Multi-omics Boot Camp: Analysis of Omics Data for Research Studies

Columbia SHARP Multi-omics TrainingMost recent live-stream Multi-omics Boot Camp was June 28-29, 2021. Sign up below to hear about the next training.

 

The Multi-omics Boot Camp is a two-day intensive boot camp of seminars and hands-on sessions to provide an overview of concepts and methods used to analyze omics data in observational studies. Specific topics will include integrating germline genetic, gene expression, and exposomic data, gene-environment interaction, mediation, and polygenetic risk scores to for assessing risk, estimating subgroups, and selecting relevant features.
  
 

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BOOT CAMP OVERVIEW

Summer 2021 dates: Live-stream, online training June 28-29, 2021; 12pm EDT - ~8pm EDT

Many observational studies are now leveraging modern technologies to measure multiple types of omic data. Omic tools can assist in better characterizing risk factors (e.g. germline genetics, exposomics), providing measurements for intermediate variables that may capture the underlying mechanism (e.g. transcriptomics, proteomics, metabolomics, and the microbiome), or defining an outcome of interest. In this context, the investigator is often confronted with an analytic decision on a continuum between simplicity and complexity. Simple approaches often treat sets of variables in a pairwise independent manner, sacrificing joint evaluation for benefits in interpretability. At the other extreme, complex methods may more-completely model the joint omics structure, but can sacrifice interpretability. This workshop will cover several different approaches to the analysis of multiple omic data, with a focus on the tradeoffs between simple and complex approaches.

This two-day intensive workshop will provide an overview of multiple approaches to analyze multiple omic data types measured on the same individuals or via the use of summary statistic data. Instructors have experience in developing and applying methods for omic analysis in genetic and environmental epidemiology and are members of an active program project focused on developing statistical methods for integrated analysis. The workshop will include seminar lectures with hands-on computer lab sessions to put concepts into practice. Since the analysis of multi-omic data is broad in scope, the workshop will survey a range of approaches and highlight the appropriate application and interpretation of each approach for specific research questions. The lab sessions will provide an opportunity to work hands-on with different types of omic data.

By the end of the workshop, participants will be familiar with the following topics:

  • Data reduction, including clustering.
  • Regression analysis, including regularized regression, hierarchical models, and partial least squares.
  • Interaction analysis and Genome-wide interaction scans (GWIS).
  • Mediation analysis.
  • Polygenic/polyexposure analysis.
  • Integrative analysis using genome-wide association study (GWAS) summary statistics.

Investigators at all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate.

PREREQUISITES AND REQUIREMENTS

There are three prerequisites and requirements to attend this training:

  1. Each participant must have an introductory background in statistics and epidemiology.
  2. Each participant must be familiar with R.
  3. Each participant is required to have a personal laptop with R and RStudio downloaded and installed prior to the first day of the workshop as all lab sessions will be done on your personal laptop. R is available for free download and installation on Mac, PC, and Linux devices.

R TUTORIALS

Knowing basic R platform and commands is required for the Boot Camp as noted in prerequisites above. If you are new to R or need a refresher, you can review the below tutorials to be well prepared:

  • Download R: R is the free software programming language we will use. Choose the correct version for your laptop: Mac/Windows 

  • Download R Studio: R studio is free software that will help us develop programs in R. Choose the correct version for your laptop: Mac/Windows

  • How to Download R and R studio: A tutorial on how to download R and R Studio

  • How to Install a Package in R studio: Steps to install a package in R Studio

  • Best tutorial for Boot Camp Prep: R Programming Tutorial - Learn the Basics: A free datalab.cc class on R fundamentals

  • Boot Camp Attendees: There will be a pre-course tutorial to step through specific to the Boot Camp closer to the training

If you have any specific questions about R and R studio in the context of the Multi-omics Boot Camp, please email us.

INSTRUCTORS

Training Director: David Conti, PhD, Professor of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC.

William Gauderman, PhD, Professor of Preventive Medicine, Preventive Medicine, Keck School of Medicine of USC.

Nicholas Mancuso, PhD, Assistant Professor of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC.

Kimberly Siegmund, PhD, Professor of Preventive Medicine, Keck School of Medicine of USC.

 

SCHOLARSHIPS

Training scholarships are available for the Multi-omics Boot Camp.

LOCATION

COVID-19 Update: The Multi-omics Boot Camp will no longer take place in person due to the COVID-19 pandemic. With the instructors on the west coast, the Boot Camp will instead be a live-stream, remote training that takes place over live, online video on June 28-29, 2021 from 12pm EDT - ~7pm EDT (9am - ~4pm PDT). Please note this training is not a self-paced, pre-recorded online training.

Testimonials

"This camp improved my knowledge and abilities to employ cutting-edge statistical principles and modelings to explore the high dimensional omics data and address the scientific hypothesis." - Faculty member at Eastern Virginia Medical School, 2021

"Extremely useful course with a great balance of theoretical concepts and hands-on application using R code. Covered state-of-the-art techniques with experienced and knowledgeable instructors." - Faculty member at Brigham and Women's Hospital, 2021

"This bootcamp was fantastic! The instructors did a great job of clearly explaining complex topics and I feel like I left with the practical skills to be able to apply them to my own research." - Postdoc at Columbia University Mailman School of Public Health

"Well prepared and organized. All teachers very helpful and patient." - Beata M., Postdoc at Albert Einstein College of Medicine, 2021 

"A great methods-driven overview of multi-omics, with applications to multiple research areas in observational research. I found the examples and overview of programming to be a great pairing, as it makes the tools learned immediately applicable." - Student at University of Texas Health Science Center at Houston, 2021

 

REGISTRATION FEES

COVID-19 Update: With the training being offered virtually, we are passing along any and all costs saved to attendees.

  Early-Bird Rate (through 4/15/21) Regular Rate (4/16/21 - 6/21/21) Columbia Discount*
Student/Postdoc/Trainee      $875 $975  10%
Faculty/Academic Staff/Non-Profit Organizations/Government Agencies $975  $1,175 10%
Corporate/For-Profit Organizations $1,175 $1,375 NA

*Columbia Discount: This discount is valid for any active student, postdoc, staff, or faculty at Columbia University. To access Columbia discount, email ColumbiaSHARP.Multiomics@gmail.com for instructions and specify if you are paying by credit card, or internal transfer within Columbia.

Invoice Payment and Group Registrations: If you would prefer to pay by invoice/check, or would like to pay for a group of registrants, please email ColumbiaSHARP.Multiomics@gmail.com with details.

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 ColumbiaSHARP.Multiomics@gmail.comDue 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 ColumbiaSHARP.Multiomics@gmail.com. In the event Columbia must cancel the event, your registration fee will be fully refunded. 

ADDITIONAL INFORMATION

 

 

 

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Questions? Email the Boot Camp team here.

The Multi-omics Boot Camp is hosted by the Columbia Mailman School of Public Health's SHARP Program.