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Blood Biopsy Results, Tissue Biopsy Possible, Proteomics, Treatment Options, Medical Data [Linnea Olson Hackathon]

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

Blood Biopsy Results: The Foundation Medicine blood biopsy report is in and can be seen on the Slack, and Linnea has received the Lucence report. Foundation Medicine reported variations of unknown significance. David Marshak noted that two of the variants included MCL1 and BNMP3A, and noted that these are potentially worth researching. Lucence identified a pathogenic mutation at a very low frequency in the TP53 gene. It is not directly druggable. Lucence tests 80 genes. The low frequency TP53 is consistent with other lung cancer results. The Lucence test goes deeply on their 80 genes, while the Foundation Medicine test looks at 300+ genes. The variations of unknown significance on the Foundation Medicine panel were not examined on the Lucence panel. We will be posting the Lucence results to the Slack soon.

Tissue Biopsy Possible: Linnea will be talking soon to her oncologist about getting a tumor biopsy, which will open up options for testing. We will be taking time on our next call about the testing options this will open up and prioritizing them.

Proteomics: Grace Cordovano has arranged with SomaLogic to get a proteomics analysis of a blood sample from Linnea. We need to organize a group to interpret the results (proteins that are up- or down-regulated) when they become available. This will be the subject of a future call.

Treatment options: The list of treatment options is expanding, based on research by Kimary Kulig and others. For example, Kimary thought Linnea might want to look at metformin and hydroxychloroquine. She also found that some of the variants of unknown significance are known in other cancers, and asked if Linnea has a family history of cancer. Linnea said her father had pancreatic cancer and melanoma, and her mother had kidney and breast cancer. Emily Vanzani shared a spreadsheet on ALK clinical trials. Please see the spreadsheet for Slack for more details.

Medical data: Linnea’s medical records from Mass General are now hosted on Ciitizen (5000 pages!), including her scans, and she can grant access to those who want to see them. Ciitizen will be developing a cancer summary — a timeline of care to date including source data. We are working on a way to host and share Linnea’s raw sequencing data (BAM files). Linnea has access to the files on Foundation Medicine and can grant access to others. Kimary Kulig is checking to see whether PathPresenter might host all of Linnea’s scans for a mini hackathon to analyze the scans.

For more details from the update, you can see and hear the update recording below (April 30, Round 4), and the recordings of the previous weekly updates in their respective posts.

Thanks again to all of the participants in the Linnea Olson hackathon.

At the request of Grace Cordovano and Glenn Sabin, I will be posting a list of participants: name, affiliation, and email address, unless you ask me not to by mid-week.

The Review Board is my first cut at people I nominate to review the options surfaced by the crowd. We will be looking to add more lung cancer researchers, in case you know any.

Please check the Slack for further background, discussion, and ongoing updates.


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