Section outline

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  • Tuesday, January 8, 2019; 1:10 PM - 3:00 PM

    Lecture: Introduction: The Big Picture

    The process of genetic epidemiology; general approaches to assess the genetic basis of disease.

    Faculty:  John Witte

    Location:      Mission Hall 1407

    • Session Slides:

    • Lecture 1 slides File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL

    • Required Reading:

      Relevant journal articles will be assigned throughout the quarter. These should be read before the corresponding class meeting. Each student will be responsible for leading discussion of one week's journal article(s).

    • Genetic Epi chapter File
    • Harry Potter reading File

    • Assignment:

    • Assignment 1 File

    • Final Exam: Optional narrative description

    • Final project File

    • Written Final Project Due Date: Due on 3/15 by email to all of Elizabeth Mercado <MariaElizabeth.Mercado@ucsf.edu>, Thomas Hoffmann <hoffmannt@humgen.ucsf.edu>, and John Witte <John.Witte@ucsf.edu>

      Also, Brief Presentation of Project in the Final Class on 3/19

  • Tuesday, January 15, 2019; 1:00 PM - 3:00 PM

    Lecture: Population Genetics, Heritability, Familiality 

    Faculty:  John Witte

    Location:      Mission Hall 1407

    • Session Slides:

    • Lecture 2 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

    • Visscher File

    • Assignment:

    • Assignment 2 File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, January 22, 2019; 1:00 PM - 3:00 PM

    Lecture: Association Studies

    Faculty:  John Witte

    Location:  Mission Hall 1407

    • Session Slides:

    • Lecture 3 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:


    • GWAS and beyond File

    • Assignment:

    • Assignment 3 File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, January 29, 2019; 1:00 PM - 3:00 PM

    Lecture: Genome-wide Association Studies (GWAS)

    Introduction to genome-wide association studies (GWAS): study design, array design, and initial analysis

    Faculty:  Thomas Hoffmann

    Location:      Mission Hall 1407

    • Session Slides:

    • Lecture4 GWAS File
    • Lecture4 GWAS File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Assignment:

    • Assignment 4 File
    • bycroft2018-ukb File
    • MTHFR File
    • MTHFR File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, February 5, 2019; 1:00 PM - 3:00 PM

    Lecture: GWAS (Continued)

    Imputation, etc.

    Faculty:  Thomas Hoffmann

    Location:      Mission Hall 1407

    • Session Slides:

    • Lecture5 GWAS File
    • Lecture5 GWAS File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Assignment:

    • Assignment 5 File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, February 12, 2019; 1:00 PM - 3:00 PM

    Lecture: GWAS (Still continued)

    Faculty: Tom Hoffmann

    Location:  Mission Hall 1407

    • Session Slides:

    • Lecture6 GWAS File
    • Lecture6 GWAS File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Assignment: Optional narrative description

    • Assignment 6 File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, February 19, 2019; 1:00 PM - 3:00 PM

    Lecture: Gene-Environment Interactions, Rare Variants, Pleiotropy. Microbiome 

    Faculty:  Iona Cheng

    Location:  Mission Hall 1407

    • Session Slides:

    • Feb 19 2019 GxE interactions Pleiotropy Gut Microbiome File
      Not available unless: You belong to a group in Registered Students Only

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

    • NSAID Colorectal Cancer GxE JAMA 2015 File
    • Pleiotropy PheWAS PLoS Genetics 2013 File

    • Assignment: Optional narrative description

    • Assignment 7 File

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, February 26, 2019; 1:00 PM - 3:00 PM

    Lecture: Non-mendelian Genetics

    Mitochondrial (MT); de novo; parent-of-origin; methylation, functional genetics

    Faculty:  Eric Jorgenson

    Location:  Mission Hall 1407

  • Tuesday, March 5, 2019; 1:00 PM - 3:00 PM

    Lecture: Next Generation Sequencing

    Faculty:  Eric Jorgenson

    Location:  Mission Hall 1407

    • Session Slides:

    • Lecture 9: Next generation sequencing File

    • Session Audio/Video Recording:

    • Final Exam: Optional narrative description

    • Final Project File

    • Written Final Project Due Date: Due on 3/15 by noon by email to all of Elizabeth Mercado <MariaElizabeth.Mercado@ucsf.edu>, Thomas Hoffmann <hoffmannt@humgen.ucsf.edu>, and John Witte <John.Witte@ucsf.edu>

      Also, Brief Discussion of Project in the Final Class on 3/19

    • Assignment: Optional narrative description

  • Tuesday, March 12, 2019; 1:00 PM - 3:00 PM

    Lecture: Genetic epidemiology in diverse populations, ancestry, admixture mapping 

    Faculty:  Laura Fejerman

    Location:  Mission Hall 1407

    • Session Slides:

    • Lecture 10 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Required Reading:

    • Popejoy et al File
    • Martin et al File

    • Assignment: Optional narrative description

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, March 19, 2019; 1:00 PM - 3:00 PM

    Lecture: Putting it all Together: Incorporating Molecular and Genetic Measures into Your Research

    Final Project Presentations.

    Faculty:  John Witte, Tom Hoffmann

    Location:      Mission Hall 1407

    • Session Audio/Video Recording (Access restricted to registered students):

    • Required Reading:


    • Assignment: Optional narrative description

    • Assignment Answer Key (Access restricted to registered students):