Course catalogue doctoral education - HT19

  • Application can be done between 2019-04-15 and 2019-05-15
Application closed
Title High throughput functional genomic technologies in biomedical research
Course number 2537
Programme Development and regeneration (DevReg)
Language English
Credits 1.5
Date 2019-04-01 -- 2019-04-05
Responsible KI department Department of Biosciences and Nutrition
Specific entry requirements
Purpose of the course The purpose of the course is to give participants an introduction to high-throughput genomic technologies. Additionally, the participants will be able to understand which high throughput technology to apply in order to answer a specific scientific question.
Intended learning outcomes After the course the students should be familiar with high throughput genomic technologies, including high throughput sequencing and various microarray platforms for gene expression profiling, genome wide DNA-binding and human genetics applications and know how these could be applied in biomedical research including in their own projects.
Contents of the course Technological platforms such as high throughput sequencing and microarray based platforms such as those provided by Affymetrix, and Illumina. Applications of these platforms for gene expression profililng, global DNA-binding, methylation and human genetic studies. Analysis of data from the above platforms and applications.
Teaching and learning activities Lectures, seminars, demonstrations and data analysis.
Compulsory elements The students have to take active part in all activities. An alternative time for demonstrations and data analysis will be provided, if possible, if they are absolutely unable to attend. If it is not possible to provide an alternative time, this part will need to be taken at the next course occasion. Other absence can be compensated for by an additional task in agreement with the course organizers.
Examination The students, will in groups of three students, select a paper of a relevant topic for the course. The course leaders will help them with this if necessary. The paper should be presented for the whole group of students, 15 min per group, with specific focus on the technologies used. The students should be able to discuss with the other participants and the examiner(s): Were the technologies appropriate for the study? Could they have used alternative technologies? Advantages and disadvantages. This seminar will take 2-3 hours.
Literature and other teaching material Recommended literature: Reviews: 1. Trevino, V., Falciani, F., and Barrera-Saldana, H.A. (2007). DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol. Med. 13, 527-541. 2. Morozova, O., and Marra, M.A. (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics 92, 255-264. 3. Mardis, E.R. (2011). A decade's perspective on DNA sequencing technology. Nature 470, 198-203. 4. Werner, T (2010). Next generation sequencing in functional genomics. Brief. Bioinform. 11, 499-511. 5. Hurd, P.J., and Nelson, C.J. (2009). Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief. Funct. Genomic Proteomic 8, 174-183. 6. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012 May 29;13(7):484-9 Reports: 1. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., thurman, R.E., et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. 2. Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science New York, NY 326, 289-293. 3. Visel, A., Blow, M.J., Li, Z., Zhang, T., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009). ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858. 4.Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A., et al. (2009). mRNA-Seq whole-transcriptome analysis of a single cell. Nature methods 6, 377-382. 5. Kulasingam, V., Pavlou, M.P. and Diamandis, E.P. (2010). Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer. Nat. Rev. Cancer 10, 371-378. 6. Zhang, J. et al. (2011). The impact of next-generation sequencing on genomics. J. Genet. Genomics 38, 95-109. 7. Macarron, R., Banks, M.N., Bojanic, D.J., Cirovic, D.A., Garyantes, T., Green, D.V.S., Hertzberg, R.P., Janzen, W.P., Paslay, J.W., Schopfer, U. and Sittampalam, G.S. (2011). Impact of high-throughput screening in biomedical research. Nat. Rev. Drug Discov. 10, 188-195. 8. Stower, H. (2012). Technology: High-throughput enhancer screening. Nat. Rev. Genet. 13, 223.
Number of students 8 - 30
Selection of students Selection will be based on 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)
More information The course will take place at campus Flemingsberg, at NEO, Blickagång 16 Huddinge.
Additional course leader
Earlier evaluation of the course Evaluation report
Course responsible Patrick Muller
Department of Biosciences and Nutrition
Contact person Patrick Muller
Institutionen för biovetenskaper och näringslära