THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Week 1: April 5-9 |
1.1 General introduction. Mendel's laws. 1.2 Terminology. Pedigrees. Passwords are available for new Biostat accounts. |
Audio lecture: Chapter 1 Part1 Get set up for your StatGen computing Homework 1 due April 12 |
| - | ||
| Week 2: April 12-16 |
1.3 Allele and genotype frequencies; 1.3 Hardy-Weinberg equilibrium. 1.3 Population subdivision. 1.3 Estimating allele freqs: recessive case 1.3 Estimating allele frequencies from relatives |
Audio lecture: Chapter 1 Part 2 Background on likelihood Help on meaning of expectations Homework 2 due April 19 Lab 1 due April 21 |
| - | ||
| Week 3: April 19-23. |
1.4 Testing HWE: goodness of fit 1.4 Testing the ABO blood group models 1.5 The EM algorithm for multinomial data 1.5 EM algorithm: examples. |
Homework 3 due Apr 26 Audio lecture: Chapter 1 Part 3 |
| - | ||
| Week 4: April 26-30 |
1.6 Haplotypes and allelic association 1.6 Estimating phase and haplotype frequencies. 1.7 Mutation, selection, and random genetic drift 2.1 Introduction to pedigrees 2.2 Kinship and inbreeding coefficients 2.2 Computation of kinship by path-counting and by recursion. |
Audio lecture: Chapter 1 Part 4 Audio lecture: Chapter 2 Part 1 Homework 4 due May 3 Lab 2: Due Wed May 5 |
| - | ||
| Week 5: May 3 -May 7 |
2.2 Recessive traits in inbred individuals 2.3 IBD between pairs of relatives 2.3 Triangle-representation of relationships. 2.3 Back to IBD; quadruple half first cousins. 2.4 Data on pairs of relatives |
Audio lecture: Chapter 2 Part 1 (Last part) Audio lecture: Chapter 2 Part 2 (First half) Homework 5 due May 10 |
| - | ||
| Week 6: May 10-14 |
2.4 General relationship of IBD to data. Chapter 3: Linkage and recombination 3.1 Haplotypes and allelic association. The sources of allelic association. Decay of allelic association over generations |
Audio lecture: Chapter 2 Part 2 (Last bit) Audio lecture: Chapter 3 Part 1 Lab 3 due May 19 (goal!) : (info updated) Project info |
| - | ||
| Week 7: May 17-21 |
3.2 Counting recombinants and estimating recombination. Testing for linkage. 3.3 Linkage designs and information 3.4 Power, sample size and information |
Projects:
Email 1 paragraph of thoughts about your
project Audio lecture: Chapter 3 Part 2 (Sec 3.2) Audio lecture: Chapter 3 Part 3 (Sec 3.3,3.4) Homework 6 due May 24 |
| - | ||
| Week 8: May 24-28 |
3.5 Two-locus gene ibd (omit 2-locus kinship) 3.6 Homozygosity mapping 4.1 Meiosis, maps and map functions |
Audio lecture: Chapter 3 Part 4 (Sec 3.5,3.6) Audio lecture: Chapter 4 Part 1 (Sec 4.1) Project update Homework 7 will be due June 1 Lab 4 will be due June 2 (goal!) |
| - | ||
| Week 9: June 1-4 (May 31 is HOLIDAY) |
4.2 Multilocus recombination: the HMM dependence structure. Map-specific lod scores and the Lander-Green algorithm. EM for genetic map estimation. |
Audio lecture: Chapter 4 Part 2 (Sec 4.2) Homework 8 due June 7 |
| - | ||
| Week 10: June 7-11 |
4.3 Bigger pedigrees ; Elston-Stewart algorithm 4.3 SIMLINK and Monte Carlo sampling on pedigrees. |
Audio lecture: Chapter 4 Part 3 (Sec 4.3) Lab 5 due June 15. |
| - | ||
| Week 11: "Exams week" |
PROJECTS due June 18 |