Overview
The Qiagen EZ1 Advanced XL CDC COVID-19 RT-PCR is part of the CDC COVID-19 RT-PCR protocols that include the following functionality.
Preconfigured CDC COVID-19 RT-PCR protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
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.
Protocol 1: Qiagen EZ1 Advanced XL (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Sample Type (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Sample Type (CDC COVID-19 RT-PCR v1.1)
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 'if (input.::Extraction Sample Type:: == ::Urine::) {nextStep = ::Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Whole Blood::) {nextStep = ::Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Dried Swabs::) {nextStep = ::Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Viscous Respiratory Samples::) {nextStep = ::Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::Extraction Sample Type:: == ::Isolation of gDNA of Gram Positive Bacteria::) {nextStep = ::Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Urine (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Manual button
Copy 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 'if (step.::Final Sample Volume (uL):: == 100) {output.::Volume of Urine (uL):: = 75 ; output.::Volume of ATL (uL):: = 25} ; \
if (step.::Final Sample Volume (uL):: == 200) {output.::Volume of Urine (uL):: = 150 ; output.::Volume of ATL (uL):: = 50} ; \
if (step.::Final Sample Volume (uL):: == 400) {output.::Volume of Urine (uL):: = 300 ; output.::Volume of ATL (uL):: = 100}' \
-log {compoundOutputFileLuid0}" Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 3: Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Whole Blood (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Manual button
Copy 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 'if (step.::Final Sample Volume (uL):: == 100) {output.::Volume of Whole Blood (uL):: = 50 ; output.::Volume of ATL (uL):: = 50} ; \
if (step.::Final Sample Volume (uL):: == 200) {output.::Volume of Whole Blood (uL):: = 100 ; output.::Volume of ATL (uL):: = 100} ; \
if (step.::Final Sample Volume (uL):: == 400) {output.::Volume of Whole Blood (uL):: = 200 ; output.::Volume of ATL (uL):: = 200}' \
-log {compoundOutputFileLuid0}" Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 4: Pretreatment of Stool (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Stool (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Copy 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.::Volume of Buffer ASL (uL):: = 900' \
-log {compoundOutputFileLuid0}" Trigger Location = Record Details
Trigger Style = Manual button
Copy 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 'if (output.::Stool (mg):: != 30) {output.::Volume of Buffer ASL (uL):: = output.::Stool (mg):: * 9}' \
-log {compoundOutputFileLuid0}" Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 5: Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Dried Swabs (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 6: Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Viscous Respiratory Samples (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 7: Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Isolation of gDNA of Gram Positive Bacteria (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 8: Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral Nucleic Acids and Bacterial DNA (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Report File - Manually uploaded
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)
Automations
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 'if (input.::RT-qPCR Assay:: == ::Thermofisher TaqPath 1-Step RT-qPCR::) {nextStep = ::Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Promega GoTaq Probe 1-Step RT qPCR::) {nextStep = ::Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix::) {nextStep = ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio UltraPlex 1-Step ToughMix (4X)::) {nextStep = ::Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
Catalog Number = A15299; A15300
Automations
Trigger Location = Placement
Trigger Style = Automatic upon entry
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI} Trigger Location = Record Details
Trigger Style = Automatic upon entry
Copy 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.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::TaqPath 1-Step RT-qPCR Master Mix (4x) (uL):: = step.::Total Samples:: * 5 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}" Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy 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 = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}" Trigger Style = Automatic upon exit
Copy 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 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}" Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 3: Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)
