Syllabus database for doctoral courses
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Syllabus database for doctoral courses
SYLLABI FOR DOCTORAL COURSES
| Swedish title | Analys av associationsdata från helgenomsstudier |
|---|---|
| English title | Analysis of genome wide association data |
| Course number | 2767 |
| Credits | 1.5 |
| 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. |
| Grading | Passed /Not passed |
| Established by | The Board of Doctoral Education |
| Established | 2017-09-22 |
| 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: http://zzz.bwh.harvard.edu/plink/ Scientific articles and introductory material distributed by course teachers. |
Course responsible |
Boel Brynedal Institutet för miljömedicin 0739802410 Boel.Brynedal@ki.se |
| Contact person |
Johanna Bergman Institutet för miljömedicin johanna.bergman@ki.se Nobels väg 13 17177 Stockholm |
