Webinar Series - Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions

The NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome has put together a webinar series, Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions. The goal of this series is to transverse the path from trait variance to QTL to gene variant to molecular networks to mechanisms to therapeutic and interventions. The target audience for this series are those new to the field of quantitative genetics, so please pass this information on to your trainees or colleagues.

Title/Description Presentation

Webinar #01 - Introduction to Quantitative Trait Loci (QTL) Analysis

Friday, May 8th, 2020
10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT

Goals of this webinar (trait variance to QTL):

  • Define quantitative trait locus (QTL)
  • Explain how genome scans can help find QTL

Presented by:
Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

Link to course material: [https://github.com/OSGA-OPAR/quant-genetics-webinars/blob/master/2020-05-08/README.md]

Webinar #02 - Mapping Addiction and Behavioral Traits and Getting at Causal Gene Variants with GeneNetwork

Friday, May 22nd. 2020 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT

Goals of this webinar (QTL to gene variant):

  • Demonstrate mapping a quantitative trait using GeneNetwork (GN)
  • Explore GN tools to identify genes and genetics variants related to a QTL

Presented by:
Dr. Rob Williams
Professor and Chair
Department of Genetics, Genomics, and Informatics
University of Tennessee Health Science Center

Link to course material: [https://github.com/OSGA-OPAR/quant-genetics-webinars/blob/master/2020-05-22/Using_GeneNetwork_22May2020v8.pdf]

Webinar #03 - Introduction to expression (e)QTL and their role in connecting QTL to genes and molecular networks

Friday, June 12, 2020 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT

Goals of this webinar (QTL to gene/molecular networks):

  • Define eQTL
  • Examine the role of eQTL in the relationship of genes and molecular networks with phenotypic QTL
  • eQTL for co-expression networks

Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Webinar flyer (pdf)
Link to course material: [https://github.com/OSGA-OPAR/quant-genetics-webinars/tree/master/2020-06-12]

Webinar #04 - From Candidate Genes to Causal Variants—Strategies for and Examples of Identifying Genes and Sequence Variants in Rodent Populations

Friday, June 26, 2020 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT

Goals of this webinar (candidate genes to causal variants):

  • To understand when it is practical or (just as often) not practical to try to "clone" the gene or nucleotide variant modulating trait variants
  • To understand that defining the crucial causal nucleotide variant is usually a bonus and often not for the translational or even mechanistic utility of discoveries.
  • To review new sequence-based methods to identify common and rare variants—the reduced complexity cross and epoch-effects in reference populations

Presented by:
Dr. Rob Williams
Professor and Chair
Department of Genetics, Genomics, and Informatics
University of Tennessee Health Science Center

Link to course material in pdf: [P30_Webinar_on_QTGenes_26Jun2020v3.pdf]
Link to course material in powerpoint pptx: [P30_Webinar_on_QTGenes_26Jun2020v3.pptx]

Webinar #05 - Identifying genes from QTL using RNA expression and the PhenoGen website (http://phenogen.org)

Friday, August 28, 2020 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar (candidate genes to causal variants):

Demonstrate how to use the PhenoGen website to identify transcripts:

  • Physically located within a QTL
  • Physically located within a QTL and expressed in brain
  • With a brain cis eQTL within the QTL
  • With any brain eQTL within the QTL
  • Within a co-expression network controlled from the same region as the QTL

Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Link to course material in pdf: [PhenoGen_webinar.pdf]

Webinar #06 - Sex as a Biological Covariate in QTL Studies

Friday, September 11th, 2020 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar (trait variance to QTL):

  • Review QTL mapping
  • Understand the role of sex in QTL study design
  • Use sex as a covariate in QTL analysis
  • Understand X chromosome segregation in crosses
  • Make adjustments for X chromosome in QTL analysis

Presented by:
Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

Webinar #07 - Introduction to Weighted Gene Co-expression Network Analysis

Friday, September 25th at 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar (molecular networks):

  • Introduction and motivation for co-expression network analysis
  • Basics of weighted gene co-expression network analysis
  • Step-by-step guide to WGCNA using the wgcna package in R.

Background reading available at: http://bit.ly/osga_wgcna

Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Webinar #08 - Using genetic and non-genetic covariates in QTL studies

Friday, October 9th at 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar (quantitative trait to genetic loci):

  • Identify covariates and mediators in QTL studies
  • Adjust for covariates in QTL scans
  • Review genetic relatedness in segregating populations
  • Adjust for genetic relatedness using linear mixed models

Presented by:
Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

Webinar #09 - Introduction to GeneWeaver: Integrating and analyzing heterogeneous functional genomics data

Friday, October 23th at 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar:

  • Compare a user's gene list with multiple functional genomics data sets
  • Compare and contrast gene lists with data currently available and integrated in GeneWeaver
  • Explore functional relationships among genes and disease across species

Presented by:
Dr. Elissa Chesler
Professor The Jackson Laboratory

Dr. Erich Baker
Professor and Chair
Department of Computer Science
Baylor University

Webinar #10 - Sketching alternate realities: An introduction to causal inference in genetic studies

Friday, November 20th at 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT
1-hour presentation followed by 30 minutes of discussion

Goals of this webinar:

Determination of cause is an important goal of biological studies, and genetic studies provide unique opportunities. In this introductory lecture we will frame causal inference as a missing data problem to clarify challenges, assumptions, and strategies necessary for assigning cause. We will survey the use of directed acyclic graphs (DAGs) to express causal information and to guide analytic strategies.

  • Express causal inference as a missing data problem (counterfactual framework)
  • Outline assumptions needed for causal inference
  • Express causal information as (directed acyclic) graphs
  • Outline how to use graphs to guide analytic strategy

Presented by:
Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

This webinar series is sponsored by the NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome (P30 DA044223).