THIS SCHEDULE IS PRELIMINARY, AND SUBJECT TO CHANGE
| Monday, March 26 8.30-9.20 |
1.1 General introduction. Mendel's laws. 1.2 Terminology. Pedigrees. |
Background on Genetics Background on likelihood Notes 1.1, 1.2 (posted 3/21/2012) Homework 1 (posted 3/21/2012) due 3/30. |
| Wednesday, March 28 8.30-9:20 |
1.3 Allele and genotype frequencies; 1.3 Hardy-Weinberg equilibrium. 1.3 Population subdivision. | Notes 1.3, 1.4 (posted 3/21/2012) |
| Friday, March 30 8.30-9:20 |
Computing setup; getting started; Homework 1 discussion |
Passwords will be available for new Biostat
accounts. Get set up for your StatGen computing Homework 1 (posted 3/21/2012) due |
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| Monday, April 2 8.30-9.20 |
1.4 MLE of allele frequencies ---Recessive alleles and data on relatives | Homework 2 (posted 3/28/2012) due 4/6. |
| Wednesday, April 4 8.30-9:20 |
1.5.1 Testing HWE 1.5.2 Testing the ABO blood groups |
Thornton example:
graph;
text. Notes 1.5, 1.6 (posted 3/28/2012) Jan to summarize. |
| Friday, April 6 8.30-9:20 |
Finish ABO testing example Homework 2 discussion; Lab 1 discussion |
Lab 1 (posted 3/28/2012) due Homework 2 (posted 3/28/2012) due |
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| Monday, April 9 8.30-9.20 |
1.6.1-2 Gene counting; the EM algorithm 1.6.3-4 The ABO blood types example. | Homework 3 (posted 4/5/2012). |
| Wednesday, April 11 8.30-9:20 |
1.6 ctd: A review on EM and ECDLL 2.1,2.2 Pedigrees, kinship and inbreeding. |
Notes 2.1, 2.2 (posted 4/4/2012) Steven to summarize |
| Friday, April 13 8.30-9:20 | 2.2 ctd. Computing kinship and inbreeding coefficients. | Homework 3 (posted 4/5/2012) due |
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| Monday, April 16 8.30-9.20 |
2.2.4 Inbreeding and genotype probabilities. (with example from Qu.3 on hwk 3). |
Homework 4 (posted 4/10/2012)
Lab 2 (posted 4/12/2012) |
| Wednesday, April 18 8.30-9:20 | 2.3.1-2 The four genes of two individuals |
Notes 2.3, 2.4 (posted 4/4/2012) Julie to summarize |
| Friday, April 20 8.30-9:20 |
Brief Homework/lab discussion. 2.3.3-4 The IBD probabilities for two non-inbred relatives. |
Zhihao, Chisheng presented. Homework 4 (posted 4/10/2012) due Lab 2 (posted 4/12/2012) due |
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| Monday, April 23 8.30-9.20 | 2.4 The probabilities of data on relatives. |
Data prob: example (posted 4/17/2012) Homework 5 (updated 4/19/2012) |
| Wednesday, April 25 8.30-9:20 |
The processes of meiosis and mitosis. 3.1 Haplotypes and recombination. |
meiosis and
recombination
(posted 4/17/2012) Notes 1.7 (also 1.8) (posted 4/17/2012) Notes 3.1 (posted 4/17/2012) Kara to summarize |
| Friday, April 27 8.30-9:20 | 3.1 Haplotype frequencies and linkage disequlibrium | Homework 5 (updated 4/19/2012) due |
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| Monday, April 30 8.30-9.20 | AWAY; NO CLASS |
A good week to think about
final projects Homework 6 and Lab 3 (Due May 11): posted 4/25/2012. |
| Wednesday, May 2 8.30-9:20 |
Inferring IBD between two haplotypes Details of HMM computation (for info only) |
IBD and HMM slides(posted 4/24/2012) |
| Friday, May 4 8.30-9:20 | AWAY: Chris Glazner (with Jean) | The BEAGLE model and beaglesim. |
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| Monday, May 7 8.30-9.20 | AWAY: Jean Morrison (with Chris) |
Imputation and Phasing with BEAGLE: Jean's slides |
| Wednesday, May 9 8.30-9:20 | AWAY: Chris Glazner |
Modeling LD, vs a better ibd model; FastIBD vs IBD_Haplo |
| Friday, May 11 8.30-9:20 |
3.2 Testing for linkage and estimating recombination fractions. Selected papers (updated 5/13/2012). |
Homework 6 and
Lab 3 due
(posted 4/25/2012). Notes 3.2 (posted 5/2/2012) Homework 7 (emailed 5/11/2012) |
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| Monday, May 14 8.30-9.20 |
Bits from Hwk 6 3.3 More testing for linkage and estimating recombination fractions. |
Notes 3.3,3.4 (posted 5/2/2012) Selected papers (updated 5/13/2012). |
| Wednesday, May 16 8.30-9:20 |
3.4 Measuring linkage information. 3.5 (part) Identity by descent at two loci. |
Notes 3.5,3.6 (posted 5/2/2012) Jared to summarize from Chris/Jean. Lab 4 (Due May 25): |
| Friday, May 18 8.30-9:20 |
3.6 Homozygosity mapping (in brief) and discussion of homeworks etc. | Homework 7 due. |
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| Monday, May 21 8.30-9.20 | Chaper 4 overview. Intro to lm_auto and lm_linkage. MCMC on pedigrees to estimate probabilities of ibd and of of data. |
Notes 4.1,
Notes 4.2 and
Notes 4.3 (posted 5/16/2012) |
| Wednesday, May 23 8.30-9:20 | 4.1 Meiosis, recombination, genetic distance, and interference models. |
Fiona to summarize; parts Ch 3 only Homework 8 and Lab 5 posted 5/22/2012. |
| Friday, May 25 8.30-9:20 |
More on genetic interference models. Discussion of Lab-4 (lm_auto). | Lab 4(posted May 16) due. |
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| Monday, May 28 8.30-9.20 | HOLIDAY | |
| Wednesday, May 30 8.30-9:20 | MCMC linkage lod scores. | Student evaluations. |
| Friday, June 1 8.30-9:20 | HMM and EM for genetic marker map estimation. | Homework 8 and Lab 5 (posted May 22) due |
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| EXAMS WEEK, June 4-8 | Projects due. | Projects due June 7 |
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