The topic this quarter is Genetic Epidemiology: Beyond Standard GWAS. Themes include the analysis of genetic variation outside the autosomes, association testing of unusual outcome data types, how to ask new questions with existing summary statistics, and the estimation of individual risk using polygenic risk scores and transcriptomic data. Each paper presents a novel method, usually providing theory, simulation, and an application.
This course is a journal club, with students presenting and leading a discussion each week. Students may also present their research in progress/capstone projects, with a separate reading and discussion board assignment for those weeks.
Students will read each week's paper in advance, join the in-class discussion, and contribute to the online discussion board by noon each class day (Tuesday). The weekly discussion leader(s) will create a short presentation of the paper that provides an overview of the paper and facilitates further discussion.
Classes meet in-person for Spring 2022, although we will have Zoom as a backup if the instructor or presenters cannot attend as per instructions across the UW. Class meets in K069 in the Health Sciences Building, near the Rotunda. Class begins at 4:00 pm Tuesdays, starting with five minutes for announcements, followed by 45 minutes of discussion, ending at 4:50. If you send these announcements to me at em27@uw.edu, I will post them to Canvas.
SPEAKER: Liz Blue
TOPIC: Introduction, review of resources, and speaker assignments.
You may be interested in a review of the limitations and benefits of genome-wide association studies (GWAS) and a primer for
conducting them. You may also be interested in this infographic or this blog post describing how to read a scientific paper.
SPEAKER: TBD
TOPIC: An atlas of mitochondrial DNA genotype-phenotype associations in the UK Biobank by Yonova-Doing et al. (2021).
SPEAKER: TBD
TOPIC: The X factor: a robust and powerful approach to X-chromosome-inclusive whole-genome association studies by Chen et
al. (2021).
SPEAKER: TBD
TOPIC: JEM: A joint test to estimate the effect of multiple genetic variants on DNA methylation by Sarnowski et
al. (2021).
SPEAKER: TBD
TOPIC: Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests
improves the power of transcriptome-wide association studies by Feng et al. (2021).
SPEAKER: TBD
TOPIC: Approximate conditional phenotype analysis based on genome wide association summary statistics by Wu et al. (2021).
SPEAKER: TBD
TOPIC: Simultaneous estimation of bi-directional causal effects and heritable confounding from GWAS summary statistics by Darrous et al. (2021).
SPEAKER: Seth Temple
TOPIC: Inferring natural selection using identity-by-descent segments.
The reading assignment is Embracing Genetic Diversity to Improve Black Health by Oni-Orison et al. (2021).
SPEAKER: TBD
TOPIC: Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories by Lali et al. (2021).
SPEAKER: TBD
TOPIC: Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries by Liang et al. (2022).