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Tissue Is The Issue [Linnea Olson Hackathon]

In our weekly lightning update meeting on the Linnea Olson Hackathon on Friday we learned:


Scan: Linnea rescheduled her scan to Sunday (May 23) and will have a scan review the following Thursday (May 27) and a discussion with her oncologists (Jess Lin and Alice Shaw) about getting a biopsy and prioritizing uses of the tissue. Linnea will also ask if they will participate in a virtual molecular tumor board.


Blood biopsy: Natera has agreed to perform their blood biopsy test for Linnea. It will be interesting to contrast their results with the test results from Foundation Medicine and Lucence. The Foundation Medicine and Lucence reports are available on the Slack. Raw sequencing data is available on request.Proteomics analysis: We are working with SomaLogic to get an agreement with them to run their test. We will need help in analyzing the results.


Data access: Ciitizen should be finishing the summary report of Linnea’s medical history data in the next week or so. 5,000 pages have produced 35,000 “statements” = something happened at this time, which are extracted by an algorithm, over the 15 years of care. Linnea noted this is the first time she has been able to see all of her scans.


Tissue uses: Candidates to use Linnea’s tumor tissue (should it become available) include Oncocyte (measures whether tumor is hot or cold and whether it will respond to immunotherapy), Certis Oncology (will build a mouse model to test therapies), Akoya Biosciences CODEX (characterizes the tissue microenvironment using spatial analysis to understand the molecular and cellular mechanisms driving the disease and therapeutic responses), NanoString (single-cell cancer genomics studies and spatial biology enables insights on tumor heterogeneity, exploration of the complex interactions with the tumor microenvironment), and Foundation Medicine (tumor sequencing oncopanel). [Are there any other tissue tests we should add?]


You can see the video recording below for more details (13 minutes).




Here are some notes from the roundtable discussion — “Tissue is the issue.”


Kimary Kulig: To play devil’s advocate, Linnea’s oncologists may not want to risk the biopsy to get scarce tissue now. They may want to wait for progression.


Linnea: They will be looking at my latest scan to determine progression. I’m afraid that it is progressing.


Kimary Kulig: You will also want to know what clinical trials are requiring tests from biopsies, to know how much tissue to reserve for them. A core needle biopsy can yield 20 4-5 micron sections. A pharma company will ask for 10 slides, which could use half the sample.


Peggy Zuckerman: Is the tumor stable? Will it be heterogeneous?


Grace Cordovano: No more than 30-40% of issue blocks and unstained tissue should ever be used. 60-70% should be reserved for Linnea. Is there anyone who could culture the cells, or create cell cultures?


Kristein King (Certis): We could do this. We will check.


Kimary Kulig: Make sure in the consents that you reserve tissue for your use. You want to own it.


Sophia Cornew (Ciitizen): Deven McGraw of Ciitizen is an expert on this.


Grace Cordovano: We should get a legal review of the consent language.


Jason Crites: I am working with MGH pathology and could possibly avoid the legal formalities.


Devon Snedden: It will help if Linnea has clinicians to argue for this with her oncologists.


Brad Power: Our plan is to arm Linnea with arguments with her oncologists and we will be having a virtual molecular tumor board where expert clinicians can have discussions about the best diagnosis and treatments. Each treatment option should have an advocate.


Brad Power: Kimary, you suggested metformin and several other therapies. Can you explain whether these might be parts of a cocktail? Are there combinations of the various drugs that have been suggested?


Rene Roach: The Care Oncology Clinic has a cocktail of four drugs, of which metformin is one.


Kimary Kulig: Plus fasting.


Glenn Sabin: Will Lavalley can suggest other complementary therapies.

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