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ISAC initiative-minimum reporting

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mleipold

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Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Dec 04, 2019 9:59 pm

ISAC initiative-minimum reporting

Hi all,

Cytometry A just published a Review/cytometry reporting requirements initiative announcement:

"MiSet RFC Standards: Defining a Universal Minimum Set of Standards Required for Reproducibility and Rigor in Research Flow Cytometry Experiments"
https://doi.org/10.1002/cyto.a.23940


"To produce such a list of gold‐standard parameters that assess whether a research flow cytometry experiment has been planned, conducted, interpreted, and reported at the highest standard, a new initiative defining the minimum set of standards a robust and rigorous research flow experiment must fulfill (MiSet RFC Standards) was proposed at CYTO 2019. MiSet RFC Standards will integrate and simplify existing resources to provide a universal benchmark a flow cytometry experiment can easily be measured against."

"Identification of Special Circumstances and Needs

Survey data and expert review/evaluation will be used to create a preliminary set of minimum standards. We will re‐engage with collaborators and stakeholders to assess the suitability of these preliminary minimum standards for different research settings pursuing a beta‐testing/user acceptance testing approach. This will enable us to make relevant revisions to MiSET RFC Standards and tailor implementation strategies to “real‐world” needs.
Composition and Implementation of MiSet RFC Standards

Surveys, expert evaluations, and testing phases will produce data‐driven progress reports that will be submitted to CYTO and other suitable meetings during the first 18 months of the initiative. We anticipate that a final consensus document will be written, and the manuscript submitted for rigorous peer‐review within 2 years. The final set of minimum standards will then be implemented via publication of peer‐reviewed guidelines, and direct presentation to collaborators and stakeholders by 2023.
Progress Updates and Monitoring of Suitability of MiSet RFC Standards

We envision the entire composition and implementation of MiSET RFC Standards to be a dynamic interactive process that is driven by data, exchange, and collaboration. Throughout the entire process, ISAC leadership and all collaborating parties will be updated yearly. It is the task of the multidisciplinary Steering Committee to hold the group accountable for meeting milestones. After publication of ISAC minimum standards by 2023 at the latest, the task force will continue to regularly monitor the suitability of the guidelines in the context of latest development and changing technologies through integration into AI‐based reagent and experiment search databases, and via surveys and quality assessment experiments."


As you can guess, I'm generally in support of standardizing reporting (along with reporting/releasing datasets...). However, I know I've run into issues with MiFlowCyt reporting when uploading CyTOF data to FlowRepository. Some of it is a clunky interface (which will hopefully be streamlined in FRv2.0), but some other things don't seem to apply as-yet to CyTOF data.

Specifically, some of the instrument set-up checks with things like Rainbow or other QC beads don't have a counterpart in CyTOF (no matter how many years I and others have been pushing Fluidigm for them.....).


Question for the Cytoforum crowd: looking particularly at Table 1 and Figure 3 of this new paper, what parts do you feel *do* apply to CyTOF data, and which ones *don't* (either currently, or at all)?


Mike
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Fri Dec 20, 2019 4:16 pm

Re: ISAC initiative-minimum reporting

The Purdue Cytometry list had this posting this week:

" Minimum Set of Research Flow Cytometry Standards (MiSET RFC Standards) - where publishing reproducible flow cytometry data starts



MiSET RFC Standards is a recently launched ISAC Marylou Ingram Scholar-led initiative that aims to integrate quality-defining parameters of a flow cytometry experiment into peer-review and publication procedures. Over a three-year period, MiSET RFC Standards will assemble a universally applicable, evidence-based checklist that helps to quickly and confidently assess the overall quality of flow cytometry data.



Be part of the first major strategic goal of MiSET RFC Standards by participating in our SURVEY! Your answers will help us understand the current approach to flow cytometry practices. Click here to answer a few questions (max. 10 minutes required) https://forms.gle/XdX4HfW6sebxAo5Z9.

The survey will be followed by EXPERT EVALUATION to compose a preliminary MiSET RFC consensus checklist highlighting the minimum requirements for an entire flow cytometry experiment. We will test the suitability of the preliminary MiSET RFC consensus checklist for real world biomedical research settings through USER ACCEPTANCE TESTING. The FINAL PRODUCT is envisioned to be a benchmark for any research flow cytometry experiment that is an integral part of manuscript and grant submissions across biomedical fields that rely on the use of flow cytometry.

Do you want to learn more about MiSET RFC? The MiSET RFC mission statement, highlighting the strategic goals and milestones, is published in Cytometry A – click here to check it out https://www.ncbi.nlm.nih.gov/pubmed/31769204. More information can also be found on our website https://misetrfc.com/.


I'm bringing this up because I think the CyTOF community needs to be involved in the establishment of any flow standards. If you feel the same, please take part in the survey link above.


Mike

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