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Barbera van Schaik Bioinformatics Laboratory, AMC

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Presentation on theme: "Barbera van Schaik Bioinformatics Laboratory, AMC"— Presentation transcript:

1 Barbera van Schaik Bioinformatics Laboratory, AMC

2 Overview Technique Applications Bioinformatics LaboratoryBarbera van Schaik

3 Bioinformatics LaboratoryBarbera van Schaik

4 Sequencing methods Synthetic chain-terminator chemistry Sequencing by hybridisation Pyrosequencing Base-by-base sequencing by synthesis Sequencing by ligation Nanopore technology Single-molecule sequencing by synthesis in real time Bioinformatics LaboratoryBarbera van Schaik

5 Methods Bioinformatics LaboratoryBarbera van Schaik Bentley 2006, Curr opinion in genetics Synthetic chain-terminator chemistry Sanger sequencing Sequencing by hybridisation Pyrosequencing (454) Pyrophosphate release after each nucleotide incorporation Base-by-base sequencing by synthesis (Solexa) Sequencing by ligation (SOLiD) Nanopore technology Single-molecule sequencing by synthesis in real time

6 Illumina - Solexa Bioinformatics LaboratoryBarbera van Schaik solexa.com

7 Illumina - Solexa Bioinformatics LaboratoryBarbera van Schaik solexa.com

8 Illumina - Solexa Bioinformatics LaboratoryBarbera van Schaik solexa.com

9 Illumina - Solexa Bioinformatics LaboratoryBarbera van Schaik solexa.com

10 Roche Bioinformatics LaboratoryBarbera van Schaik 454.com

11 Roche Bioinformatics LaboratoryBarbera van Schaik Nature Methods 2007 advertisement 454.com

12 Roche Bioinformatics LaboratoryBarbera van Schaik Nature Methods 2008

13 Roche Bioinformatics LaboratoryBarbera van Schaik Nature Methods 2008 and 454.com

14 Roche Add adaptors with different sequences Analyze samples in one run Bioinformatics LaboratoryBarbera van Schaik

15 Bioinformatics LaboratoryBarbera van Schaik

16 Overview Bioinformatics LaboratoryBarbera van Schaik

17 Whole genome De novo sequencing Re-sequencing Copy number variations Rearrangements New insertions/deletions/mutations Bioinformatics LaboratoryBarbera van Schaik

18 Copy number variation Bioinformatics LaboratoryBarbera van Schaik The Human Genome Structural Variation Working Group, Nature 2007

19 SNP/Haplotype analysis Linkage studies Forensic research Bioinformatics LaboratoryBarbera van Schaik

20 Gene regulation studies Chip-on-sequencing Protein-DNA Protein-RNA Bioinformatics LaboratoryBarbera van Schaik

21 Chip-seq Bioinformatics LaboratoryBarbera van Schaik

22 Gene expression Full-length transcripts EST sequencing 5' transcript ends (5'-RATE, CAGE) SAGE ditag sequencing SAGE-like 3' end sequencing Nebulized fragments ncRNA sequencing Bioinformatics LaboratoryBarbera van Schaik

23 SAGE Bioinformatics LaboratoryBarbera van Schaik

24 CAGE Bioinformatics LaboratoryBarbera van Schaik

25 Epigenetics Treatment with sodium bisulfite Unmethylated cytosines change into uracil Methylated cytosines are unchanged Compare sequences with reference sequence Bioinformatics LaboratoryBarbera van Schaik

26 Bisulfite sequencing Bioinformatics LaboratoryBarbera van Schaik

27 Paleogenomics Sequencing of ancient DNA Mummies Sabretooth Mammoth Neanderthal Bioinformatics LaboratoryBarbera van Schaik

28 Metagenomics & microbial diversity Study genomic content in a complex mixture of microorganisms (bacteria or viruses in some environment) Identify new species Bioinformatics LaboratoryBarbera van Schaik

29 Metagenomics Bioinformatics LaboratoryBarbera van Schaik

30 Bioinformatics LaboratoryBarbera van Schaik

31 Topics of interest Large-scale population studies: mutations, cnv's, rearrangements (e.g. tumors, T- and B-cells) Other organisms (viruses, bacteria): metagenomics, whole genome (e.g. identify new bacteria, HIV1 variants) Gene expression studies: SAGE-like, multiple samples in one run Bioinformatics LaboratoryBarbera van Schaik

32 Bioinformatics LaboratoryBarbera van Schaik

33 Overview Bioinformatics LaboratoryBarbera van Schaik


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