChip (Infinium XT Assay Manual v1.2)

• Master Step Name = Wash BeadChip-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• 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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  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

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	BeadChip Barcode	Text	Read Only
    Derived Sample	BeadChip Position	Text	Read Only
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text

Step 3: Extend and Stain BeadChip (Infinium XT Assay Manual v1.2)

• Master Step Name = Extend and Stain BeadChip-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • 70% EtOH

  • ATM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • EDTA

  • EML-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • LX1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • LX2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • PB1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • RA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • SML-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC3-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Array Instrument

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

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 -exp 'input.::Array Instrument:: = ::iScan::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• 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}"

Routing Script - iScan

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ️ The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Extend Instruction Notes	Multiline Text	Read Only	Default = Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows: 150 µl RA1. Incubate for 30 seconds. Repeat 5 times. 225 µl LX1. Incubate for 10 minutes.Repeat once. 225 µl LX2. Incubate for 10 minutes. Repeat once. 300 µl EML. Incubate for 15 minutes. 250 µl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat twice.Incubate 5 minutes. Set the the chamber rack temperature to the temperature indicated on the SML tube. 250 µl XC3. Incubate for 1 minute. Repeat twice.
  Stain Instruction Notes	Multiline Text	Read Only	Default = Fill the reservoir of each flow-through chamber as follows: 250 µl SML. Incubate for 10 minutes. 250 µl XC3. Incubate for 1 minute. Repeat twice. Wait 5 minutes. 250 µl ATM. Incubate for 10 minutes. 250 µl XC3. Incubate for 1 minute. Repeat twice. Wait 5 minutes. g 250 µl SML. Incubate for 10 minutes. 250 µl XC3. Incubate for 1 minute. Repeat twice. Wait 5 minutes. 250 µl ATM. Incubate for 10 minutes. 250 µl XC3. Incubate for 1 minute. Repeat twice. Wait 5 minutes. 250 µl SML. Incubate for 10 minutes. 250 µl XC3. Incubate for 1 minute. Repeat twice. Wait 5 minutes.
  Wash and Coat Beadships 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

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Array Instrument	Text		Default = iScan
    Derived Sample	BeadChip Barcode	Text	Read Only
    Derived Sample	BeadChip Position	Text	Read Only
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text