Obi L. Griffith, PhD

Obi L. Griffith, PhD

Associate Professor

Address:
Division of Oncology
Mail Stop 8501-0029-10
Washington University
660 South Euclid Avenue
St. Louis, MO 63110

Room 10116, Mid Campus Center (lab)

Research Interests
  • Cancer informatics
  • Clinical statistics
  • Breast cancer
Research

My research career began during the earliest phase of reference genome sequencing and helped to address basic questions such as the relationship between genome size (C-value) and organism complexity and longevity. Subsequently, I contributed to the Mammalian Gene Collection, publishing some of the first full-length sequences for many human genes. I was also part of a small team of bioinformaticians that, under extreme time pressure, sequenced, assembled, finished and published the first whole genome sequence for the severe acute respiratory syndrome (SARS-CoV-1) virus at the height of the 2003 epidemic. As a member of large-scale genome science centers for over 15 years, I have led the genomic characterization of a number of cancer types and subtypes. This has involved both cancer cohort analyses and case studies representing thousands of tumors in total. This work has contributed to the discovery of novel drivers of tumorigenesis, diagnostic and prognostic markers, and drug targets for breast cancer, liver cancer, small cell lung cancer (SCLC), leukemia, lymphoma, and others. I have also made significant contributions to understanding the genetic basis and fidelity of experimental cancer models. This has included identifying the critical drivers of tumor development in several genetically engineered mouse models, quantifying genomic heterogeneity in xenograft models, and comprehensively characterizing the molecular landscape and drug sensitivities of cell line models.

My current research is focused on the development of personalized medicine strategies for cancer using genomic technologies. I was one of two primary informaticians that completed the analysis for the first cancer patient to have whole genome and transcriptome sequencing performed with the goal of identifying personalized treatment options. More recently, I co-led the analysis of whole genome and transcriptome data that identified FLT3 as a target for Sunitinib and resulted in the successful treatment of a patient with adult ALL. I am currently leading the development of the first completely open-source and open-access public domain knowledgebase for expert-crowd-annotation of clinically actionable variants in cancer (civicdb.org). My lab focuses on the identification of molecular markers at the DNA, RNA and protein level that are useful for diagnosis and prognosis of cancer. Using bioinformatics methods and machine learning, we have developed biomarkers, panels and assays that can accurately classify malignant versus benign thyroid neoplasms, predict relapse in ER+ breast cancer, detect high-risk colorectal adenomas, and others.

Through my lab’s research activities and leadership roles in the Variant Interpretation for Cancer Consortium, Cancer Genomics Consortium, ClinGen, and GA4GH I have helped establish widely used standards, guidelines, knowledgebases and informatics resources for the clinical interpretation of cancer somatic variants. I am a strong advocate for open-access science and open-source tool development. All software and resources developed in my lab are completely open and free for academic use. I helped release an end-to-end pipeline for clinical cancer sequencing which automates state-of-the-art methods for sequence alignment, somatic variation detection, RNA sequence analysis, and the integration of these data types into a user-friendly report of the most clinically relevant genome and transcriptome changes in a tumor or group of tumors (github.com/genome). I developed a database and web tool for interrogating the druggable genome (dgidb.org). To accompany workshops that I help teach at CSHL, CBW and elsewhere I have released complete tutorials for RNA-seq analysis on the cloud (rnabio.org), precision medicine bioinformatics (pmbio.org), and genomic visualization (genviz.org).

Griffith Lab
Profiles (publications)

Biosketch

Education

  • 2008-2003: PhD in Medical Genetics, University of British Columbia, Vancouver, BC, Canada
  • 2004-2003: Molecular Biology Graduate Exchange, Simon Fraser University, Burnaby, BC, Canada
  • 2002-1996: BSc in Biology (Honours) and Biochemistry, University of Winnipeg, Winnipeg, MB, Canada

Academic Positions & Employment

  • present-2019: Associate Professor, Departments of Medicine and Genetics, Washington University, St. Louis, MO
  • present-2014: Assistant Director, The Genome Institute, Washington University, St. Louis, MO
  • 2019-2014: Assistant Professor, Departments of Medicine and Genetics, Washington University, St. Louis, MO
  • 2014-2012: Genome Fellow, The Genome Institute, Washington University, St. Louis, MO
  • 2014-2012: Research Assistant Professor, Department of Medicine, Washington University, St. Louis, MO
  • 2012-2011: Visiting Scientist, Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR
  • 2012-2010: Post-Doctoral Fellow, Cancer & DNA Damage (Joe Gray; Paul Spellman), Lawrence Berkeley National Laboratory, Berkeley, CA
  • 2010-2008: Post-Doctoral Fellow, Medical Genetics (Steven Jones), BC Cancer Agency, Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
  • 2003-2002: Computational Biologist/Sequence Finisher (Steven Jones; Marco Marra), BC Cancer Agency, Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada

University & Hospital Appointments & Committees

  • present-2021: Member, Research Infrastructure & Applications Governance Committee
  • present-2021: Member, Biomedical Informatics and Data Science PhD Admissions Committee
  • present-2018: Emergency Preparedness Coordinator, McDonnell Genome Institute
  • present-2017: Member, Master of Science in Clinical Investigation Curriculum Committee
  • present-2016: Mentor, Initiative for Maximizing Student Development Program
  • present-2016: Faculty, Molecular Oncology Training Program
  • present-2016: Faculty, Clinical Informatics Fellowship Program
  • present-2014: Member, Siteman Cancer Center
  • present-2014: Member, Division of Biology and Biomedical Sciences

External Committees

  • present-2022: Member, CCDI Molecular Targets Platform Advisory Panel
  • present-2022: Member, AACR Project SPIRIT Technical Working Group
  • present-2021: Annual Meeting Program Chair, Cancer Genomics Consortium
  • present-2021: President-Elect, Cancer Genomics Consortium
  • present-2020: Member, AACR Education and Training Committee
  • present-2020: Member, ClinGen Cancer Variant Interpretation (CVI) Committee
  • present-2018: Member, ClinGen VHL Expert Panel
  • present-2018: Education Advisory Board Member, bioinformatics.ca
  • present-2018: Communication Committee Member, Cancer Genomics Consortium
  • present-2018: Member, ClinGen Cancer Somatic Work Group
  • present-2017: Steering Committee Member, Global Alliance for Genomic Health
  • present-2017: Board of Directors Member, Cancer Genomics Consortium
  • present-2016: Founder/Co-Chair, Variant Interpretation for Cancer Consortium (VICC), GA4GH
  • 2022-2019: Communication Committee Chair, Cancer Genomics Consortium
  • 2020-2019: Co-Chair, AACR Annual Meeting Education Committee
  • 2020-2019: Co-Chair, AACR Annual Meeting Program Committee
  • 2020-2012: Editor, Biostar Consulting LLC
  • 2019-2018: Genomics Resource Development Committee, Cancer Genomics Consortium
  • 2018: ITCR 2018 Annual Meeting Steering Committee
  • 2018: Cancer Genomics Consortium Annual Meeting Organizing Committee
  • 2018-2017: Co-Chair, AACR Annual Meeting Program Committee
  • 2018-2017: Co-Chair, AACR Annual Meeting Education Committee
  • 2017: Session Chair, Resources Section, NCI-ITCR Annual Meeting
  • 2017-2016: Member, AACR Annual Meeting Education Committee
  • 2017-2014: Member, Canadian Bioinformatics Workshops Planning Committee
  • 2016: Program Co-Chair, Clinical Interpretation Knowledgebase Hackathon and Curation Jamboree, Amsterdam, Netherlands
  • 2016-2013: Member, Network of Biothings
  • 2016-2013: Member, Transcription Factor Target Gene Consortium
  • 2014-2013: Member, Illumina Sequencing Experts Panel
  • 2011-2010: Program Committee Member, GTC Next Gen Sequencing Conference
  • 2011-2010: Program Committee Member, NIH ICBP Junior Investigator Meeting
  • 2010-2008: Founding Member, Open Regulatory Annotation Consortium
  • 2008: Sponsorship and Registration Coordinator, Brain Tumor Foundation of Canada
  • 2007-2004: Member, Let’s Talk Science Partnership Program, University of British Columbia
  • 2006: Program Committee Member, The RegCreative Conference, Ghent, Belgium

Honors & Awards

  • 2020: AACR Most-Cited Article Published in 2020
  • 2015: University of Winnipeg Annual Alumnus Speaker Award
  • 2015: National Academy of Sciences Kavli Fellow
  • 2012-2010: CIHR Fellowship
  • 2008-2005: CIHR Canada Graduate Scholarship Doctoral Award
  • 2007: Lloyd Skarsgard Research Excellence Prize
  • 2006: MSFHR Senior Trainee Award
  • 2006-2003: UBC PhD Tuition Fee Award (4 years)
  • 2005-2003: MSFHR Junior Trainee Award
  • 2005-2003: NSERC PGS-A Award
  • 2004: John Bosdet Memorial Fund Travel Scholarship
  • 2004: CIHR National Poster Competition Award (Silver)
  • 2004: Albert B. and Mary Steiner Summer Research Award
  • 2003: UBC Graduate Entrance Scholarship

Editorial Boards

  • Cell Reports
  • Cancer Genetics

Professional Societies & Organizations

  • present-2016: Member, Cancer Genomics Consortium (CGC)
  • present-2016: Member, American Society of Human Genetics (ASHG)
  • present-2014: Professional Member, International Society for Computational Biology (ISCB)
  • present-2010: Active Member, American Association for Cancer Research (AACR)

Resources Created