Eli Van Allen Profile picture
Aug 20, 2019 3 tweets 1 min read Read on X
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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More from @VanAllenLab

Sep 30, 2021
Our latest - introducing the Molecular Oncology Almanac (MOAlmanac): paired clinical interpretation algorithm + knowledge base for precision cancer medicine @moalmanac
Congrats @brendan_reardon et al! @DanaFarber @broadinstitute nature.com/articles/s4301… @NatureCancer [1/12]
(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…
Read 12 tweets
Sep 8, 2021
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!

cell.com/cell-reports/f… @CellReports

[1/n]
(See also co-published/co-submitted wonderful story by @Chris_Barbieri1 lab with convergent science! cell.com/cell-reports/f…)
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
Read 11 tweets
Jun 8, 2021
Here’s our latest, a deep dive into fusions and partner or "collateral" cancer dependencies

Interesting findings for pediatric and adult cancers...

Congrats Dr. Riaz Gillani @BostonChildrens @DanaFarber @broadinstitute et al! @CR_AACR @AACR cancerres.aacrjournals.org/content/early/… [1/n]
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
Read 8 tweets
Jun 22, 2020
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! )
1) Technical:
- Many non-biological factors affect TMB calculation, like sample quality, tumor purity, sequencing artifacts, and NGS fails.

Difference btwn NGS from TCGA samples vs. clinical trial samples vs. real world clinical samples is large. Also: nejm.org/doi/full/10.10…
Read 15 tweets
Dec 3, 2019
A brief thread on our latest study, as well as a more general chat on biology & biomarkers for cancer immunogenomics - w/ longtime friend Dirk Schadendorf + rockstar jr faculty @dliu_ccb + more friends! @NatureMedicine @DanaFarber @broadinstitute
nature.com/articles/s4159… [1/n]
Many current biology & biomarkers blurry lines in cancer immunogenomics - e.g. our TMB melanoma work:

2014-15: Correlation btwn TMB + clinical benefit to ICB in melanoma → neoantigen biology

Though our 2015 data (ncbi.nlm.nih.gov/pubmed/26359337) suggested weak predictive effect...
...and then:

2018: TMB confounded by mutational signatures (ncbi.nlm.nih.gov/pubmed/30150660)

Here: TMB also confounded by histologic subtype

Cool biology: Yes!
Clinical biomarker: Err...probably not
Read 14 tweets
Nov 19, 2018
Here, we partnered w/ cancer patients + friends @KDeutsch @adamhayden @CultPerfectMoms @CurrentIncurSci @stephanie_mul to liberate their cancer genomic data from clinical labs.

It was a struggle…

...but there’s hope & we have a plan! [1/n] @OSFramework osf.io/gupvq
(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.

hhs.gov/hipaa/for-prof… cc @EricTopol @TheLizArmy
Read 13 tweets

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