Semester 2 2015/16

Thursday 13-16, Dan-David 202

Home page on http://www.tau.ac.il/ ∼ saharon/StatsGenetics.html

Thursday 13-16, Dan-David 202

Home page on http://www.tau.ac.il/ ∼ saharon/StatsGenetics.html

Lecturer: | Saharon Rosset |

Schreiber 022 | |

saharon@post.tau.ac.il | |

Office hrs: | Thursday 16-17 or by appointment (coordination needed in any case). |

Special dates: | Extra classes on Sunday 17.4 and Tuesday 19.4 (same hour and room). |

We will start with a brief introduction to Genetics concepts, and gradually start elaborating on statistical aspects of the questions that come up. As needed, we will introduce relevant areas of statistics in some detail.

In the latter part of the course we will pick a hot current research topic and concentrate on it for a few weeks.

The final grade will be based on a combination of homework (3-4), a final take home exam, and possibly a class presentation.

Tentative topics list (each topic 1-2 weeks):

- Introduction to Genetics and quantitative Genetics
- Mutation models: stochastic processes; estimation from data
- Phylogenetic analysis: algorithms and inference
- Human population genetics: statistical inference about human history
- Estimation of ancestry
- Principal component analysis in Genetics
- Genome-wide association studies (GWAS)
- Major public data sources like HapMap, 1000Genome project and their analysis
- Linear mixed models (LMM) in Genetics

African mtDNA paper which describes the data used.

- 4*4 Mutation models: definitions, estimation and hypothesis
testing/model selection.

Relevant reading material: any textbook in statistical genetics, such as Yang (2006), review by Huelsenbeck and Crandall which we discussed in class. - STR mutation models: simple random walk and (δμ)
^{2}method; more complex and realistic models; existence of stationary distribution; estimation and model selection.

Relevant reading material: Chap. 11 in Nielsen (2005) on models of microsatellite evolution, Whittaker et al. (2003) whose data is used in HW1.

mtDNA mutation counts for problem 1.

mtDNA loci list for problem 1.

The paper by Whittaker et al. (2003) for problem 3 is available in pdf or html.

There are plenty of resources to read about this, including the review by Huelsenbeck and Crandall and the book Inferring phylogenies by Felsenstein.

Homework 2 due 19 April in class. PHYLIP homepage for problem 1.

The primate data for problem 1.

HapMap YRI Chromosome 22 dataset for problem 3.

R code implementing the approach.

Code: Running PCA on movies example and simulated genetic data. Comparable example using the EM approach.

Homework 3 due 5 May in class.

Book chapter on mixed models in genetics.

Yang et al. (2010) famous paper applying mixed models to GWAS.

Undergraduate courses in: Probability; Theoretical Statistics

Statistical programming experience in

Prior basic knowledge in Biology and Genetics is an advantage

An excellent introduction to Human Genetics, with a quantitative flavor

Comprehensive overview of computational methods in Genetics

Collection of tutorials and reviews on major topics in Statistical Genetics

R Project website also contains extensive documentation.

A basic "getting you started in R" tutorial. Uses the Boston Housing Data (thanks to Giles Hooker).

File translated from T

On 08 May 2016, 16:19.