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Statistical genetics, spring 2015


Lecturer

Sirkka-Liisa Varvio

Scope, type, prerequisites

5-10 cr, intermediate / advanced studies
If you have already taken this course, do not plan to take Statistical genetics spring 2015. Although the courses are not identical, there will be too much overlapping content in order to regard the credits as non-overlapping.

Time schedule

III period (5 cr option),  Wednesday 14-18 (-20 if needed)  in computer class C128. 
IV period (additional 5 cr option), time schedule negotiable. We discuss about this during the III-period part, and some assignments for these additional credits will be given already during the III-period.

Passing the course and the grade

  • Five assignments or assignment sets / home-exercise sets. These will be graded. There will not be an exam.
  • You get 1 point from each assignment /assignment set  if your performance is excellent, 0.7-0.8 from good performance, 0.5 from moderate, and 0.2 from an acceptable performance.
  • Final grade 5 comes from 4.2 assignment points and final grade 1 comes from 2.5 points.
  • The spirit of the two first assignment sets, which are  probability calculus and basic statistics applied on genetic problems: You submit your own solutions to STAGE-Moodle during the given deadline. Then you will get the correct answers and you are asked to evaluate your own solutions in the face of the corrects answers. You are supposed to write a report from your evaluations, explain why your solution(s) is/are wrong, what is it that you did not understand or take into account, etc. -  so you give report on your own learning process. This report  will be graded! This means that you can get full points by completely correct solutions (you only state in your report that your solution(s) are correct) but also by giving an excellent report about your learning process.
  • The other three assignments (tba, they will be data-analysis, getting familiar with scientific articles, etc.)
Wed 21.1

The current mainstream of statistical genetics, see here

Basic concepts 1_Inheritance, probability, Hardy-Weinberg.pdf, assignment set 1 included, simulations: http://www.radford.edu/~rsheehy/Gen_flash/popgen/

A century of Hardy Weinberg equilibrium.pdf
LD_understanding the evolutionary past and mapping the medical future.pdf

Wed 28.2

Basic concepts 2_Selection, mutation, drift.pdf, assignment set 2 included

Revising human mutation rate, understanding human evolution.pdf
Human genomic disease variants, A neutral evolutionary explanation.pdf

Wed  4.2

Christian Benner from FIMM: Statistical_Concepts_In_A_Nutshell_Part1.pdf, Statistical_concepts_in_a_nutshell_Part2.pdf

Wed (11.2),
18.2,
25.2

Coalescence theory and selection tests.pdf,
An illustrative guest lecture on coalescence.pdf
,
Kingman´s Coalescence paper.pdf


Assignments for 3 more credits (2cr come from assignment sets 1 and 2): You can choose, whether writing essays or doing data-analysis, or both. If you want to get the 5 cr before IV period, then you submit your work for 3 cr  8. March, at the latest. Then you can continue for more credits during period IV. In data-analysis assignments the definition 1-2 cr means that you can do a "small" work for 1 cr (to obtain the credits for the 5 cr option), and continue for a more comprehensive work later. However, you don´t have to do first 1 cr and then continue for the other credit, you can start by doing a 2 cr work.

Assignment 3, 1-3 cr by writing essays. One essay, 1 cr, is about 5 pages text. Below are review-type recent scientific papers. For one essay, you pick one paper and find another paper by yourself (for example on the basis of the original paper´s reference list). The additional paper is a kind of specific example on the the general topic introduced in the original review-paper.

  • Topics, the review-type scientific papers:

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.pdf
Recent human adaptation, genomic approaches, interpretations and insights.pdf
Natural selection and infectious diseases in human populations.pdf
Molecular sprandels, tests of adaptation at the genetic level.pdf
How culture shaped the human genome.pdf

Assignment 4.docx, 1-2 cr by analysing human population data:

Assignment 5.pdfAssignment 5 clarification.docx,  1-2 cr by analysing bacteria data:

Assignment 6 , (TBA) , 1-2 cr by analysing virus data

  • data TBA

Software (installed in C128; you can also install these free programs to your own computer):

DnaSP 5.10.1 , DnaSP Manual.pdf
Network 4.6.1.1
, Network Manual.pdf , Median-joining networks.pdf



 

STAGE-MOODLE


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