BIOST 581 A Statistical Genetics Seminar

Winter 2024

Contact information

Instructor: Guanghao Qi, PhD. (he/him/his)

Assistant Professor

Department of Biostatistics, School of Public Health

Contact: gqi@uw.edu

206-543-5657 (office)

HRC 359 (office)

Office hours: By appointment

Course times and locations

Tuesdays, 4:00-4:50pm PT, HST T359

Course Description

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.

Classes meet in-person for Winter 2024. 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 Dr. Qi at gqi@uw.edu, who will post them to Canvas.

The topic this quarter is expression quantitative trait loci (eQTL) analysis. We will discuss different methods for eQTL mapping: single-tissue, cross-tissue, incorporation of allele-specific expression, cell type-specifc mapping using deconvolution, single-cell eQTL studies, potential limitations.

Reading List

Week 1 – January 9

TOPIC: Introductions and sign up

PAPER: GTEx Consortium. "The GTEx Consortium atlas of genetic regulatory effects across human tissues." Science 369.6509 (2020): 1318-1330.

Week 2 – January 16

TOPIC: Fast eQTL testing

PAPER: Shabalin, Andrey A. "Matrix eQTL: ultra fast eQTL analysis via large matrix operations." Bioinformatics 28.10 (2012): 1353-1358.

Week 3 – January 23

TOPIC: eQTL analysis across multiple tissues

READING: Urbut, Sarah M., et al. "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions." Nature genetics 51.1 (2019): 187-195.

Week 4 – January 30

TOPIC: Leveraging allele-specific expression

READING: Liang, Yanyu, et al. "A scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction." Nature communications 12.1 (2021): 1424.

Week 5 – February 6

TOPIC: Cell type deconvolution and eQTL

READING: GTEx Consortium. "Cell type–specific genetic regulation of gene expression across human tissues." Science 369.6509 (2020): eaaz8528.

Week 6 – February 13

TOPIC: Single-cell eQTL study in PBMCs

READING: Perez, Richard K., et al. "Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus." Science 376.6589 (2022): eabf1970.

Week 7 – February 20

TOPIC: Single-cell eQTL mapping without pseudobullk

READING: Cuomo, Anna SE, et al. "CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq." Molecular Systems Biology 18.8 (2022): e10663.

Week 8 – February 27

TOPIC: Trait heritability mediated by gene expression

READING: Yao, Douglas W., et al. "Quantifying genetic effects on disease mediated by assayed gene expression levels." Nature genetics 52.6 (2020): 626-633.

Week 9 – March 5

TOPIC: eQTL and GWAS overlap

READING: Mostafavi, Hakhamanesh, et al. "Systematic differences in discovery of genetic effects on gene expression and complex traits." Nature Genetics (2023): 1-10.