THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Week 1: March 31-April 4 |
1.1 General introduction. Mendel's laws. 1.2 Terminology. Pedigrees. Passwords are available for new Biostat accounts. Discussion and questions re homework1: April 7. |
Audio lecture: Chapter 1 Part1 Get set up for your StatGen computing Homework 1 due April 8 |
| Week 2: April 7-11 |
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 15 and Lab 1 due April 17 |
| - | ||
| Week 3: April 14-18. |
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. |
Lab 1 due April 17 Homework 3 due Apr 21 Audio lecture: Chapter 1 Part 3 |
| - | ||
| Week 4: April 21-25 |
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 Apr 29 |
| - | ||
| Week 5: Apr 25-May 2 |
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) Lab 2 due May 1 Homework 5 due May 6 |
| - | ||
| Week 6: May 5-9 |
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 15 |
| - | ||
| Week 7: May 12-16 |
3.2 Counting recombinants and estimating recombination. Testing for linkage. 3.3 Linkage designs and information 3.4 Power, sample size and information |
No graded Homework Email 1 paragraph of thoughts about your project (uploaded May 8) Audio lecture: Chapter 3 Part 2 (Sec 3.2) Audio lecture: Chapter 3 Part 3 (Sec 3.3,3.4) (uploaded May 12) Homework 6 will be due May 20 |
| - | ||
| Week 8: May 19-23 |
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) Homework 6 due May 20 Papers list Homework 7 will be due May 27 Lab 4 will be due May 29 |
| - | ||
| Week 9: May 27-30 (May 26 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) uploaded May 28 Homework 7 due May 28, and Lab 4 due May 30. Homework 8 will be due June 3 |
| - | ||
| Week 10: June 2-6 |
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) uploaded May 29 Homework 8 due June 3 Lab 5 will be due June 9. |
| - | ||
| Week 11: "Exams week" |
PROJECTS due June 12 |
Lab 5 due June 9. |