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As a clinician I want noiseless coverage profiles and accurate CNV calls. We have PONs for 3 panels built, but the samples used in their construction have been sequenced or prepped or analysed bioinformatically with methods with carry their own inherent coverage-biases and which may not be consistent with the biases existing in the current production workflow. This means that the PONs may not be working optimally, as has been raised in ticket: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=69121
Beyond these updates we are also currently underway with a new update to the TGA workflow, where UMIs will be used to remove duplicates, which may most likely also affect the coverage profiles in some ways. Probably here we would be forced to rebuild the PONs anyway, and it would be a good opportunity to get more recent samples that also reflect the new lab methods.
Suggested approach
Collect recent samples for existing panels and rerun about 50 - 100 for each panel (mixed sexes) with the updated UMI collapsed TGA workflow.
Considered alternatives
No response
Deviation
No response
System requirements assessed
Yes, I have reviewed the system requirements
Requirements affected by this story
No response
Risk assessment needed
Needed
Not needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered:
Need
As a clinician I want noiseless coverage profiles and accurate CNV calls. We have PONs for 3 panels built, but the samples used in their construction have been sequenced or prepped or analysed bioinformatically with methods with carry their own inherent coverage-biases and which may not be consistent with the biases existing in the current production workflow. This means that the PONs may not be working optimally, as has been raised in ticket: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=69121
Beyond these updates we are also currently underway with a new update to the TGA workflow, where UMIs will be used to remove duplicates, which may most likely also affect the coverage profiles in some ways. Probably here we would be forced to rebuild the PONs anyway, and it would be a good opportunity to get more recent samples that also reflect the new lab methods.
Suggested approach
Collect recent samples for existing panels and rerun about 50 - 100 for each panel (mixed sexes) with the updated UMI collapsed TGA workflow.
Considered alternatives
No response
Deviation
No response
System requirements assessed
Requirements affected by this story
No response
Risk assessment needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
The text was updated successfully, but these errors were encountered: