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cfDNA sample type abbreviation - simplify to L #1432

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ao508 opened this issue Mar 4, 2025 · 2 comments
Open

cfDNA sample type abbreviation - simplify to L #1432

ao508 opened this issue Mar 4, 2025 · 2 comments

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@ao508
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ao508 commented Mar 4, 2025

Sample origin isn't collected anymore and other similar fields like tissueLocation aren't reliably set or filled in during sample intake.

Ronak suggested simplifying cfDNA sample type abbreviations to L, which would also mean no longer requiring sampleOrigin to be populated. To make sure that Normal samples aren't accidentally getting labeled as cfDNA though we should also exclude cases where cmoSampleIdFields.sampleType = cfDNA and sampleType (aka IGO CMO sample class) = Normal

One thing to consider:
A normal sample should always be identified as Normal (i.e., ignore that it's a cfDNA).

@ao508 ao508 changed the title cfDNA resolve where sample origin can be captured from cfDNA sample type abbreviation - simplify to L Mar 4, 2025
@ao508
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ao508 commented Mar 5, 2025

draft pr mskcc/smile-label-generator#111

@ao508
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ao508 commented Mar 5, 2025

Please add your planning poker estimate with Zenhub @qu8n

@ao508 ao508 added the DEPLOYED label Mar 6, 2025
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