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---
title: "PUBH 8878: Statistical Genetics"
subtitle: "Fall '25"
format: gfm
---
*Article links direct to files hosted on the Zotero group library*
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| Week | Lecture | Readings | Assignment |
+=========+=======================================================================================================================================================================================================================================+================================================================================================================================================================================================================================================================================================================================================================================================+=================================================+
| 1 | [Foundations: Mendelian genetics & statistical basics](lectures/lecture-01.qmd) | - Sorensen Chapter 1 | [Problem Set 01](assignments/assignment-01.qmd) |
| | | - Edwards, A. W. F. (2008), [“G. H. Hardy (1908) and Hardy–Weinberg Equilibrium,”](https://www.zotero.org/groups/6113424/pubh-8878/items/K7VHXW7X/attachment/CABRB84T/reader) *Genetics*. | |
| | Mendel’s laws, Hardy–Weinberg equilibrium, $\chi^2$goodness‑of‑fit. Sampling distributions; linking population parameters to sample estimates. One‑locus likelihood: building and interpreting likelihood functions. | - [Introduction to Probability Theory](http://users.stat.umn.edu/~helwig/notes/ProbabilityTheory.pdf) | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 2 | [Heritability, segregation, and the gene-mapping toolkit](lectures/lecture-02.qmd){target="_blank"} | - Sorensen Chapter 2.1-2.2, 2.4, 2.8 | [Problem Set 02](assignments/assignment-02.qmd) |
| | | - Visscher, P. M., et al., (2008), [“Heritability in the genomics era — concepts and misconceptions,”](https://www.zotero.org/groups/6113424/pubh-8878/items/3WV5AULA/attachment/SKL5CU9C/reader) *Nature Reviews Genetics*. | |
| | Narrow and broad sense heritability; variance-component interpretation. Segregation analysis and modelling genetic inheritance without marker data. | | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 3 | [Likelihood algorithms & practical gene mapping](lectures/lecture-03.qmd){style="target: _blank;"} | - Sorensen, Chapter 3 | [Problem Set 03](assignments/assignment-03.qmd) |
| | | - Lander, E. S., and Green, P. (1987), [“Construction of multilocus genetic linkage maps in humans.,”](https://www.zotero.org/groups/6113424/pubh-8878/items/TUHQAN7Q/attachment/CC5K3VW6/reader) *Proceedings of the National Academy of Sciences of the United States of America*. | |
| | Newton-Raphson, EM, and stochastic gradient algorithms for complex likelihoods. Pedigree linkage analysis, LOD-score calculation, and missing-data EM steps. Single-marker and haplotype association tests with basic quality control | | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 4 | [Population structure & Bayesian fundamentals](lectures/lecture-04.qmd){style="target: _blank;"} | - Sorensen 4.1-4.5, 4.7-4.8, 5.1 | [Problem Set 04](assignments/assignment-04.qmd) |
| | | - Porras-Hurtado, L. et al., (2013), [“An overview of STRUCTURE: applications, parameter settings, and supporting software,”](https://doi.org/10.3389/fgene.2013.00098) *Frontiers in Genetics*. | |
| | Detecting and correcting for population stratification and admixture confounding. Priors, posteriors, and the Bayes-frequentist debate in genetic inference. Bayesian admixture/STRUCTURE-style modelling implemented in Stan. | - Lawson, D. J. et al., (2018), [“A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots,”](https://doi.org/10.1038/s41467-018-05257-7) *Nature Communications*. | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 5 | [GWAS at Scale](lectures/lecture-05.qmd) | - Loh, P.-R. et al., (2015), [“Efficient Bayesian mixed model analysis increases association power in large cohorts,”](https://doi.org/10.1038/ng.3190) *Nature Genetics*. | |
| | | | |
| | End to end GWAS workflow: sample QC, variant QC. Linear mixed models. Genomic inflation and calibration. | | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 6 | [Prediction models in genetics](lectures/lecture-06.qmd) | - Sorensen Chapters 6, 7.1-7.2, 10.1, 10.5, 11.3-11.5 | |
| | | - Wu, T. T., Chen, Y. F., Hastie, T., Sobel, E., and Lange, K. (2009), “Genome-wide association analysis by lasso penalized logistic regression,” *Bioinformatics*, 25, 714–721. <https://doi.org/10.1093/bioinformatics/btp041>. | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 7 | [Multiple testing & false-discovery control](lectures/lecture-07.qmd) | - Sorensen Chapter 8 | [Assignment 05](assignments/assignment-05.qmd) |
| | | - Otani, T., Noma, H., Nishino, J., and Matsui, S. (2018), “Re-assessment of multiple testing strategies for more efficient genome-wide association studies,” *European Journal of Human Genetics*, Nature Publishing Group, 26, 1038–1048. <https://doi.org/10.1038/s41431-018-0125-3>. | |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 8 | [Binary traits](lectures/lecture-08.qmd) | - Sorensen Chapter 9 | |
| | | - Zhou, W., Bi, W., Zhao, Z., Dey, K. K., Jagadeesh, K. A., Karczewski, K. J., Daly, M. J., Neale, B. M., and Lee, S. (2022), “SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests,” *Nature Genetics*, Nature Publishing Group, 54, 1466–1469. <https://doi.org/10.1038/s41588-022-01178-w>. | |
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| 9 | [Causal inference (Mendelian randomization)](lectures/lecture-09.qmd) | - Sanderson, E., Glymour, M. M., Holmes, M. V., Kang, H., Morrison, J., Munafò, M. R., Palmer, T., Schooling, C. M., Wallace, C., Zhao, Q., and Davey Smith, G. (2022), “Mendelian randomization,” *Nature Reviews Methods Primers*, 2, 1–21. [https://doi.org/10.1038/s43586-021-00092-5](https://www.zotero.org/groups/6113424/pubh-8878/items/ECYBM54E/attachment/3F33AJN2/reader){.uri}. | [Assignment 06](assignments/assignment-06.qmd) |
+---------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------+
| 10 | Advanced AI Topics in Statistical Genetics: Language Models for Genomics | **Recommended:** | |
| | | | |
| | | - [Ji et al., 2021](https://academic.oup.com/bioinformatics/article/37/15/2112/6128680) | |
| | | - [Avsec et al., 2021](https://www.nature.com/articles/s41592-021-01252-x) | |
| | | - [Cheng et al., 2023](https://www.science.org/doi/10.1126/science.adg7492) | |
| | | - [Baghbanzadeh et al., 2025](https://www.biorxiv.org/content/10.1101/2025.03.12.642848v1) | |
| | | - [Mollerus et al., 2025](https://www.biorxiv.org/content/10.1101/2025.07.08.663767v1) | |
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