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d3b-center / ticket-tracker-OPC

A repo to generate and track tickets for ped OT
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Proposed Analysis: Review JAX/PIVOT PDX DNA Pipeline #276

Closed migbro closed 1 year ago

migbro commented 2 years ago

What are the scientific goals of the analysis?

To evaluate the efficacy of the JAX PDX pipeline

What methods do you plan to use to accomplish the scientific goals?

Use this pipeline: https://cavatica.sbgenomics.com/u/d3b-bixu/open-targets-pdx-workflow-dev/apps/#d3b-bixu/open-targets-pdx-workflow-dev/pdx-wes-tumor-only-xenome-with-variant-calling-msi-and-tmb-score

Alternatively, this one: https://github.com/kids-first/kf-tumor-workflow by using xenome + continue with wf, is a recent candidate. Major advantage being CNV, SV and WGS capability. However, it is still beta.

What input data are required for this analysis?

Results from existing paper, similar to #271

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

A couple weeks to a month

Who will complete the analysis (please add a GitHub handle here if relevant)?

What relevant scientific literature relates to this analysis?

jharenza commented 2 years ago

@migbro once you are back, or @dmiller15, if you know- has this been started? If so, can you link to the CAVATICA project/ update here?

migbro commented 2 years ago

So, Alvin created this ticket, #283 which I think outlines how we want to test this out. It has not been started yet, I'll try to work out how/when it will be started as cBio has regained priority.

jharenza commented 2 years ago

@migbro this is the manifest of all DNA samples for which we should have MAFs for this project

pptc-dna-mafs.txt

chinwallaa commented 1 year ago

Do we need permission to run the CHOP data thru the updated pipelines (PIVOT pipelines). @afarrel will follow up with John Marris. Do we have other PDX data - PDXFinder? - Nothing processed yet. WIll need to get an analysis plan together with FNL/NCI for this new data type. Have starfusion/ariba for PPTC PDX data. Expression table, SNV calls, fusion calls - ability to look at mutations in patients and PDX models.