Modern DNA Sequencing Methods

[schedule]

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.

Welcome!

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