# TruSight Oncology 500 ctDNA v1.1

## Overview

TruSight Oncology 500 ctDNA v1.1 includes the following functionality:

* Preconfigured TruSight Oncology 500 ctDNA v1.1 protocol that supports the preparation of 48 libraries from cfDNA.
* Automated calculation of sample and buffer volumes.
* Automated calculation or display of reagents at every step in the protocol.
* Automatic step transition when required.
* Automatic placement of samples (when necessary).
* Automated assignment of QC Pass/Fail, based on user-selected threshold values. A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

## Protocol 1: TruSight Oncology 500 ctDNA v1.1

Protocol Type = Library 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-b6ccaa8acdb95c0118129f07c0531d03671488c1%2Ftrusight-oncology-500ctdna-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Prepare cfDNA, Perform End Repair and A-Tailing (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 2
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 3
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Prepare cfDNA, Perform End Repair and A-Tailing master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3afa413041d8333df499bfd7dfa2cd394ccf074e%2Ftrusight-oncology-500ctdna-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Count Samples and Calculate Master Mix</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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /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.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
step.::ERA1-B (uL):: = step.::Total Samples:: * (26/3) ; \
step.::ERA1-A (uL):: = step.::Total Samples:: * (10/3) ' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Calculate Normalization</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 'output.::Sample Volume (uL):: = (step.::Desired Input (ng):: / output.::Concentration:: ) ; \
output.::Buffer Volume (uL):: = step.::Final Volume (uL):: - output.::Sample Volume (uL):: ' \
-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 = Row
  * 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** |
  | ------------------ | -------------- | -------------- | ----------------------------------------- |
  | Desired Input (ng) | Numeric        | Required Field | Default = 30                              |
  | ERA1-A (uL)        | Numeric        |                | Decimal Places Displayed = 2              |
  | ERA1-B (uL)        | Numeric        |                | Decimal Places Displayed = 2              |
  | Final Volume (uL)  | Numeric        |                | Default = 50                              |
  | Total Samples      | Numeric        |                | Default = 0                               |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Row
  * Table Columns - Global Fields

    | **Category**   | **Field Name**     | **Field Type** | **Options**    | **Additional Options and Dropdown Items** |
    | -------------- | ------------------ | -------------- | -------------- | ----------------------------------------- |
    | Derived Sample | Buffer Volume (uL) | Numeric        |                | Decimal Places Displayed = 2              |
    | Derived Sample | Concentration      | Numeric        | Required Field | Decimal Places Displayed = 2              |
    | Derived Sample | Conc. Units        | Text           | Required Field |                                           |
    | Derived Sample | Sample Name        | Built-in       |                |                                           |
    | Derived Sample | Sample Volume (uL) | Numeric        |                | Decimal Places Displayed = 2              |

### Step 2: Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Ligate Adapters (TruSight Oncology 500 ctDNA v1.1)
* Step Type = No Outputs
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 1
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 2
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Ligate Adapters master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b28583e05ae007e688337e5833449fc1d923273c%2Ftrusight-oncology-500ctdna-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** |
  | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | 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**         |
  | -------------------------- | -------------- | ----------- | ------------------------------------------------- |
  | Add ALB1 (uL) to each well | Numeric        |             | Default = 60                                      |
  | Add LIG3 (uL) to each well | Numeric        |             | Default = 5                                       |
  | Add UMI1 (uL) to each well | Numeric        |             | Default = 10                                      |
  | Note                       | Multiline Text |             | Default = Immediately after ligation: add 5ul STL |
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 3: Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Clean Up Ligation (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 3
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Clean Up Ligation master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-e0904f19bd8d4f87c6af3892ce0805e6f41672f1%2Ftrusight-oncology-500ctdna-step3-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** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 4: Index PCR (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Index PCR (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

{% hint style="info" %}
The version of Index PCR master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8743c222b463191de1a40cb8be82f612cc4259af%2Ftrusight-oncology-500ctdna-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       |             |                                           |

