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GTAC-MGI / GTAC-ESP-LIMS

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CLE Lab: Specimen Assessment pt.2 #423

Open billtell opened 5 months ago

billtell commented 5 months ago

This is a branch for the continuation of work begun on #307

billtell commented 5 months ago
billtell commented 3 weeks ago

Changing Sample Name to Accesssion Number Changing Tissue Type to Sample Type This work was completed on #493

billtell commented 3 weeks ago

Calculated Yield (ng) changed to match entity value Yield (ng) on #493

billtell commented 3 weeks ago

Need to add protocol actions to sync Assessed Concentration (ng/µl) and 260/280 & 260/230

abohanno commented 3 weeks ago

Hi Guys, I figured out how to annotate the Qubit Flex file today. We should now be able to scan the accession sticker to add it to the file prior to ESP upload. This can then act as a double check that the samples were in the right order. I will have the next person who does assessments label their files this way and I can export them and give them to you guys.

billtell commented 2 weeks ago

bringing in pass/fail thresholds from #307

Concentration/Purity:

Updated QC metrics for specimen assessment listed below:

IDT Tumor-Normal = Yield >250ng, 260/280 = 1.4 - 2.4 SOMA = Yield >250ng, 260/280 = 1.4 - 2.4 IDT Germline Exome = Yield >250ng, 260/280 = 1.4 - 2.4 Gateway Seq = Yield >250ng, 260/280 = 1.4 - 2.4 MyeloSeq = Yield >250ng, 260/280 = 1.4 - 2.4 (any MyeloSeq that is also a ChromoSeq should have >500ng) ChromoSeq = Yield >250ng, 260/280 = 1.4 - 2.4 (any ChromoSeq that is also a MyeloSeq should have >500ng) Positive Controls = Yield >250ng, 260/280 = 1.4 - 2.4 Negative Controls = Concentration <0.2ng/uL Anything that does not meet the above conditions will need to be marked as a QC fail.

Things to consider for a possible error handler

Our preferred input for library construction is 500ng. Mark any samples between 250ng and 500ng. Any blood or bone marrow specimen with less than 750ng should get another extraction in case we need more DNA. (Any blood or marrow that is both MyeloSeq and ChromoSeq will get another extraction if it has less than 1000ng) May need to come up with an "aliquot status" column during accessioning or assessment. If status = true, the yield must also be greater than the amount required for NGS and aliquot.

Volume:

QIACube DNA (blood and bone marrow eluted in 100uL, 1 reaction): QC Range = 50uL - 125uL QIACube DNA (blood and bone marrow eluted in 100uL, 2 reactions): QC Range = 150uL - 225uL QIACube DNA (blood and bone marrow eluted in 100uL, 3 reactions): QC Range = 250uL - 325uL QIACube DNA (blood and bone marrow eluted in 100uL, 4 reactions): QC Range = 350uL - 425uL Manual Prep DNA (fresh tissue and FFPE eluted in 60uL): QC Range = 40uL – 70uL Manual Prep DNA (Buccal Swabs eluted in 150uL, 2 reactions pooled): QC Range = 250uL – 310uL Manual Prep DNA (cell pellets and fibroblasts eluted in 200uL): QC Range = 150uL – 225uL

billtell commented 2 weeks ago
billtell commented 5 days ago