# Infinium LCG Assay Manual v1.2

## 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**

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-aca369b77a828249efdc3718d75d0451257a83f8%2Finfinium-lcg-protocol1-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### 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

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-6aa034c3d6dadf4e5e474e531951a60180b9d873%2Finfinium-lcg-protocol1-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Infinium LCG Kit Name</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 'input.::Infinium Kit Name:: = step.::Infinium LCG Kits::' -log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### 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 | <p>Presets</p><ul><li>Infinium Omni2.5Exome-8 Kit</li><li>Infinium OmniExpressExome-8 Kit</li><li>Infinium Global Diversity Array-8 v1.0 Kit</li><li>Infinium OmniZhongHua-8 Kit</li><li>Infinium Multi-Ethnic AMR/AFR-8 Kit</li><li>Infinium Multi-Ethnic EUR/EAS/SAS-8 Kit</li><li>Infinium Multi-Ethnic Global-8 Kit</li><li>Infinium Omni2.5-8 Kit</li></ul> |
* 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

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-1b07fd15a971c17e858a359925d9bd2498cf219b%2Finfinium-lcg-protocol1-step2-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Stock Lambda DNA and PicoGreen Dilution</summary>

* 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 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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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   | <ul><li>Default =<br>Add 66.7 uL 1X TE to well B1.<br>Add 100 µl 1X TE to the remaining wells of column 1.<br>Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.<br>Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.<br>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.</li></ul> |
  | No. of QDNA Plates                       | Numeric Dropdown |             | <ul><li><p>Presets</p><ul><li>1</li><li>2</li><li>3</li></ul></li><li>Default = 1</li></ul>                                                                                                                                                                                                                                                                                                                                                                                 |
  | PicoGreen (uL)                           | Numeric          | Read Only   |                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
  | Sample QDNA Plate instruction notes      | Multiline Text   | Read Only   | <ul><li>Default =<br>Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate.<br>Add 2 µl DNA sample to each well containing PicoGreen/1xTE</li></ul>                                                                                                                                                                                                                                                                                          |
  | Standard QDNA Plate instruction notes    | Multiline Text   | Read Only   | <ul><li>Default =<br>Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.<br>Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.</li></ul>                                                                                                                                                                                                    |
  | 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](https://www.illumina.com)
  * MSM-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * NaOH
  * RPM-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-bc28df21e0ff362d74bef536d4f5ae76bf5c0f89%2Finfinium-lcg-protocol1-step3-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Validate MSA6 Plate Barcode and Set Sample Placement Information</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon exit

{% 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 -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}"
```

{% endcode %}

</details>

<details>

<summary>Copy Infinium Kit Name</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 'output.::Infinium Kit Name:: = input.::Infinium Kit Name::' -log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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   | <p>Default =<br>Add 20 µl MA1 to each well of the MSA3 plate.<br>Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate<br>Add 4 µl 0.1N NaOH in to each sample well of the plate<br>Add 68 μl RPM in to each sample well of the plate.<br>Add 75 μl MSM in to each sample well of the plate<br>Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.</p> |
* 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

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-2e4d09def65caf4e977c4d7d7ea5fe3c4d518e5a%2Finfinium-lcg-protocol1-step4-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3a0d9a62eadbeceb60a2af911bb2698f259b13ec%2Finfinium-lcg-protocol1-step5-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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 (HD Methylation & LCG) | Multiline Text | Read Only   | Default = Add 50 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 6: Precipitate DNA (Infinium LCG 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](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b30eed8dc6acbe774d704ff85d4f10a70e3c5b53%2Finfinium-lcg-protocol1-step6-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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 (HD Methylation & LCG) | Multiline Text | Read Only   | <p>Default =<br>Add 100 μl PM1 to each well of the plate.<br>Add 300 μl 100% 2-propanol to each well of the plate.</p> |
* 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 7: Resuspend DNA (Infinium LCG 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](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-e295a1c6dc85a132b9f841be7449f9e490ab9b5c%2Finfinium-lcg-protocol1-step7-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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 |             |                                                   |
  | Instruction Notes (HD Methylation & LCG) | Multiline Text | Read Only   | Default = Add 46 µl RA1 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           |             |                                           |

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

Protocol Type = Sample Prep

**Next Steps Configuration**

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3adfb7f0c28eb658a2ea6a857e863d7ca7d27e33%2Finfinium-lcg-protocol2-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Hybridize DNA to LCG BeadChip (Infinium LCG 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](https://www.illumina.com)
  * XC4-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-bbbbe304b1a0355298018d10cc5ebf74ca33769f%2Finfinium-lcg-protocol2-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Generate Sample Placement for Infinium BeadChip</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
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"
```

{% endcode %}

</details>

<details>

<summary>Validate BeadChip Barcode</summary>

* Trigger Location = Placement
* Trigger Style = Automatic upon exit

{% code overflow="wrap" %}

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

{% endcode %}

</details>

<details>

<summary>Copy Sample Information</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% 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 '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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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

  * 8x1 LCG BeadChip

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-c3b9ff229a00092a24dcf9be146efb8552904f33%2F8x1-lcg-beadchip.png?alt=media" alt=""><figcaption></figcaption></figure>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**        | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                       |
  | --------------------- | -------------- | ----------- | ----------------------------------------------------------------------------------------------- |
  | Comment               | Multiline Text |             |                                                                                                 |
  | LCG Instruction Notes | Multiline Text | Read Only   | Default = Transfer 35 µl each sample from the plate to the appropriate section of the BeadChip. |
* 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 LCG 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](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-c1b9249d39b699ccd879fcf60b2a0143116db57e%2Finfinium-lcg-protocol2-step2-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

#### 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 LCG 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](https://www.illumina.com)
  * EML-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * LX1-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * LX2-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * PB1-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * RA1-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * SML-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * XC3-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)
  * XC4-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8f505fa42c587e13330e1650fc69b18fec912199%2Finfinium-lcg-protocol2-step3-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Array Instrument</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

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

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% 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 %}

</details>

<details>

<summary>Routing Script - iScan</summary>

* Trigger Location = Step
* Trigger Style = Automatic upon exit

{% code overflow="wrap" %}

```markup
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'"
```

{% endcode %}

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

</details>

#### 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   | <p>Default =<br>Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows:<br>150 µl RA1. Incubate for 30 seconds. Repeat 5 times.<br>225 µl LX1. Incubate for 10 minutes.Repeat once.<br>225 µl LX2. Incubate for 10 minutes. Repeat once.<br>300 µl EML. Incubate for 15 minutes.<br>250 µl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat twice.Incubate 5 minutes.<br>Set the the chamber rack temperature to the temperature indicated on the SML tube.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.</p>                                                                   |
  | Stain Instruction Notes                   | Multiline Text | Read Only   | <p>Default =<br>Fill the reservoir of each flow-through chamber as follows:<br>250 µl SML. Incubate for 10 minutes.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.<br>Wait 5 minutes.<br>250 µl ATM. Incubate for 10 minutes.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.<br>Wait 5 minutes. g 250 µl SML. Incubate for 10 minutes.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.<br>Wait 5 minutes.<br>250 µl ATM. Incubate for 10 minutes.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.<br>Wait 5 minutes.<br>250 µl SML. Incubate for 10 minutes.<br>250 µl XC3. Incubate for 1 minute. Repeat twice.<br>Wait 5 minutes.</p> |
  | Wash and Coat Beadships Instruction Notes | Multiline Text | Read Only   | <p>Default =<br>Add 310 ml PB1 to the PB1 wash dish.<br>Add 310 ml XC4 to the XC4 wash dish</p>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
* 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           |             |                                           |