Robert West Dissertation

Abstract

Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis.

View details for DOI 10.1371/journal.pgen.1003464

View details for PubMedID 23637631


[I moved to EPFL in December 2016, so this website isn't updated any longer. My new website lives at http://dlab.epfl.ch/people/west/.]

Hi, I'm Robert West, but you can call me Bob, or His Bobness, or Bobber, or El Boberino if you're not into the whole brevity thing.

My research aims to understand, predict, and enhance human behavior in social and information networks by developing techniques in data science, data mining, network analysis, machine learning, and natural language processing.

Previously, I received a PhD in Computer Science from Stanford University (advised by Jure Leskovec), an MSc from McGill University in Montreal, and a Diplom from Technische Universität München in Munich.

Contact

Email: click here to see it
Office location: William Gates Computer Science Building, Room 450

News

  • 2016/12/23: Co-organizing Wiki Workshop 2017 @ WWW 2017 in Perth, Australia, on April 3 or 4, 2017 (exact date TBD) — consider submitting a paper or extended abstract!
  • 2016/12/23: Co-organizing Applied Machine Learning Days at EPFL on January 30/31, 2017 — register now!
  • 2016/06/22: Super excited to start as a tenure-track assistant professor at EPFL in Switzerland in late 2016
  • 2016/04/19: PhD thesis successfully defended
  • 2016/04/13: Our paper on "Growing Wikipedia across Languages via Recommendation" was featured as a best-paper runner-up at WWW'16.
  • 2015/12/30: Co-organizing Wiki Workshop 2016 @ WWW and ICWSM — consider submitting a paper or extended abstract!
  • 2015/12/15: Two papers accepted to WWW'16
  • 2015/12/03: Plenary talk on "Death of famous people in the media" at GESIS Computational Social Science Winter Symposium in Cologne, Germany
  • 2015/10/14: Paper with Ashwin Paranjape, Jure Leskovec, and Leila Zia (Wikimedia) accepted to WSDM'16
  • 2015/09/08: Invited talk at GESIS Leibniz Institute for the Social Sciences in Cologne, Germany
  • 2015/08/07: Gave a guest lecture to the super smart and curious girls taking part in the Stanford Artificial Intelligence Laboratory's Outreach Summer.
  • 2015/06/02: Invited talk at the Language and Network Science Symposium at NetSci 2015 in Zaragoza, Spain
  • 2015/05/26: I won the 2015 ICWSM Science Slam with a talk about Unfun.me! :)
  • 2015/05/26: Our ICWSM Workshop on Wikipedia, a Social Pedia: Research Challenges and Opportunities in Oxford was a great success!
  • 2014/11/26: Invited talk at the Max Planck Institute for Software Systems in Saarbrücken, Germany
  • 2014/11/20: Guest lecture in Stanford's "Minds and Machines" class (SymSys-100)
  • Try Unfun.me — a fun language game!

Publications [Google Scholar]

2017

2016

2015

2014

2013

2012

2011

2010

2009

Writings &c.

Deutsches

  • A long time ago I had my three minutes of fame on Bavarian state TV
  • About ten years later, I made a three-line reappearance in the Frankfurter Allgemeine Zeitung
  • Ein rechnergestützter Vergleich von Jacob Baldes Encomium toruitatis mit der übrigen lateinischen Literatur [PDF] — Ergebnisse (siehe PDF für Erklärung): [sortiert nach Stelle bei Balde] [sortiert nach Stelle bei anderem Autor]
  • Venus' Rede in der Götterversammlung (Vergil, Aeneis 10.18–62) [PDF]
  • Inhalt der Bücher VII, VIII und XII von Vergils Aeneis [PDF]
  • Agricolas Statthalterschaft in Britannien (Tacitus, Agricola 19–21) [PDF]

Last modified on April 26, 2017 

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