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Cancer Data Science @CancerDataSci

Fighting cancer with machine learning @ Broad Institute

Joined January 2017
  • Tweets 18
  • Following 24
  • Followers 405
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While the focus in the clinical setting has been on finding DNA-based cancer biomarkers, in a study led by Josh Dempster we show that, at least in vitro, gene expression is generally a more powerful biomarker for cancer vulnerabilities biorxiv.org/content/10.1101/… @CancerDepMap

Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics

Achieving precision oncology requires accurate identification of targetable cancer vulnerabilities in patients. Generally, genomic features are regarded as the state-of-the-art method for stratifying...

biorxiv.org
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
21 Jan 2020
Congratulations to @corsellos on the Drug Repurposing paper published today @NatureCancer! An unexpectedly large number of non-oncology drugs selectively inhibit subsets of cancer cell lines: nature.com/articles/s43018-0…

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We've just released the MIX-seq manuscript, data and code. Congrats James, Brent, Allie, Katie and the rest of the team for this cool work!
The Cancer Dependency Map@CancerDepMap
9 Dec 2019
Excited to share our preprint describing MIX-seq [biorxiv.org/content/10.1101/…]! MIX-seq is an approach for multiplexed transcriptional profiling of chemical and genetic perturbations in large pools of co-treated cancer cell lines, with single-cell resolution. (1/5)
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
9 Aug 2019
REPURPOSING HUB DATA AND PREPRINT NOW OUT!! See how >4500 existing compounds performed when used across >550 cancer cell lines 💊 biorxiv.org/content/10.1101/…, data can be found on the #DepMap portal: depmap.org/portal/download/

Non-oncology drugs are a source of previously unappreciated anti-cancer activity

Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. We sought to create a public resource containing the growth inhibitory...

biorxiv.org
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
7 Aug 2019
19Q3 Cancer Dependency data now live! #CRISPR knockout screening data for 64 (😲!) new #cancer cell lines, plus accompanying gene expression, copy number and mutation profiles: depmap.org

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Are the CRISPR screens published by Sanger today consistent with those done at Broad? We teamed up with @DepMapSanger to find out. The results are in: biorxiv.org/content/10.1101/… @CancerDepMap @biorxivpreprint #OpenScience

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency datasets

Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic targets. As multiple large-scale screens...

biorxiv.org
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
10 Apr 2019
We’re excited to announce the release of a paper describing a new synthetic lethal target in MSI tumors as part of our GI Dependency Map! nature.com/articles/s41586-0… #Cancer #DepMap
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The largest dataset of cancer genetic dependencies to date includes RNAi data for 712 cell lines from Achilles, DRIVE and Marcotte et al., created using our new method DEMETER2, now out in Nat Comms. depmap.org/R2-D2 for data, code and paper @CancerDepMap @broadinstitute
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A great example of how @CancerDepMap genetic screens can be used to study protein complex function. doi.org/10.1016/j.cels.2018.… Congrats to @joshbiology and @_robin_meyers_!
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
10 May 2018
18Q2 data release is here! depmap.org
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The largest dataset of cancer genetic dependencies: More than 970 RNAi screens in 713 cell lines from @broadinstitute Achilles, Novartis DRIVE and Marcotte et al., 2016 processed together by the new DEMETER2 method. biorxiv.org/content/early/20… @CancerDepMap @biorxivpreprint
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Cancer Data Science retweeted
The Cancer Dependency Map@CancerDepMap
13 Apr 2018
We have a new portal! depmap.org/ Integrated genome-scale #CRISPR LoF, sm mol sensitivity & #RNAi knockdown screen data on 500 #cancer cell lines together w/ user-friendly analysis & #dataviz tools
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Now available from @CancerDepMap: #CRISPRscreen data from 391 #cancer lines, incl 51 new lines (representing 14 tumor types): broad.io/achilles Accompanying #RNAseq #WES profiles: broad.io/CCLEdata. More to come on a quarterly basis!
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342 CRISPR KO screens in cancer cell lines and our method to correct for CRISPR/CN effect, now live nature.com/ng/journal/vaop/n… @broadinstitute
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Our first effort to define a Cancer Dependency Map is now live at cell.com/cell/fulltext/S0092… and depmap.org/rnai @broadinstitute
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CERES corrects the copy-number effect of CRISPR-Cas9 essentiality screens in 342 cancer cell lines #bioRxiv biorxiv.org/content/early/20…
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