Epigenetics Boot Camp: Planning and Analyzing DNA Methylation Studies for Human Populations
June 29-30, 2023 | Subscribe to hear about the next training
The most recent Epigenetics Boot Camp on June 29-30, 2023. Sign up below to hear about the next training!
The Epigenetics Boot Camp is a two-day intensive boot camp of seminars and hands-on analytical sessions to provide an overview of concepts, techniques, and data analysis methods utilized in human epigenetics studies and focused on DNA methylation array.
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Boot Camp Overview
Summer 2023 dates: Livestream, online training June 29-30, 2023; 10:00am EDT - ~5:00pm EDT.
This two-day intensive boot camp integrates the principle concepts of epigenetics and the effects of risk factors on the epigenome as we step through the key components of designing and executing DNA methylation studies. Led by a team of scientists with more than 50 years of combined expertise in the field of environmental epigenetics, this epigenetics training will integrate seminar lectures with hands-on computer sessions to put concepts into practice. Emphasis will be given to leveraging existing resources from ongoing studies and initiating new investigations. The afternoon lab sessions will provide an opportunity to work hands-on with real methylation data generated by the Illumina Infinium MethylationEPIC (850k) BeadChip platform. Participants will learn and practice data handling, cleaning, and basic analysis of epigenome-wide DNA methylation data. This training will not cover WGBS or analyses from sequencing experiments in animal models.
By the end of the epigenetics training, participants will be familiar with the following topics:
- Principles of epigenetics
- Concept ideation and study design
- Sample collection and processing
- Laboratory methods and platforms for analysis
- Data handling and cleaning
- Analysis of 450K/EPIC data
- Study design advantages and pitfalls
- Emerging epigenetic topics and laboratory platforms
Investigators at all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate. There are two requirements to attend this boot camp:
- Each participant is required to have a personal laptop/computer and a free, basic RStudio Cloud account. All lab sessions will be done using RStudio Cloud.
- The Boot Camp will use data sets in R, therefore participants must have a basic understanding of this platform prior to attending the Boot Camp. If you have never used this platform before, make sure to step through all the tutorials outlined below so you have the basic skills needed for Boot Camp success.
Knowing basic R platform and commands is required for the Boot Camp as noted in prerequisites above. This training will use RStudio Cloud. If you are new to R or need a refresher, you can review the below tutorials to be well prepared:
- R Programming Tutorial - Learn the Basics: A free datalab.cc class on R fundamentals
- Once you create your free, basic RStudio Cloud account for the training: Primers on Programming Basics and Visualization Basics.
- SHARP Program RStudio Cloud Tutorial: This self-paced tutorial from the Columbia SHARP Program walks through the Cloud Platform you will use at the training, as well as some basic exercises. We recommend this tutorial if you have not used the Cloud version of RStudio before, or if you are a beginner user of R.
If you have any specific questions about R and R studio in the context of the Epigenetics Boot Camp, please email us.
Riccardo Marioni, PhD, Chair of Translational Epidemiology at the Centre for Genomic & Experimental Medicine, University of Edinburgh. His primary research goal is to use computational models to understand the molecular mechanisms that underlie Alzheimer's disease and to enhance prediction of the disease.
Boot Camp Director: Andres Cardenas, PhD, MPH, School of Medicine, Stanford University.
Andrea Baccarelli, MD, MPH, PhD, Mailman School of Public Health, Columbia University.
Alexandra Binder, ScD, Department of Cancer Epidemiology, University of Hawai'i.
Anne Bozack, PhD, School of Public Health, University of California, Berkeley.
Elena Colicino, PhD, Icahn School of Medicine at Mount Sinai.
Jonathan Heiss, PhD, GRAIL.
Allison Kupsco, PhD, Mailman School of Public Health, Columbia University.
Former Keynote Speakers and Instructors
John Greally, DMed, PhD, Center for Epigenomics, Albert Einstein College of Medicine. Keynote Speaker, 2017-2022.
Allan Just, PhD, Icahn School of Medicine at Mount Sinai. Instructor 2017-2020.
Chris Mason, PhD, Weill Cornell Medical College. Keynote Speaker, 2017.
Caroline Relton, PhD, Professor of Epigenetic Epidemiology and MRC Investigator, Bristol Medical School (PHS). Keynote Speaker, 2022.
Cavin Ward-Caviness, PhD, Environmental Public Health Division, US Environmental Protection Agency. Instructor, 2017.
Kasey Brennan, MS, Mailman School of Public Health, Columbia University. Instructor, 2017-2018.
Scholarships are available for the Epigenetics Boot Camp.
Summer 2023: The Epigenetics Boot Camp is a live-stream, remote training that takes place over live, online video June 29-30, 2023 from 10am EDT - ~5pm EDT. Please note this training is not a self-paced, pre-recorded online training.
