BNF073: Statistics in Genetics

Department/Division:

Mathematical Statistics, Centre of Mathematics

Goal of the course:

The goal of the course is to give acquaintance with statistical methods to map genes, i.e. to locate their positions on the chromosomes. Most often the mapping concerns genes associated with inheritable human diseases. In particular we discuss parametric and nonparametric linkage analysis, association analysis, and methods for quantitative trait loci (QTL). Students will also get an introduction to commonly used statistical software for analysing linkage data sets.

Course content:

The basic notions of probability and statistical inference theory underlying the presented methods are introduced when considered vital for the understanding of the course material. Parametric linkage analysis is discussed, including definition of allele frequencies, penetrances, recombination fractions and lod score statistics. The treatment of nonparametric linkage analysis introduces affected relatives methods, the identical-by-descent (IBD) notion, inheritance vectors and nonparametric score statistics. Further, methods for mapping of loci governing the expression of quantitative traits are considered, including an introduction to quantitative genetics. Finally, we discuss several methods for association analysis, both in a case-control setting and using family based designs.

Examination:

The course consists of lectures and two compulsory computer assignments. The computer assignments are based on the Genehunter and Fastlink statistical software packages. (No programming experience is needed.) The examination is written and consists of both theoretical matters and by-hand calculations.

Credits:

The BNF073 course is given as a 2 credit course (3 ECTS credits) within the Master's program in bioinformatics, organized by the biomedical research school, cf. http://www.medfak.lu.se/bioinfo/, http://www.medfak.lu.se/bmf/ and http://www.medfak.lu.se/biomed/.

Prerequisites:

Some acquaintance with calculus, such as derivatives, integrals and the laws of logarithms is helpful.

Course start:

January 8th, 2007.

Updated preliminary course schedule (061221):

Preliminary schedule (PDF).

Literature:

Lecture notes;
Hand-out articles;
Statistics in Genetics. Compendium. Revised version, November 25, 2003. Available for download in Postscript or PDF format. Version history, see CHANGELOG.txt. Errata, see ERRATA.txt.
A. Read and T. Strachan. Human Molecular Genetics. 3rd ed. Taylor & Francis Inc, UK, 2003.

Some other books of interest:

J. Ott. Analysis of Human Genetic Linkage. 3rd ed. Johns Hopkins University Press, Baltimore, 1999.
J.D. Terwilliger, J.Ott. Handbook of Human Genetic Linkage. Johns Hopkins University Press, Baltimore, 1994.
P. Sham. Statistics in Human Genetics. Arnold applications of Statistics, New York, 1998.
J.L. Haines, M.A. Perica-Vance. Approaches to Gene Mapping in Complex Human Diseases. Wiley-Liss, New York, 1998.
J. Lynch and B. Walsh. Genetics and Analysis of Quantitative Traits. Sinaure Associates Inc., Sunderland, MA, 1998
D.C. Thomas. Statistical Methods in Genetic Epidemiology. Oxford University Press, New York, 2004.