THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Monday, April 1 8.30-9.20 |
1.1 Mendel's laws. 1.1 Hardy-Weinberg equilibrium. 1.1 Meiosis and Recombination |
Background on Genetics Background on likelihood Homework 1 (due 4/5/2013)) Chap 1.1 to 1.4 (posted 3/31/2013) |
| Wednesday, April 3 8.30-9:20 |
1.2 Allele and genotype frequencies; 1.2 Estimating frequencies 1.2 Population subdivision. | |
| Friday, April 5 8.30-9:20 |
Computing setup; getting started; Homework 1 discussion |
Some computing/software info Homework 1 due |
| - | ||
| Monday, April 8 8.30-9.20 |
1.2.5 Another estimation example 1.3 Testing HWE 1.3 Testing the ABO blood groups |
Chap 1.5 to 1.6 (posted 4/07/2013) Biblio to date-- will get updated Homework 2 (due 4/12/2013)) |
| Wednesday, April 10 8.30-9:20 | 1.4 Gene counting and the EM algorithm | Qian to summarize 1.1 and 1.2. |
| Friday, April 12 8.30-9:20 |
Homework 2 discussion; More on computing/software. |
Homework 2 due Computing on statgen.stat.washington.edu |
| - | ||
| Monday, April 15 8.30-9.20 | 1.5 Haplotypes and Phasing. |
Homework 3 (due 4/19/2013)) Lab 1 (due 4/19/2013) Stephens' ppt on Clark |
| Wednesday, April 17 8.30-9:20 |
1.6 Linkage disequilibrium. 2.1 Defining pedigrees |
Seely to summarize, 1.3 and 1.4. Chap 2.1 to 2.2 (updated April 21) |
| Friday, April 19 8.30-9:20 |
2.1 A bit more on pedigrees Lab 1 and Homework 3 discussion. |
Homework 3 and
Lab 1 due From Mohamad, on question 3 of the homework: Likelihood vs q1 & q4. and Likelihood vs q1 & q2. |
| - | ||
| Monday, April 22 8.30-9.20 |
2.1 Pedigrees and relationships 2.2 Gene identity by descent (ibd) |
No homework this week. Lab 2 (due 4/26/2013) Additional Pedfiddler information |
| Wednesday, April 24 8.30-9:20 |
2.2 Gene identity by descent (ibd) 2.3 ibd of more than two genes |
Alice to summarize 1.5, 1.6 See under April 17 for updated 2.1,2.2 notes. Chap 2.3 to 2.4 (May 1) |
| Friday, April 26 8.30-9:20 | Discussion of Lab 2 and more from homework 3. Hutterite pedigrees. |
Lab 2 due April 26 slides |
| - | ||
| Monday, April 29 8.30-9.20 | 2.3 IBD in pairs of non-inbred relatives | Homework 4 Due Friday May 3. |
| Wednesday, May 1 8.30-9:20 | 2.4 Probabilities of data on relatives. |
Alex to summarize 2.1, 2.2 Note on the COGA study Lab 3 (due 5/10/2013) |
| Friday, May 3 8.30-9:20 |
Finish up section 2.4; Discuss Hwk 4. Reference on power to detect LD |
Chap 2.3 to 2.4 (Updated May 1) Homework 4 due. |
| - | ||
| Monday, May 6 8.30-9.20 | 3.1 Linkage, recombination and genetic maps. |
Chap 3.1 to 3.2 (Posted May 5; updated) Homework 5 Due Friday May 10. (posted May 1). |
| Wednesday, May 8 8.30-9:20 | 3.2.1-4 Likelihoods for linkage: the lod score. |
Sen to summarize 2.3, 2.4 |
| Friday, May 10 8.30-9:20 | Lab 3 and Homework 5 due. | |
| - | ||
| Monday, May 13 8.30-9.20 | 3.2 ctd., 3.3: Designs for testing for linkage |
Chap 3.3 (Posted May 12) Homework 6 Due Friday May 17. (posted May 9). Project info. Lab 4 (posted May 16: due May 24) |
| Wednesday, May 15 8.30-9:20 |
3.3 ctd; Power and sample size 3.4 Two-locus ibd |
Robin to summarize 3.1, 3.2.1-4 Chap 3.3,3.4 (Posted May 14) |
| Friday, May 17 8.30-9:20 |
Homework 6 discussion 3.4 Example of 2 sibs with putative aunt/half-sib/niece. | Homework 6 due. |
| - | ||
| Monday, May 20 | 8:30-9:203.5 Homozygosity mapping |
Chap 3.3-3.5 (Updated May 19,21) Project and Papers update. |
| Wednesday, May 22 8.30-9:20 |
3.5 Final bits 4.1 Multilocus meiosis |
Aaron to summarize, 3.3, 3.4 Chap 4.1,4.2 (Posted May 21,23) |
| Friday, May 24 8.30-9:20 | Discussion of Lab-4. |
Lab 4 due. (No Homework) |
| - | ||
| Monday, May 27 | HOLIDAY: MEMORIAL DAY |
Homework 7
Due Monday June 3. (posted May 23). Lab 5 Due Friday June 7. (Posted May 26). |
| Wednesday, May 29 8.30-9:20 |
4.2 If we could observe inheritance .... 4.3 Summing over unobserved inheritance |
(Sandrine to summarize, 3.5, 4.1) Chap 4.3, 4.4 (Posted May 27) Papers: final list (almost). |
| Friday, May 31 8.30-9:20 | 4.4 Monte Carlo versions of the HMM (Baum) algorithm. |
Homework 7 due on Monday June 3. Student evaluations. |
| - | ||
| Monday, June 3 8.30-9.20 |
Homework 7. 4.5 Summing over genotypes on large pedigrees |
Homework 7 due. Chap 4.5, 4.6 (Posted Jun 4) |
| Wednesday, June 5 8.30-9:20 |
4.5 Large pedigrees ctd; SIMLINK 4.6 Monte Carlo estimation and MCMC. |
Michael to summarize, 4.2,4.3 |
| Friday, June 7 8.30-9:20 |
4.6 Final comments and updates Lab 5 discussion. |
Lab 5 due. Chap 4.5, 4.6 and bibliography (Updated Jun 6) |
| - | ||
| EXAMS WEEK, June 10-14 | Projects due. : late projects ok, but you must let me know, and class grade will almost certainly be delayed. | Projects due June 11, hard copy (PDLFD B313) or electronic (PDF much preferred) no later than 5:00 p.m., as I leave then for travel to a meeting. |
| - |
