PRS
In this tutorial section, we will focus on describing and comparing different methods of calculating polygenic risk scores. Generally, a polygenic risk score is the combined effect of multiple genetic variants on a trait, and is most basically calculated as a sum of risk allele effects across the genome.
In this section you will hear about many different methods for calculating PRS: In the first video, Dr. Ni gives a comprehensive overview and comparisons of different PRS methods, such as LDPred2, PRS-CS, SBayesR, and LASSOSUM, and the benefits and limitations of each method. In the next two videos, Drs. Ge and Ruan give tutorials on how to calculate PRS using PRS-CS/PRS-CSx software using both individual-level genotypes and GWAS summary statistics. In the following video, Dr. Privé demonstrates how to calculate PRS using LDPred2. Next, Dr. Choi gives an introduction to PRSice2 for calculating PRS, and a background into the theory of this method using LASSOSUM. We have content on SBayesR coming soon! Lastly, Dr. Balbona discusses methods of determining vertical transmission, or the effect of parental phenotype on the offspring, through PRS methods.
Comparison of PRS Methods
Title: Comparison of PRS methods
Presenter(s): Guiyan Ni, PhD (Institute for Molecular Bioscience, University of Queensland)
Level: Intermediate
Length: 13:52
Link to video transcript here.
PRS-CS and PRS-CSx
PRS-CSx to perform PRS analysis
Title: Hands-on tutorial of using PRS-CSx to perform multi-ancestry PRS analysis
Presenter(s):
Tian Ge, PhD (Center for Genomic Medicine, Mass General Research Institute)
Yunfeng Ruan, PhD (Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard)
Level: Intermediate
Length: 8:28
Link to video transcript here.
PRS in Ancestrally-Diverse Populations
Title: PRS-CSx: Improving Cross-Population Polygenic Prediction using Coupled Continuous Shrinkage Priors
Presenter(s): Tian Ge, PhD (Center for Genomic Medicine, Mass General Research Institute)
Level: Intermediate
Length: 56:46
Link to video transcript here.
LDpred2
Title: How to run LDpred2
Presenter(s): Florian Privé, PhD (National Centre for Register-Based Research, Aarhus University)
Level: Intermediate
Length: 15:00
Link to video transcript here.
Link to tutorial test datasets here.
PRSice2 and LASSOSUM
Title: PRSice: Basic Polygenic analysis
Presenter(s): Shing Wan Choi, PhD (Regeneron)
Level: Intermediate
Length: 25:35
Link to video transcript here.
SBayesR
[Note]: At the moment the video input does not have sound. We are working on getting a working version up very soon!
Title: How to run SBayesR
Presenter(s): Jian Zeng, PhD (Institute for Molecular Bioscience, University of Queensland)
Level: Intermediate
Length: 8:09
Link to video transcript here.
Vertical Transmission and Genetic Nurture with PRS
Title: Estimating Vertical Transmission and Genetic Nurture using Polygenic Scores
Presenter(s): Jared Balbona, PhD (Institute for Behavioral Genetics, University of Colorado Boulder)
Coauthor(s):
Yongkang Kim, PhD (Janssen Pharmaceutical Companies of Johnson & Johnson)
Matthew Keller, PhD (Institute for Behavioral Genetics, University of Colorado Boulder)
Level: Intermediate
Length: 21:30
Link to video transcript here.
Link to code and practice data on Google drive.
Link to OpenMx R package.