"As a translational exercise physiologist learning how to integrate multi-omic data into my research, this Epigenetics Boot Camp provided a great overview of background, study design, pre-processing and analysis considerations, and highlighted recent findings in this rapidly developing field of research. I feel I have a better grasp on concepts to take into consideration when consulting with our bioinformaticians for upcoming projects and how to interpret results." - Postdoc at Duke University, 2022
"Excellent crash course in the analysis of epigenetic data that goes into great depth on the assumptions and limitations for responsible application of methods." - Faculty member at University of Massachusetts, Amherst, 2022
"Great course! Have done some epigenetic work previously, but these two days (and the preparatory exercises) really deepened my understanding and improved my R skills significantly." - Student at Umea University, Sweden, 2022
"This was a great experience for me since I had no prior experience. It quickly caught me up on the field. I would recommend this course to my friends." - Trainee at the NIH, 2022
"I feel like my participation in this boot camp has sharpened my skillset and given me new techniques and tools to apply to my ongoing and future research. I appreciate how responsive and helpful all of the presenters and organizers were in responding to questions from the participants, who had a diverse range of experiences and research interests, thank you!" - Postdoc at the University of Arizona, 2022
|Early-Bird Rate (through 4/17/23)||Regular Rate (4/18/23-6/22/23)||Columbia Discount*|
|Faculty/Academic Staff/Non-Profit Organizations/Government Agencies||$1,175||$1,375||10%|
*Columbia Discount: This discount is valid for any active student, postdoc, staff, or faculty at Columbia University. If paying by credit card, use your Columbia email address during the registration process to automatically have the discount applied. If paying by internal transfer within Columbia, submit this Columbia Internal Transfer Request form to receive further instructions. Please note: filling out this form is not the same as registering for a training and does not guarantee a training seat.
Invoice Payment: If you would prefer to pay by invoice/check, please submit this Invoice Request form to receive further instructions. Please note: filling out this form is not the same as registering for a training and does not guarantee a training seat.
Registration Fee: This fee includes course material, which will be made available to all participants both during and after the conclusion of the training.
Cancellations: Cancellation notices must be received via email at least 30 days prior to the training start date in order to receive a full refund, minus a $75 administrative fee. Cancellation notices received via email 14-29 days prior to the training will receive a 75% refund, minus a $75 administrative fee. Please email your cancellation notice to Columbia.EBC@gmail.com. Due to workshop capacity and preparation, we regret that we are unable to refund registration fees for cancellations <14days prior to the training.
If you are unable to attend the training, we encourage you to send a substitute within the same registration category. Please inform us of the substitute via email at least one week prior to the training to include them on attendee communications, updated registration forms, and materials. Should the substitute fall within a different registration category your credit card will be credited/charged respectively. Please email substitute inquiries to Columbia.EBC@gmail.com. In the event Columbia must cancel the event, your registration fee will be fully refunded.
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The Epigenetics Boot Camp is hosted by Columbia University's SHARP Program with additional support from Illumina, Inc.
"Excellent. I was very impressed by the breadth and depth of coverage of epigenetics and data analysis. I will highly recommend it to others." - Faculty member at Michigan State University, 2021
"Excellent course that provides a foundation in the quality control and analyses of epigenome-wide DNA methylation data. The course is very practical, providing tools that can be immediately applied, and the instructors are very knowledgable and clearly experts in the field." - Faculty member at Brigham and Women's Hospital, 2021
"This bootcamp was an immersive experience for a deep dive into DNA methylation analysis. As a novice, it was a lot of information, but I feel like I learned a ton!" - Postdoc at University of Colorado Boulder, 2021
"As a novice in this field, I felt the instructors made this course thorough and accessible for all levels of experience. I left with a greater understanding of DNA methylation and can now speak intelligently about the subject with collaborators and now know how to approach the inclusion of DNA methylation in my future study designs." - Faculty member at the University of California, Davis, 2020
"The Epigenetics Boot Camp was very helpful! The instructors provided all the tools to start analyzing DNA methylation datasets, showed us how to use them, and provided information on how make decisions based on the data and research question." - Postdoc Fellow at University of Texas, Austin, 2020
"The instructors were friendly and enthusiastic. The material and activities were accessible and the format allowed participants to engage at their desired level." - Dawn M., Faculty member at Wayne State University, 2019
"The boot camp provided a great overview of important considerations from study conception through design, analysis, and interpretation. The provided information would be useful to researchers with all levels of experience in methylome analyses." - Mark G., Postdoc Fellow at the American Cancer Society, 2019
"As someone new to epigenetics, this workshop provided a great introduction to key concepts and strategies that will allow me to effectively implement epigenetic data into my research." - Student at Virginia Commonwealth University, 2018
"This was a very useful, all-encompassing dive into the epidemiologic methods required for epigenome-wide DNA methylation analyses. The instruction was high-quality, and there was a strong lab component that supported application of skills to real-world data. I would only hope for a part 2 to this quick course." - Alonzo F., Faculty Member at Cincinnati Children's Hospital Medical Center, 2018
"The level of knowledge and experience as well as careful planning by all instructors made the entire two-day experience worthwhile. Best applied training I have been to, I now feel equipped to work with my own data and collaborate with bioinformatics colleagues in cleaning and analyzing our data." - Kristen M., Faculty Member at the University of Wisconsin-Madison, 2017
"Overall, I found the Epigenetics Boot Camp to be a very useful and comprehensive tool for learning basic principles surrounding DNA methylation analysis and interpretation. It provided a good foundation from which to build upon as I advance my knowledge in this field." - Postdoc at Emory University, 2017
"The Boot Camp gives a very comprehensive overview of the epigenetic research with enough technical details that all levels of participants will find informative and educational. I especially appreciate how knowledgeable the speakers are. Thank you for putting such a great workshop together!" - Staff Member at Harvard University, 2017