With the introduction of next-generation sequencing platforms, it is now feasible to use high-throughput approaches to address many research questions. This is especially true in cancer research, which has rapidly embraced high-throughput technologies. Dedicated compute clouds such as the Cancer Genome Collaboratory also facilitate complex analyses on large cancer data sets from projects such as the International Cancer Genome Consortium (ICGC) and the Pan-Cancer Analysis of Whole Genomes (PCAWG). Now more than ever, it is crucial to know what bioinformatic tools and resources are available in cancer research, and it is necessary to develop informatic skills to analyze high-throughput data using those tools.
The Canadian Bioinformatics Workshops (CBW), in collaboration with Cold Spring Harbor Laboratory, has developed a comprehensive six-day course covering key bioinformatics concepts and tools required to analyze cancer genomic data sets. This course combines the material and concepts from established CBW workshops; see a full outline here. In this course, participants will gain practical experience and skills to:
- visualize genomic data
- analyze cancer data sets for gene expression, genome rearrangement, somatic mutation, and copy-number variation
- analyze and conduct pathway analysis on candidate gene lists
- integrate -omic and clinical data
- launch, configure, customize, and scale virtual machines (VMs)
- navigate cloud repositories and work with data sets in them
- follow best practices in data and workflow management
Target Audience: Graduate students, postdoctoral scholars, clinical scientists, and principal investigators currently working with cancer genomics data, or about to embark on projects that require analysis of such data.
Prerequisites: You must have basic familiarity with UNIX/Linux and R to participate in this course. Specifically, you will need to understand material in the following tutorials before attending the course: UNIX for Beginners (tutorials 1-3) and Introductory R Tutorial (chapters 1-5). You can also review material from the prior CBW workshop on Exploratory Analysis of Biological Data Using R. A useful hands-on tool for getting started in R is Swirl. Pre-work and pre-course readings can be found on GitHub.
Computer requirements: If selected for the course, you will need to bring your own laptop computer. The minimum specifications are as follows: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, and a recent version of the Windows, Mac OS X or Linux operating systems. Most laptops purchased in the past 3-4 years likely meet these requirements. If you do not have access to your own laptop, you may be able to borrow one from CSHL.
Confirmed Speakers and Module Instructors:
Lauren Erdman, The Hospital for Sick Children
Brian Haas, The Broad Institute
Robin Haw, Ontario Institute for Cancer Research
Zhibin Lu, Princess Margaret Cancer Centre
George Mihaiescu, Ontario Institute for Cancer Research
Sorana Morrissy, University of Calgary
Brian O’Connor, University of California Santa Cruz
Mark Phillips, McGill University
Trevor Pugh, Princess Margaret Cancer Centre
Juri Reimand, Ontario Institute for Cancer Research
Jared Simpson, Ontario Institute for Cancer Research
Fouad Yousif, Ontario Institute for Cancer Research
Christina Yung, University of Chicago
Support & Financial Aid
Major support for this course is generously provided by the Helmsley Charitable Trust
Access to cloud computational resources may be supported by an education grant from Amazon Web Services
Financial aid is available to help offset tuition costs as follows:
1) Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) are provided by the Helmsley Charitable Trust
2) Financial aid for international applicants is provided by the Howard Hughes Medical Institute
Please indicate your eligibility for either of these funding sources in a financial aid request submitted as part of your application materials. Financial aid requests do not affect selection decisions made by the instructors.
Cost (including board and lodging): $2,910
No fees are due until you have completed the full application process and are accepted into the course. Students accepted into the course should plan to arrive in Cold Spring Harbor by the evening of Sunday, March 11, and depart the morning of Sunday, March 18.
Before applying, ensure you have 1) Personal statement/essay; 2) Letter(s) of recommendation; 3) Curriculum vitae/resume (optional); and, 4) Financial aid request (optional). More details about the course application process can be found here.
If you are not ready to fully apply, but wish to express interest in the course and receive an application reminder two weeks prior to the deadline, click below: