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0STAT 537 - Statistics for Molecular Genetics


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0Reading Assignments
Week 1 (2007-01-08): read chapters 1 through 3 of the text
Week 2 (2007-01-15): read chapter 5 (We'll tackle it out of order: first familial risk, then identity coefficients, then continuous phenotypes, but eventually we'll get it all.)
Week 4 (2007-01-29): read chapter 6
Week 5 (2007-02-05): read chapter 7
Week 6 (2007-02-12): Mendel manual: Intro, 7 (optional), 14, 19.
Week 7 (2007-02-19): Still at chapter 7
Week 8 (2007-02-26): busy in reviewing
Week 9 (2007-03-05): Mid-term
Week 10 (2007-03-12): Spring Break

0Lecture Notes
Complete Lecture Notes: all pdf files listed below are included in this large file.
Introduction to Statistical Genetics
Genetics Background (including introduction to linkage)
Family Risk:
lecture 1 (corrected again 2007-01-24 1/3 should be 1/4 on last page)
lecture 2 (corrected again 2007-01-31, one of identities for covariance of continuous traits)
Segregation Analysis:
lecture 3
lecture 4
lecture 5: Genotype elimination; allele consolidation; polygenic model; penetrance functions (sorry, some overlap with the next lecture)
lecture 6: corrected for errors noticed during lecture
Linkage Analysis
lecture 7: corrected for errors noticed during lecture and (1) category probabilities for coupling-repulsion intercross and (2) allele frequencies for paternity testing example
lecture 8 (lab)
lecture 9: map functions I
lecture 10: map functions II (corrected for 3 errors detected during lecture)
lecture 11: two-point with intro to linkage analysis (numbering corrected)
lecture 12: multipoint linkage analysis (corrected for errors; also better explanation of 3-point locus ordering)
lecture 13: troubles with parametric linkage analysis
lecture 14: nonparametric linkage analysis (updated 2007-04-30: IBS probabilities and example calculation corrected)
LD lectures: linkage disequilibrium analysis (updated 2007-04-30: Admixture example corrected for numerical errors)
QTL mapping lectures: QTL mapping


0Local Resources

Please post your correct solutions for participation credit.  Consider scanning and uploading pdfs of your correct solutions.
Homework1: Due January 26 at 5pm (electronic is OK; delivery of written solutions can go to either office, but let me know where it is). Solution Q1_Solution_XW
Homework2: Due Feb 2 at 5pm (Saturday was a typo - now I understand why you were asking certain questions -; you can turn it in on Monday by 5)  Solution
Homework3: Due Feb 12 at 5pm Solution
Homework4: Due Feb 19 at 5pm Solution Q2&3_Solution_XW
Homework5: Due Feb 26 at 5pm Solution
Homework6: Not turned in for credit; provide solutions for participation credit.Solution
Homework7: Due April 2 at 5pm Solution
Homework8: Due Monday, April 23, last week of classes (final form) Solution

Project1: Due Mar 5 at 5pm
Project2: Due Apr 24 at 5pm
Project3: Due May 4 at 5pm (Take-Home | data)

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