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2011Planning

Syllabus

WebCT for grades

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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:

##### 0Exams

##### 0Local Resources

##### 0Homework

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

##### 0Project

Project1: Due Mar 5 at 5pm

Project2: Due Apr 24 at 5pm

Project3: Due May 4 at 5pm (Take-Home | data)

##### 0Web Resources

##### 0Other Courses

Syllabus

WebCT for grades

How to edit this Wiki

- first login via the Login link in the lower, right corner
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- Firefox handles MathML by default.

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

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 2 (corrected again 2007-01-31, one of identities for covariance of continuous traits)

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 Analysislecture 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

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

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

- Midterm: covers material up through section 8.4.3 in lecture 12.
- Final: Thursday 12-2 in regular room

- Nonhomogeneous Poisson Process: read this for some justification of the absolute risk formula for non-constant hazard rate
- Notes on path analysis
- Glossary
- Algorithms / Hypothesis Tests
- Questions
- Data

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

Project2: Due Apr 24 at 5pm

Project3: Due May 4 at 5pm (Take-Home | data)

- http://www.math.uah.edu/stat/poisson/ : Poisson processes (related to (1) chiasmata formation on chromosomes and (2) occurrences of disease over time, in a cohort)
- Bibliography, linkage analysis
- Bibliography, allele sharing
- Bibliography, linkage algorithms
- Bibliography, variance components analysis of QTL
- Software

- http://linkage.rockefeller.edu/course/basic06.html
- http://linkage.rockefeller.edu/suzanne/munich_mapping_sch05.html
- http://www.hgsc.bcm.tmc.edu/genemapping/Berlin06/gmc2006.htm
- http://www.maths.lth.se/matstat/kurser/statgen/
- http://hg-wen.uchicago.edu/
- http://www.stat.washington.edu/thompson/Stat550/
- http://www.biostat.washington.edu/sisg06/
- http://www.genetics.ucla.edu/courses/statgene/
- http://www.wellcome.ac.uk/doc_wtx026851.html

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