This GitHub serves as a repository for STT 855 and EPI 855.
Instructor 2025: Gustavo de los Campos (gustavoc@msu.edu).
Github Team:
- Gustavo de los Campos (D&M)
- Ana I. Vazuqez (D&M)
[D: Developer, M: Maintainer]
Time & Place Tuesdays & Thursdays 12:40 PM-2:00 PM Wells Hall C506
| Topics | Slides | Handout/Script | In-class | Homework |
|---|---|---|---|---|
| Introduction to the course | ||||
| Introduction to Quantitative Genetics | Bulmer Ch. 1 | Galton | ||
| Allele and Genotype Frequency | ||||
| Allele Frequencies | binom.test() | Allele Freq. | ||
| Hardy-Weinberg Eq. | HWE | |||
| MiceGenos | ||||
| Sources of Genetic Variation | HW1; HW1 R Markdown | |||
| Single locus model | Means & Variances | Inclass 5 ; Inclass 6 | ||
| Linkage Disequilibrium | genetics R-package | Inclass 8-LD | ||
| Coancestry & Inbreeding | Inclass 9 | |||
| Resamblance between Relatives | Inclass 10 | HW2 | ||
| Computing additive relationships from pedigree | Inclass 11 | |||
| Multi-locus models | Means & Variances | Inclass 12 | ||
| Polygenic Additive Model | Means & Variances | Inclass 13 | ||
| Midterm Tuesday Oct 14 | ||||
| GWAS | HW3 | |||
| Reviews and Tutorials | MareesEtAl , UffelmanEtAl , AbdellaouiEtAl. , Pike (2010) | |||
| Introduction | GWAS 1 | Multiple Testing | ||
| Controlling for Genetic Confunding | GWAS 2 | |||
| Post-GWAS (refining GWAS peaks) | GWAS 3 | |||
| Power in GWAS | Power GWAS | |||
| Heritability estimation | ||||
| Estimation Methods | ||||
| Trait Vs SNP heritability | RMarkdown | |||
| HW 4 | HW4 | |||
| Genomic Prediction | ||||
| Conceptual Framework | ||||
| Building models using independent screening | ||||
| Forward regression | ||||
| Principal component regression | ||||
| Penalized Regression | ||||
| Bayesian Srhinkage and Variable Selection | PGS prediciton using summary statistics: BGLR LDPred GPTL | |||
| Kernel Regression | ||||
| Neural Networks | ||||
| HW 5 | HW5 |