The DataShed5 Assay Manager with MDS v4.6.5 provides the ability to apply QC policies during assay loading and pass (accept) or fail (reject/query) a batch.
Assay Management in the MDS
Prior to MDS v4.6.5, the AssayMergeResultPreferredValue in tblSYSParam by default is set to 0. In MDS v4.6.5, this value has been changed to -1000. This value dictates what initial Preferred value will be set in tblAssay when run assay merging process.
The QC Rule Checker (usp_DataAssayQCRuleChecker, called by usp_DataAssayMergingProcess) applies any configured QC policies, if any, on the newly imported batches.
If all data in the batch meet the policies, the Preferred value in tblAssay will be changed from -1000 to 0 and Batch_Status in tblSYSAssBatch will be set to A (Accepted). If any data in the batch failed the policies, the Preferred value in tblAssay will remain as -1000 and tblSYSAssBatch.Batch_Status will be set to other R (Rejected) or Q (Queried) depends on the policy configurations.
If no QC policy set up, then tblAssay.Preferred will be changed from -1000 to 0 and tblSYSAssBatch.Batch_Status will be set to QCNA (QC not applied).
One important change, apart from introducing the QC Checker, between the new and old assay management is that the new assay management requires all data in a batch to be processed. If any data for a given batch is still left behind in the buffer table for any reason, QC Checker will set the tblSYSAssBatch.Batch_Status to be UM (Unmerged) and tblAssay.Preferred will remain as -1000 and effectively any newly merged assay from that batch will not be able to be picked up by ranking process for tblAssayFlat.
The backend tables involved with the QC Checker process are the tblSYSAssQC* tables. It’s recommended to not manually manipulate data in these tables and always using DataShed5 frontend to make any QC configuration changes.
tblSYSAssQCPolicy: table contains all the QC policies
tblSYSAssQCPolicyLayout: table contains mapping between QC policies and assay import layouts
tblSYSAssQCPolicyRule: table contains configuration details of each QC policy
tblSYSAssQCResult: summary result from the QC Checker run.
tblSYSAssQCResultDetail: detailed result of the QC Checker run
The new assay merging process flow is as follows:
Assay Management in DataShed5
The workflow for set up and use of Assay Manager in DataShed5 is as follows:
1. Create the QC rules:
- Standards – will check standard sample results are within x standard deviations of an expected Value or within expected high/low values.
- Blanks – will check blank sample results are within x standard deviations of an expected Value or within expected high/low values.
- Repeats – will check repeat results are less than x% difference from the original value
- Screen test – will check if the size result is greater than x%
2. Create a QC policy and assign QC rule/s to it
Assign QC policy to an import layout
4. Load assays and DataShed5 will apply the QC rules relevant to import layout used
5. Check QC results and approve/reject
Security Levels for Users
- SysAdmin – maintain assay library data, configure QC policy, Configure assay administration and delete batches
- UserPlus – can edit batch data, process and approve batches
- Users – can view and filter Assay Manager, analyse assay data using QAQC dashboard & assay batch status report
DataShed5 – Assay Manager screen
The Filters across the top of screen allow the user to display the required batches by defining options such as dates, labs etc.
The Download Batch List button creates an Excel file containing the filtered Batch List details.
The Process Batches will run the incoming datadriver, merge, the QC checker and rank the data for all batches in the list.
Once the filter is applied the Batch List shows the batch details.
The process batch action allows the SysAdmin user to reprocess the specific batch which will retry merge, run the QC checker and rank the data.
The delete option allows the SysAdmin user to delete a batch.
The Batch Status values are:
- Accepted (A) – all the QC rules passed
- Queries (Q) – one or more QC rule/s failed
- Unmerged (U) – QC policy has not been applied due to batch not fully merged, eg missing sample numbers
- Rejected (R) – all QC rules failed
- QC Not Applied (QC_NA) – no QC rules applied to batch (note: all historic batches prior to upgrade to MDS 4.6.5 will have QC Not Applied batch status)
Entries in red are batches that have not been validated.
The Unmerged Assay Results screen shows details of any batches that have not been merged
The Assay Batch Header screen show the details of the assay batch including dates, sample counts and validation status.
The Assay Batch Details screen shows the details of the assays completed such as assay method, element and limits.
The QC Results screen shows the results of the QC rules applied. Each rule can be expanded to display the individual assay results.
The Batch Approval screen allows the user to approve/reject a batch and automatically email a notification with batch summary details and QC Results. Once a batch is changed to accepted and validated it is automatically ranked. If the batch is loaded by AAL and is Accepted (eg passes all QC rules) it is automatically validated.
The configuration menu button displays the following options:
Library Tables allows the user to manage the library tables associated with the assay process including labs, elements, lab methods and the QC reference tables
Assay Configuration allows the user to manage the attributes that add columns to tblAssayFlat though RHNorm > details of AM_RH_Assay
QC Rules Configuration allows the user to define the QC rules to be used. DataShed5 comes with standard QC rules for gold (Au) installed which can be used as templates for use with other elements.
The Screen Test rule setup screen has the following components:
Code – the QC rule name
Description – description of QC rule
QC type – type of QC rule
Element – element to be assayed
Lower Limit – lower size value
Upper Limit – upper size value
Pass% – percentage to pass rule for rule to be successful
Active – rule is active or not
The Standards rule setup screen has the following components:
Code – the QC rule name
Description – description of QC rule
QC type – type of QC rule
Standard Types – drop down allowing choice of standards available eg ALL, LAB, CLIENT
Element – element to be assayed
Pass% – percentage to pass rule for rule to be successful
Exclude BDL/OR – exclude Below Detection Limit/OverRange values
Reference Values – Standard Expected or Standard High Low value
Standard Deviation – 1,2 or 3 STD
Is Active – rule is active or not
The Blanks rule setup screen has the following components:
Code – the QC rule name
Description – description of QC rule
QC type – type of QC rule
Standard Types – drop down allowing choice of blanks available eg ALL, LAB, CLIENT
Element – element to be assayed
Pass% – percentage to pass rule for rule to be successful
Exclude BDL/OR – exclude Below Detection Limit/OverRange values
Reference Values – Blank Expected or Blank High Low value
Standard Deviation – 1,2 or 3 STD
Is Active – rule is active or not
The Repeat rule setup screen has the following components:
Code – the QC rule name
Description – description of QC rule
QC type – type of QC rule
Repeat Types – drop down allowing choice of repeats available eg Duplicate, Pulp, Repeat, Field, Lab
Element – element to be assayed
Pass% – percentage to pass rule for rule to be successful
% Difference from Original Reference Value – value 0-100
Value * Detection Limit (lower limit) – is a percentage that will determine if the repeat result fails or passes.
Active – rule is active or not
The QC Policy screen allows the user to create a QC Policy and name it
The QC Policy Rule screen allows the user to add QC Rules to a QC Policy
The QC Policy Layout screen allows the user to apply a QC Policy to an import layout. Each import layout can only have one QC Policy applied but one QC Policy can be applied to many different import layouts.
The QC Emails screen allows email recipients to be added to receive the Batch Approval Notifications.
Version 1 – 27/05/2021