Course catalogue doctoral education - VT18

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Title Analysis of genome wide association data
Course number 2767
Programme Epidemiologi
Language English
Credits 1.5
Date 2018-03-08 -- 2018-03-14
Responsible KI department Institutet för miljömedicin
Specific entry requirements Knowledge corresponding to Biostatistics I: Introduction for epidemiologists and Epidemiology I: Introduction to epidemiology or equivalent courses.
Purpose of the course The aim is to enable students to independently perform a complete genome wide association study (GWAS) analysis in a computationally effective and statistically correct manner.
Intended learning outcomes After the course the student should be able to execute a standard genome wide association study (GWAS) analysis using various tools (Linux, plink, R, among others). More specific the student should be able to:
- Create directories, move files and perform other standard tasks using Linux-type commands.
- Perform standard quality control procedures and filter data accordingly using plink, define the logic behind each quality assessment and explain why high quality data is essential.
- Perform tests of association and apply multiple testing correction, interpret and discuss the result.
- Investigate the presence of biases, identify reasons for their presence and manage different ways to correct for these.
- Use the language R to read and write files, and to illustrate results from each step of the GWAS analysis.
- Perform secondary analysis and review the results.
Contents of the course The course follows a standard GWAS analysis of a real data set of a complex trait, from receiving the data to processed and illustrated association results. During the course the student will use multiple different tools and computer languages.
Teaching and learning activities The course focuses on active learning and includes introductory lectures, practical hands on analysis of GWAS data sets as well as group discussions.
Compulsory elements The individual examination (summative assessment).
Examination To pass the course the student must fulfill the learning outcomes. This will be assessed through a written individual report outlining the commands used and discussing their relevance as well as the achieved results.
Literature and other teaching material Plink Manual: Scientific articles and introductory material distributed by course teachers.
Number of students 8 - 25
Selection of students Eligible doctoral students, with required prerequisite knowledge, prioritized according to 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given to earlier registration date). To be considered, submit a completed application form. Give all information requested, including a description of current research and motivation for attending, and an account of previous courses taken.
More information Course dates are March 8, 9, 12, 13 and 14. The individual examination will be performed as a take-home examination.
Additional course leader
Earlier evaluation of the course Evaluation report
Course responsible Boel Brynedal
Institutet för miljömedicin
Contact person Johanna Bergman
Institutet för miljömedicin

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