THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Week 1: March 30-April 3 |
1.1 General introduction. Mendel's laws. 1.2 Terminology. Pedigrees. Passwords are (not yet) available for new Biostat accounts. |
Audio lecture: Chapter 1 Part1 Get set up for your StatGen computing Homework 1 due April 6 |
| Week 2: April 6-10 |
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 13 Lab 1 due April 13 |
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| Week 3: April 13-17. |
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 20 Audio lecture: Chapter 1 Part 3 |
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| Week 4: April 20-24 |
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 Lab 2 is optional: see note on main course materials page. Audio lecture: Chapter 2 Part 1 Homework 4 due Apr 27 |
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| Week 5: Apr 27-May 1 |
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 Optional but try for May 1 if doing it Homework 5 due May 4 |
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| Week 6: May 4-8 |
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 13 (goal!) |
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| Week 7: May 11-15 |
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 (uploaded May 1) Audio lecture: Chapter 3 Part 2 (Sec 3.2) Audio lecture: Chapter 3 Part 3 (Sec 3.3,3.4) Homework 6 due May 18 |
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| Week 8: May 18-22 |
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 May 26 Lab 4 will be due May 26 also (goal!) |
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| Week 9: May 26-29 (May 25 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 1 |
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| 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) Lab 5 due June 9. |
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| Week 11: "Exams week" |
PROJECTS due June 15 |