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 Type = Library Prep
Next Steps Configuration
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Step Data (Master Step Fields)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Step Data (Master Step Fields)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Step Data (Master Step Fields)
Step File Placeholders
Master Step Name = Amplify Targets Replicates (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Group of Defaults
Step Data
Group of Defaults = CCP
Master Step Fields
Master Step Name = Partially Digested Amplicons with Pooling (AmpliSeq for Illumina v1.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Label Uniqueness = Off
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Defaults
Well Sort Order = Row
Placement Pattern = Column
Destination Containers
Step Data (Master Step Fields)
Step File Placeholders
Master Step Name = Ligate Indexes (AmpliSeq for Illumina CCP v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
AmpliSeq CD Indexes Set C for Illumina
Step Data (Master Step Fields)
Step File Placeholders
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
Step File Placeholders
Log - 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
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Criteria 1 - Threshold Value
Numeric
Criteria 2 - Operator
Text
Default = <=
Criteria 2 - Source Data Field
Text
Default = Concentration
Criteria 2 - Threshold Value
Numeric
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Automatically attached
Upload File - Manually uploaded
Sample Table
Enable QC Flags = Yes
Sample Display Default = Expand
Well Sort Order = Row
File Column Options
File Column Display = Hide
File Attachment Method = Auto
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
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Reagent Kits
AmpliSeq Comprehensive Cancer Panel for Illumina
Supplier = Illumina
Catalog Number = 20019160
Website = www.illumina.com
AmpliSeq Library PLUS for Illumina
Supplier = Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Website =
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
20x AmpliSeq Sample ID Panel For Illumina
Toggle Switch
Default = None Set
20x AmpliSeq Sample ID Panel For Illumina Lot#
Text
Instructions
Multiline Text
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.
Thermal Cycler Program
Text Dropdown
Custom Entries
Presets
AMP_CCP
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Reagent Kits
AmpliSeq Library PLUS for Illumina
Supplier = Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Website =
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
96 well plate
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Reagent Kits
AmpliSeq Library PLUS for Illumina
Supplier = Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Website =
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
AmpliSeq CD Indexes Set D for Illumina
AmpliSeq UD Indexes for Illumina (24 Indexes)
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Field Name
Field Type
Options
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Numeric
Range = 20 To 50
Decimal Places Displayed = 0
Directions
Multiline Text
Read Only
Field Name
Field Type
Options
Additional Options and Dropdown Items
Criteria 1 - Operator
Text
Default = >=
Criteria 1 - Source Data Field
Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Numeric
Range = 20 To 50
Decimal Places Displayed = 0
Field Name
Field Type
Options
Field Name
Field Type
Options
Additional Options and Dropdown Items
Thermal Cycler Program
Text
Default = FUPA
Field Name
Field Type
Options
Additional Options and Dropdown Items
Thermal Cycler Program
Text
Default = LIGATE
Default = If enough DNA is available, dilute to intermediate concentration of ~20-50 ng/uL.
Default = Concentration
Additional Options and Dropdown Items
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"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}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"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}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Total Volume (uL):: = input.::Total Volume (uL):: ; output.::Input Amount (ng):: = input.::Input Amount (ng):: ; output.::5X AmpliSeq HiFi Mix (uL):: = 9.0'\
-log {compoundOutputFileLuid0}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Prep Input Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Concentration:: ; \
if (output.::Prep Input Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 13.5 - output.::Prep Input Volume (uL)::} '\
-log {compoundOutputFileLuid0}"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}"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}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Queue for Plate Transfer' \
--FIELD_VALUE 'Transfer Amplicons' \
--WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "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}"bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"Container
Well
Built-in
Derived Sample
Concentration
Numeric
Required Field
Decimal Places Displayed = 2
Derived Sample
Conc. Units
Text
Required Field
Derived Sample
Sample Name
Built-in
Measurement
Concentration
Numeric
Decimal Places Displayed = 2
Measurement
Conc. Units
Text
Project
Project Name
Built-in
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
Concentration
Numeric
Required Field
Decimal Places Displayed = 2
Derived Sample
Conc. Units
Numeric
Required Field
Derived Sample
Input Amount (ng)
Numeric
Decimal Places Displayed = 0
Derived Sample
Low TE (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Sample Name
Built-in
Derived Sample
Sample Volume (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Total Volume (uL)
Numeric
Decimal Places Displayed = 2
Project
Project Name
Built-in
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
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
Concentration
Numeric
Required Field
Decimal Places Displayed = 2
Derived Sample
Conc. Units
Numeric
Required Field
Derived Sample
Input Amount (ng)
Numeric
Decimal Places Displayed = 0
Derived Sample
Low TE (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Sample Name
Built-in
Derived Sample
Sample Volume (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Total Volume (uL)
Numeric
Decimal Places Displayed = 2
Project
Project Name
Built-in
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
5X AmpliSeq HiFi Mix (uL)
Numeric
Decimal Places Displayed = 1
Derived Sample
Concentration
Numeric
Required Field
Decimal Places Displayed = 2
Derived Sample
Conc. Units
Text
Required Field
Derived Sample
Input Amount (ng)
Numeric
Decimal Places Displayed = 0
Derived Sample
Nuclease-free water (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Prep Input Amount (ng)
Numeric
Required Field
Range = 2 To 200
Decimal Places Displayed = 0
Derived Sample
Prep Input Volume (uL)
Numeric
Decimal Places Displayed = 2
Derived Sample
Sample Name
Built-in
Derived Sample
Total Volume (uL)
Numeric
Decimal Places Displayed = 2
Project
Project Name
Built-in
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
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
AmpliSeq Workflow
Text Dropdown
Required Field
Preset
Standard Workflow
Equalizer Workflow
Derived Sample
Sample Name
Built-in
Project
Project Name
Built-in
Built-in