Thinking about oncology clinic yesterday and the wide-ranging conversations I had with my patients/families - no, not about life and death, but instead:
1) Inner city violence and youth programs in Boston 2) The Sedale Threatt ‘90s Lakers 3) Flying Spirit Airlines and the horror therein 4) Pics of all the grandkids
The regular real life stuff that makes the subtext of a rising PSA after chemotherapy or a new cancer diagnosis really matter, fostered over time, trials, and tears as a patient-doctor partnership
That part, it’s really a privilege
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(Plus shout outs to @natemoore and @NickMoore [no relation] who contributed greatly to this effort during their research time in med school. The co-authors, reviewers, editors, and those mentioned in acknowledgements were instrumental to both this resource and study)
We've long been interested in how to take molecular data from individual cancer patients and search for clinically + biologically relevant events - see below for our first attempt at this for cancer exomes via PHIAL (ca. 2014) nature.com/articles/nm.35…
Here's our latest, a deep molecular dive into exceptional responders to anti-androgen therapy before surgery - congrats @aloktewar@alexorscanner Dr. Taplin @DanaFarber_GU et al!
High risk localized prostate cancer can be curable with existing modalities (e.g. surgery), though whether giving upfront anti-androgen therapy before surgery can expand the number of men who are cured is not yet known.
Many trials ongoing by Dr. Taplin + many others to assess
Gene fusions can be important for cancer development, and prior work nicely demonstrated how such events can directly affect the expression or functionality of partner genes in cell line data, e.g.: nature.com/articles/s4146…
Riaz then asked - with CRISPR screening + molecular data from 645 cell lines - whether fusions create:
(i) functional dependencies on partner genes
and/or
(ii) “collateral dependencies” on genes w/in the same topologically associating domains (TADs) as fusion partners
Interested to see how the forthcoming data behind the ‘TMB > 10 in all cancer types’ approval addresses a few key issues, having spent a long time thinking about this general topic - some thoughts to follow:
[1/n]
(Heeding wise words of @tmprowell - this is *not intended as critique*, but rather some open thoughts on the matter that I'm excited to see in the final data once available - feedback welcome!
(Updated my bio to have a disclosures link, including consulting for genomics labs which is relevant for this effort. Also pasting here: goo.gl/6kfq2E)
Patients have a right to their data, and HIPAA states that data (whether clinical, molecular, or anything in between) should come in a computable form.