Sandberg Lab

Ludwig Institute for Cancer Research & Department of Cell and Molecular Biology, Karolinska Institutet

Modern DNA Sequencing Methods


Duration: March 23 - March 27, 2009.

Location: CMB seminar room, Berzelius väg 35, room A216. See map below.

Aim: After completing the course, the student will understand the technology behind the major DNA sequencing platforms available today, and their strengths and limitations; and will know the most important applications, and how they may apply to the student's own research.

Content: The course will cover the following topics: The history of DNA sequencing. Introduction to modern DNA sequencing. Practical considerations, cost, dealing with a deluge of data. Applications - RNA sequencing, ChIP sequencing, metagenomics. Future technologies and applications.

Format: The course consists of lectures by invited speakers, and a site visit. In addition, students will be asked to prepare a presentation of how modern DNA sequecning methods could benefit their own research.

Examination: All lectures are compulsory. In case of absence, lectures can be compensated by a literature assignment and written report. Oral examination in conjunction with the presentation of an individual project of research.


Sten Linnarsson                    Rickard Sandberg
Assistant Prof, MBB                Assistant Prof, CMB
Monday, March 23
9.00 - 10.30   Introduction
               Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson
11.00 - 12.30 History of DNA sequencing [pdf] Ass. Prof. Sten Linnarsson
13.30 - 15.00 The development of Pyrosequencing and the two different formats: Qiagen (96- sample format) and Roche (454 technology). [pdf] Professor Pål Nyrén, KTH School of Biotechnology pdfs: Nyren_MMB_07, Margulies_Nature_05, Ronaghi_Science_1998 Tuesday, March 24 9.00 - 10.30 Applied Biosystems SOLiD [pdf] Inger Jonasson, BA, Lab Manager, Uppsala Genome Center
11.00 - 12.30 The Illumina Genome Analyzer II [pdf] Dr. Anna Kiialainen, Department of Medical Sciences, Uppsala University pdfs: Bentley_Nature_08, Mardis_AnnRevGenHumGen_08 13.30 - 13.45 General bioinformatics of short reads [pdf] Ass. Prof. Rickard Sandberg, CMB pdfs: Overview, Eland, MAQ, Bowtie, Novoalign, Tophat, velvet. 14.00 - 15.00 RNA-Sequencing [pdf] Ass. Prof. Rickard Sandberg, CMB pdfs: Wang_NatRevGen_09,Mortazavi_NatMethods_08,Wang_Nature_08 Wednesday, March 25 9.00 - 10.30 How to read the genetic regulatory code Prof. MD. Claes Wadelius, Dep. of Genetics and Pathology, Uppsala University pdfs: Johnson_Science_07
11.00 - 12.30 Metagenomics Professor Björn Andersson, CMB, KI
13.30 - 17.00 Site visit: 454 core facility, KTH Hosted by Professor Joakim Lundeberg, KTH
Thursday, March 26 9.00 - 10.30 Sequencing the cancer genome Assoc. Prof. Tobias Sjöblom, Uppsala University, Dep. Of Genetics and Pathology pdfs: Wood_Science_07
11.00 - 12.30 Sequencing of regulatory chromatin regions Dr. Andreas Lennartsson, Dep. Of Bioscience and Nutrition, KI NOVUM pdfs: Jiang_NatRevGen_09
13.30 - 15.00 High-throughput single-cell RNA-Seq [pdf] Ass. Prof. Sten Linnarsson, MBB
Friday, March 27 9.00 - 10.30 Project presentations (20 min per person)
11.00 - 12.30 Project presentations (20 min per person)
13.30 - 14.30 The future of DNA sequencing Ass. Prof. Sten Linnarsson, MBB
14.30 - 15.00 Wrap-up and course evaluation Ass. Prof. Rickard Sandberg & Ass. Prof. Sten Linnarsson

Additional Course Links:
Sequencing Platforms Links:Illumina/Solexa, SOLiD, 454

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