# Statistical genetics

Course
2023-2024

Statistics and probability
Linear & generalized linear models and linear algebra
Statistical computing with R

## Description

Statistical genetics is an important topic within the Life and Behavioral Sciences. The structure within families (pedigrees) and the dependency structure between genetic markers at the genome require specific statistical models and software packages for analysis. The topics addressed during this course will be: estimation of heritability, detecting new genetic factors using genome wide linkage and association studies, the analysis of candidate genes, data bases such as Hapmap. Data sets from human genetics and from animal and plant breeding will be analyzed.

## Course objectives

After completion of the course the student is able to:

Familial Aggregation:
1. understand the concept of heritability
2. analyze data to assess heritability in the sib-design
3. evaluate results from the analysis of complex families
1. understand the concept of Identity by descent and its relation to linkage analysis
2. apply standard procedures (Z-mean) in new situations and evaluate the effect of violation of assumptions
Population Genetics:
1. understand genetic drift
2. apply statistical methods to quantify population stratification
3. evaluate the consequences of population stratification in downstream analyses
Genetic association:
1. to create a Genome-wide association study (GWAS) analysis report and quality control analysis
2. critically appraise and evaluate a GWAS, by recognizing problematic results and improve the analysis
Mendelian Randomization (MR):
1. understand assumptions of MR
2. apply a MR analysis to data
3. evaluate results and recognize limitations
Principles of Plant Genetics:
1. understand experimental populations and their statistical properties
2. analyze data to evaluate experimental population
3. evaluate results from data analysis to draw conclusions on breeding experiments
1. understand segregation in experimental populations
2. evaluate data to create genetic maps and investigate segregation
3. evaluate experimental designs with respect to map resolution
Quantitative trait loci (QTL) mapping:
1. understand the relationship between QTLs and genetic/phenotypic variation
2. analyze data and model output to judge presence of QTLs
3. evaluate designs and analysis strategies with respect to suitability for QTL analyses
Genotype by environment (GxE):
1. understand the importance of GxE analyses and corresponding designs
2. analyze GxE data and interpret the output,
3. evaluate interpretations of GxE analyses and corresponding conclusions

## Timetable

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).

For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

## Mode of Instruction

Lectures, practicals, and two assignments

## Assessment method

• Obligatory computer practicals

• Oral examination

• Book “The Fundamentals of Modern Statistical Genetics”, Laird and Lange, Springer 2011 (L1 - L11)

• Book “Phenotypes and Genotypes“, Frommlet, Bogdan, and Ramsey, Springer 2016

## Registration

It is the responsibility of every student to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.

Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.
Extensive FAQ's on MyStudymap can be found here.

## Contact

Stefan Böhringer, email: s.boehringer@lumc.nl