Prospectus

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Statistical genetics

Course
2024-2025

Admission Requirements

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
Linkage (human studies):
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
Linkage analysis in Plants:
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

In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.

Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.

Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.

Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.

Mode of Instruction

Lectures, practicals, and two assignments

Assessment method

  • Obligatory computer practicals

  • Oral examination

Reading List

  • 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

As a student, you are responsible for enrolling on time through MyStudyMap.

In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.

There are two enrolment periods per year:

  • Enrolment for the fall opens in July

  • Enrolment for the spring opens in December

See this page for more information about deadlines and enrolling for courses and exams.

Note:

  • It is mandatory to enrol for all activities of a course that you are going to follow.

  • Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.

  • Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.

Contact

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

Remarks

Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.