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Modelling inheritance in pedigrees and populations, spring 2010

Lecturer

Sirkka-Liisa Varvio

Scope

4 cu - 6 cu

Type and prerequisites 

Advanced studies, no formal prerequisites. The course is tailored for Bioinformatics Master program (MBI) students and suitable to all students interested in population genetics and genomics, pedigree and haplotype inference, coalescence (see below).

Time schedule

Tue 19. Jan, 14-18 in room B120.
Tue 26. Jan - 23. Feb 14-16 in room B120, 16-18 in computer class B221 (Jussi Kollin, jussi.kollin at cs.helsinki.fi).
Tue 2. March 14-17 in room B120, homework (other than computer class execises) presentations.

Exams

There will be no exam. Grading is based on computer exercise reports, home assignments and literature surveys (scope 4-6cu).
Grading is fail/pass or, if desired, 1-5.

Contents of lectures, computer class exercises, and homework

The course is about population genetics, evolutionary factors which shape population structures, coalescence, haplotypes, an emphasis is in human populations, data analysis and simulation methods which lead to understanding human population genomic structures and human diseases (the course is not, however, a disease gene mapping course).

Week

Lectures

Recent review papers on the lecture topics

 

1

Introduction_190110..pdf
Inheritance_and_HW..pdf

Genetic relatedness.pdf


Linkage disequilibrium.pdf

LD Evol past medical future..pdf

 

3

Intro to coalescence..pdf

 

 

4

Lectures on haplotypes, LD, coalescence continue

Coalescence human origins..pdf

 

5

mtDNA haplotypes and demo: ´Median joining haplotypes´ 

 

 

6

Human population genetics, Fst,  differentiation, Wright-Fisher cont

Human population structure..pdf
Diversity programs..pdf

 

Week

Computer class

To do before next computer class session

 

1

 

Assignment 1a..pdf, PH1.pdf,PH2..pdf,PH3..pdf
Submit to Student page

 

2

Results from Assignment 1a.pdf
Introduction to Assignment 1b..pdf
PHASE demonstration,  fastPHASE..pdf, PHASE..pdf, cosi_toPHASE..txt
http://stephenslab.uchicago.edu/software.html
http://hapmap.ncbi.nlm.nih.gov/

Work for some preliminary results from  Assignment 1b..pdf

 

3

Preliminary results from Assignment 1b.pdf
For assignment 1: http://www.cs.helsinki.fi/u/jkollin/Modelling/
For assignment 2: coalescent_simulator_compilation_instructions.txt

Work further with assignment 1b, population comparisons etc.

Learn from here more haplotype tools: http://www.broadinstitute.org/mpg/haploview
Read:Calibrating coalescence simulation.pdf
        Hudson simulator..pdf

 

4

A look at assignment 1b, what is the situation now.
Coalescence simulation.

 

 

5

 

Submit results from assignment 1b to Student page
Material for Assignment 2b_the alternative.pdf, Deadline 2. March
Coalescence software:http://beast.bio.ed.ac.uk/Downloads, http://www.stats.ox.ac.uk/mathgen/software.html, http://evolution.gs.washington.edu/lamarc http://cmpg.unibe.ch/software/simcoal, http://www.stanford.edu/group/hadlylab/ssc/index.html
Example papers: mtDNA haplotypes.pdf, Neandertahl and Cro_Magnoid.pdf, Ancient DNA review.pdf,
Chimp human chromosome coalescence.pdf, Dating Mycobacterium tuberculosis success.pdf, Whale past by coalescence.pdf

 

6

Results from assignment 1b. 

Submit results from assignment 2 to Student page

 

7

Results from assignment 2

 

 

Student page

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