#### Add Labels

* Label Groups
  * TruSight Oncology 500 ctDNA NovaSeq

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**             | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Add EPM (uL) to each well  | Numeric        |             | Default = 20                              |
  | Add UPxx (uL) to each well | Numeric        |             | Default = 5                               |
  | Thermal Cycler Program     | Text           |             | Default = I-PCR                           |
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 5: Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Set Up First Hybridization (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 5
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 7
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Set Up First Hybridization master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-199198fc69198034b9009773068a59467494bf1f%2Ftrusight-oncology-500ctdna-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** |
  | -------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Add OPD2 (uL) to each well | Numeric        |             | Default = 5                               |
  | Add TCA1 (uL) to each well | Numeric        |             | Default = 10                              |
  | Add TCB1 (uL) to each well | Numeric        |             | Default = 15                              |
  | Thermal Cycler Program     | Text           |             | Default = HYB1                            |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 6: Capture Target One (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 5
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Capture Targets master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-60c37f499ffd44a0173aed929bb7e7fe165515db%2Ftrusight-oncology-500ctdna-step6-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Count Samples and Calculate Master Mix</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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /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 'step.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------- | -------------- | ----------- | ----------------------------------------- |
  | EE2 (uL)       | Numeric        |             | Decimal Places Displayed = 0              |
  | HP3 (uL)       | Numeric        |             | Decimal Places Displayed = 0              |
  | Total Samples  | Numeric        |             | Default = 0                               |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 7: Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Set Up Second Hybridization (TruSight Oncology 500 ctDNA v1.1)
* Step Type = No Outputs
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 5
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 7
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Set Up Second Hybridization master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-f19813ce6adc819a158909d1158fca5846c916bd%2Ftrusight-oncology-500ctdna-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 = 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** |
  | -------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Add OPD2 (uL) to each well | Numeric        |             | Default = 5                               |
  | Add TCA1 (uL) to each well | Numeric        |             | Default = 10                              |
  | Add TCB1 (uL) to each well | Numeric        |             | Default = 15                              |
  | Thermal Cycler Program     | Text           |             | Default = HYB2                            |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 8: Capture Target Two (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Capture Targets (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 3
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 5
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Capture Targets master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-f0d14b62dd1da09eef82d5e1a076d44809b61432%2Ftrusight-oncology-500ctdna-step8-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Count Samples and Calculate Master Mix</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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /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 'step.::EE2 (uL):: = step.::Total Samples:: * (95/3) ; \
step.::HP3 (uL):: = step.::Total Samples:: * (5/3) ' \
-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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------- | -------------- | ----------- | ----------------------------------------- |
  | EE2 (uL)       | Numeric        |             | Decimal Places Displayed = 2              |
  | HP3 (uL)       | Numeric        |             | Decimal Places Displayed = 2              |
  | Total Samples  | Numeric        |             | Default = 0                               |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 9: Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
* Step Type = No Outputs
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Amplified Enriched Libraries master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3e9c17245417acff2e7a04a9f86adfd84e8fd409%2Ftrusight-oncology-500ctdna-step9-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** |
  | -------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Add EPM (uL) to each well  | Numeric        |             | Default = 20                              |
  | Add PPC3 (uL) to each well | Numeric        |             | Default = 5                               |
  | Thermal Cycler Program     | Text           |             | Default = EL-PCR                          |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 10: Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)

* Master Step Name = Clean Up Amplified Enriched Libraries (TruSight Oncology 500 ctDNA v1.1)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSight Oncology 500 ctDNA, Box 3
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://www.illumina.com)

{% hint style="info" %}
The version of Clean Up Amplified Enriched Libraries master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-437b13aa2cbb6594aad026d347ccd749bafe13a9%2Ftrusight-oncology-500ctdna-step10-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** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * 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 | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |