The topic this quarter is Rare Variant Testing. We will review alternative strategies for statistical tests of association between rare genetic variants and complex traits, including burden, variance component, and omnibus tests.
Classes meet in-person for Autumn 2022. Class begins at 4:00 pm Tuesdays in HST T474, starting with five minutes for announcements, followed by 45 minutes of discussion, ending at 4:50pm. If you send these announcements to me at em27@uw.edu, I will post them to Canvas.
SPEAKER: Liz Blue
TOPIC: Introduction
We will assign discussion leaders for the following weeks and Liz will provide an overview of rare variant testing in complex traits to build your intuition for the rest of the course. You may be interested in this infographic or this blog post describing how to read a scientific paper.
SPEAKER: Diane
TOPIC: Collapsing tests.
PAPER: Ultra-rare genetic variation in common epilepsies: a case-control sequencing study by the Epi4K consortium and Epilepsy Phenome/Genome Project (2017). This paper references the approach applied by Cirulli et al. (2015).
SPEAKER: Abbey
TOPIC: Burden tests.
PAPER: A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic by Madsen and Browning (2009).
CANCELLED: Annual meeting of the American Society of Human Genetics.
SPEAKER: Chris
TOPIC: Variance components tests.
PAPER: Rare-Variant Association Testing for Sequencing Data with the Sequence Kernal Association Test by Wu et al. (2011).
SPEAKER: Ethan
TOPIC: Omnibus tests.
PAPER: Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies by Lee et al. (2012).
SPEAKER: Ruoyi
TOPIC: Tests accommodating sparse data.
PAPER: ACAT: A Fast and Powerful p Value Combination Method for Rare-Variant Analysis in Sequencing Studies by Liu et al. (2019).
SPEAKER: Jingheng
TOPIC: Tests incorporating functional annotations.
PAPER: Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale by Li et al. (2020).
SPEAKER: Alyna
TOPIC: When to directly test rare variants.
PAPER: Individuals with common diseases but with a low polygenic risk score could be prioritized for rare variant screening by Lu et al. (2021).
SPEAKER: Seth
TOPIC: Seth's identity-by-descent research.
PAPER: A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex by Antaki et al. (2022). This paper is the focus of the Discussion board this week, and Seth may give some highlights during his presentation.