# 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="/files/IAiMonJMQQtvu7P5JO5x" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 3
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/NoFFj4vfnL8PLO4FxloJ" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 2
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/xvbpUTYcIatrVqIikrVD" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/zXFFhBqXn83OrVkWjeD6" 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="/files/vW9BmkZgTRL1J6RZfKLD" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 7
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/X1HpthFyOzz3RrMe1BGL" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/Q2J4RBPhiDCYlOWSVDgM" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 7
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/19EUNc4HxrG3dv4zfjMs" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 5
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/www.illumina.com)
  * TruSight Oncology 500 ctDNA, Box 6
    * Supplier = Illumina
    * Catalog Number = 20039252; 20039253; 20039254
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/HiMbZE9Em1XfXM2BDA1N" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/VTu5Lx0PLKHF4ugYYEqZ" 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://help.connected.illumina.com/clarity-lims/library-prep/trusight/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="/files/nIgwb7h2HamEgCRQisYM" 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       |             |                                           |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/clarity-lims/library-prep/trusight/trusight-oncology-500-ctdna-v1.1.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.