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Infinium LCG Assay Manual v1.2

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Last updated 17 days ago

Overview

The Infinium LCG Assay Manual workflow includes the following functionality.

Preconfigured protocols to prepare 96 DNA samples for use with 8x1 LCG BeadChip products.
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 LCG Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium LCG Assay Manual v1.2)

Master Step Name = Select Infinium Kit-Infinium LCG v1.2
Step Type = No Outputs

Automations

Set Infinium LCG Kit Name

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 'input.::Infinium Kit Name:: = step.::Infinium LCG Kits::' -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
Infinium LCG Kits
Text Dropdown
Required Field
Presets
Infinium Omni2.5Exome-8 Kit
Infinium OmniExpressExome-8 Kit
Infinium Global Diversity Array-8 v1.0 Kit
Infinium OmniZhongHua-8 Kit
Infinium Multi-Ethnic AMR/AFR-8 Kit
Infinium Multi-Ethnic EUR/EAS/SAS-8 Kit
Infinium Multi-Ethnic Global-8 Kit
Infinium Omni2.5-8 Kit
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
  Well
  Built-in
  Derived Sample
  Infinium Kit Name
  Text
  Read Only
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Quantify DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

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 true -h false -exp 'step.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -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
Container
Container Name
Built-in
Container
Well
Built-in
Derived Sample
Infinium Kit Name
Text
Read Only
Derived Sample
Sample Name
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- 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
1X TE (mL)
Numeric
Read Only
1X TE for A1 (uL)
Numeric
Read Only
Lambda serial dilution instruction notes
Multiline Text
Read Only
Default = Add 66.7 uL 1X TE to well B1. Add 100 µl 1X TE to the remaining wells of column 1. Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix. Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix. Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
No. of QDNA Plates
Numeric Dropdown
Presets
1
2
3
Default = 1
PicoGreen (uL)
Numeric
Read Only
Sample QDNA Plate instruction notes
Multiline Text
Read Only
Default = Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate. Add 2 µl DNA sample to each well containing PicoGreen/1xTE
Standard QDNA Plate instruction notes
Multiline Text
Read Only
Default = Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate. Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Stock Lambda DNA (ng/uL)
Numeric
Stock Lambda DNA for A1 (uL)
Numeric
Read Only
Step File Placeholders
- Log - Automatically attached
- Results File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Collapse
- Well Sort Order = Row
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Derived Sample
  Infinium Kit Name
  Text
  Read Only
  Derived Sample
  Sample Name
  Built-in

Step 3: Amplify DNA (Infinium LCG Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium LCG v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH
- RPM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Validate MSA6 Plate Barcode and Set Sample Placement 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}-MSA6:: ) ) {fail ( ::Invalid MSA6 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA6:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

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::' -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
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 = Same Shape
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
Instruction Notes
Multiline Text
Read Only
Default = Add 20 µl MA1 to each well of the MSA3 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 68 μl RPM in to each sample well of the plate. Add 75 μl MSM in to each sample well of the plate Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.
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 4: Incubate DNA (Infinium LCG 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 5: Fragment DNA (Infinium LCG 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