The Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel is part of the AmpliSeq for Illumina Comprehensive Cancer Panel protocols that include the following functionality:
Preconfigured AmpliSeq for Illumina Comprehensive Cancer Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.
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: Standard Workflow (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Clean Up Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Amplify Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Count Samples and Calculate Master Mix
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Calculate Total Samples and Calculate Master Mix
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
AmpliSeq for CHS V2
Thermal Cycler Program = AMP
Equalizer Workflow
Thermal Cycler Program = EQUAL
Standard Workflow
Thermal Cycler Program = AMP_7
Step Data
Group of Defaults = Standard Workflow
Master Step Fields
Step 3: Perform Second Clean Up (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)
The Library Prep AmpliSeq for Illumina Comprehensive Cancer Panel is part of the AmpliSeq for Illumina Comprehensive Cancer Panel protocols that include the following functionality:
Preconfigured AmpliSeq for Illumina Comprehensive Cancer Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.
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: Library Prep (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute DNA (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Qubit (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step and Copy Concentration
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 4: Amplify Targets Replicates (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Amplify Targets Replicates (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration & Input Amount - CCP
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Prep Input
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
CCP
Recommended Prep Input (ng) = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Thermal Cycler Program = AMP_CCP
Step Data
Group of Defaults = CCP
Master Step Fields
Step 5: Partially Digested Amplicons with Pooling (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Partially Digested Amplicons with Pooling (AmpliSeq for Illumina v1.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Route AmpliSeq RNA Samples for Plate Transfer - Comp. Panel
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Pooling
Label Uniqueness = Off
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Well Sort Order = Row
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step 6: Ligate Indexes (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Ligate Indexes (AmpliSeq for Illumina CCP v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Route AmpliSeq Samples - CCP
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Add Labels
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
Record Details
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
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
Default = If enough DNA is available, dilute to intermediate concentration of ~20-50 ng/uL.
Default =
Add 5 µl 2X AmpliSeq Comprehensive Cancer Panel Pool 1 (blue cap) to the first well, and 5 µl 2X
AmpliSeq Comprehensive Cancer Panel Pool 2 (blue cap) to the second.Add 5 µl 2X AmpliSeq Comprehensive Cancer Panel Pool 3 (blue cap) to the third well, and 5 µl 2X
AmpliSeq Comprehensive Cancer Panel Pool 4 (blue cap) to the fourth.
PCR Cycles
Numeric
Decimal Places Displayed = 0
Recommended Prep Input (ng)
Multiline Text
Read Only
Default = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
The Equalizer Workflow AmpliSeq for Illumina Comprehensive Cancer Panel is part of the AmpliSeq for Illumina Comprehensive Cancer Panel protocols that include the following functionality:
Preconfigured AmpliSeq for Illumina Comprehensive Cancer Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.
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: Equalizer Workflow (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Clean Up Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Amplify Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Count Samples and Calculate Master Mix
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Calculate Total Samples and Calculate Master Mix
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
AmpliSeq for CHS V2
Thermal Cycler Program = AMP
Equalizer Workflow
Thermal Cycler Program = EQUAL
Standard Workflow
Thermal Cycler Program = AMP_7
Step Data
Group of Defaults = Equalizer Workflow
Master Step Fields
Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Perform Capture and Clean Up (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 4: Elute Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Master Step Name = Elute Library (AmpliSeq for Illumina v1.1)
