Workshop Description

High-throughput sequencing technologies have allowed researchers to extract DNA at the individual, population, and species levels. In this workshop, students will learn how to analyze and interpret population-level genetic information with PLINK and R. Students will also be exposed to the literature on the different topics, followed by hands-on exercises and paper discussion.

Workshop Materials

At the end of the workshop, the students will be able to:

  • Describe what a variant calling file (VCF) format is and how to manage those files.
  • Conduct quality assesment of a VCF.
  • Learn about population structure and how to compute it with PLINK.
  • Learn about linkage disequilibrium and how to compute it with PLINK.
  • Learn about basic association testing and genome wide association studies (GWAS).
  • Learn about copy number variants (CNVs) and how to test for common CNVs across indidviduals.
  • Discuss original literature within the subjects.
  • Background lecture (45 minutes)
    • What is a VCF?
    • What is QC, and why is it so important?
  • Break (15 minutes)
  • Hands on exercise (1 hour)
    • VCF Data management (read, recode, reorder, merge, subset, compress data)
    • QC assessement
  • Break (15 minutes)
  • Paper discussion on quality control assessment (30 minutes)
  • Assignment explanation (15 minutes)
  • Background lecture (45 minutes)
    • What is population structure?
    • What is linkage disequilibrium?
    • How does population structure and LD affect association mapping?
  • Break (15 minutes)
  • Hands on exercise (1 hour)
    • Population stratification detection
    • LD estimation
  • Break (15 minutes)
  • Paper discussion on genome wide association studies
  • Assignment explanation (15 minutes)
  • Peer review of previous assignment (15 minutes)
  • Background lecture (45 minutes)
    • What is association testing and GWAS?
    • What is a Manhattan plot and a Q-Q plot?
    • What is a copy number variant?
  • Break (15 minutes)
  • Hands-on exercise (1 hour and 30 minutes)
    • Basic association testing
    • GWAS accounting for population structure
    • CNV detection
  • Break (15 minutes)
  • Assignment explanation (15 minutes)

Technical Requirements

Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.





Workshop Details

Prerequisites: Some familiarity with basic command line, R, and genetics
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Spring 2022 Dates

May 24, 25, and 26
1:30 PM – 4:30 PM