The Roche MagNA Pure 96 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: Roche MagNa Pure 96 (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)
Step Type = No Outputs
Automations
Set Next Step - Roche MagNA Pure 96
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 2: Lysates (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Lysates (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Calculate Lysed Sample (uL)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Purification MagNa Pure 96
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 3: Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Purification MagNa Pure 96
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 4: Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Purification MagNa Pure 96
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 5: Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Purification MagNa Pure 96
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 6: Cultured Cells (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Cultured Cells (CDC COVID-19 RT-PCR v1.1)
ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.
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
Placement Pattern = Row
Destination Containers
96 well plate
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Total Volume (uL)
Numeric
Decimal Places Displayed = 2
UltraPlex 1-Step ToughMix (4x) (uL)
Numeric
Decimal Places Displayed = 2
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
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
Presets
2019-nCov Dx Panel TaqPath
2019-nCov Dx Panel Quanta
2019-nCov Dx Panel Promega
Step File Placeholders
Log - Automatically attached
Instrument Driver File - Automatically attached
Upload Result File - Manually uploaded
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
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
Criteria - Operator
Text
Read Only
Default = <=
Criteria - Source
Text
Read Only
Default = Ct Value
Result
Text
Read Only
Default = Positive
Step File Placeholders
Log - Automatically attached
Results File (.csv) - Automatically attached
File Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Column
Table Columns - Global Fields
Field Name
Field Type
Options
Additional Options and Dropdown Items
Directions
Multiline Text
Default = Suspend a dry swab in 200 l BLB; add 20 uL Proteinase K. For swabs in transport medium use 100 uL transport medium, add 100 uL BLB and 20 uL Proteinase K.
Field Name
Field Type
Options
Additional Options and Dropdown Items
Protocol Name
Text Dropdown
Required Field
Custom Entries
Presets
DNA Blood ds SV
DNA Blood SV
DNA Blood ext lys SV
Viral NA Plasma SV
Viral NA Plasma ext lys SV
Viral NA Universal SV
Pathogen Universal 200
DNA Cells SV
DNA Tissue SV
DNA FFPE SV
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Go Script RT Mix for 1-Step RT-qPCR (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Directions
Multiline Text
Template File
Text Dropdown
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Criteria - Ct Threshold
Numeric
Required Field
Required Field
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.::MagNA Pure 96 Sample Type:: == ::Whole blood::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Plasma::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Serum::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Bacteria::) {nextStep = ::Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Swabs::) {nextStep = ::Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Cultured Cells::) {nextStep = ::Cultured Cells (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Fresh-frozen Tissue::) {nextStep = ::Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::FFPE::) {nextStep = ::Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}"
