Next Gen Sequencing Summary of the short course Next Gen Sequencing at Avans hogeschool, Breda. 24/04/2013 Next gen Sequencing technologies

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1 Next Gen Sequencing Summary of the short course Next Gen Sequencing at Avans hogeschool, Breda 24/04/2013 Next gen Sequencing technologies 1

2 2nd Gen Sequencing Summary of the short course Next Gen Sequencing at Avans hogeschool, Breda 24/04/2013 Next gen Sequencing technologies 2

3 Generations of sequencing technologies 1st gen: Sanger sequencen 2nd gen (Next gen) massive parallel sequencing 3rd gen 2012-? Single molecule sequencing Next gen Sequencing technologies 24/04/2013 3

4 Overview History NGS (2nd gen) platforms Illumina (former: Solexa) SoLID: Life technlogies (former: Applied Biosystems) (SOLID) Roche (Pyrosequencing) Ion Torrent (semiconductor hydrogen ion detection) 3rd gen platforms Helicos Pac bio Oxford Nanopore Sequencing strategies Not covered NGS subjects Next gen Sequencing technologies 24/04/2013 4

5 1973 First sequence published Next gen Sequencing technologies 24/04/2013 5

6 1977 Frederick Sanger Next gen Sequencing technologies 24/04/2013 6

7 1985 Human genome project proposed Start of the project in 1987 Next gen Sequencing technologies 24/04/2013 7

8 1987 first automated sequencer ABI370 Next gen Sequencing technologies 24/04/2013 8

9 1997 first next gen patents filed 2003 Human genome project finished 2005 first next gen sequencer available 2012 first 2nd gen sequencer available Next gen Sequencing technologies 24/04/2013 9

10 Illumina The illumina sequencer family: Genome AnalyzerIIx, HiSeq 2500, HiSeq 2000, HiSeq 1500, HiSeq 1000, HiScanSQ instruments, MiSeq TruSeq chemistry: sequencing by synthesis. Next gen Sequencing technologies 24/04/

11 Illumina sample prep Next gen Sequencing technologies 24/04/

12 Illumina sequencing Next gen Sequencing technologies 24/04/

13 Illumina sequencing Next gen Sequencing technologies 24/04/

14 SOLiD (Life technologies) Sequencing by ligation Next gen Sequencing technologies 24/04/

15 SOLiD sample prep Ligate biotinilated adapters to fragmented DNA Bind fragments to beads in a 1:1 ratio Emulsion PCR or on chip amplification Next gen Sequencing technologies 24/04/

16 Emulsion PCR Next gen Sequencing technologies 24/04/

17 Emulsion PCR Next gen Sequencing technologies 24/04/

18 Emulsion PCR Next gen Sequencing technologies 24/04/

19 NEW: In stead of emulsion PCR: The wildfire chemistry Next gen Sequencing technologies 24/04/

20 SOLiD sequencing chip Next gen Sequencing technologies 24/04/

21 SOLiD sequencing surface Individual sequence colonies Next gen Sequencing technologies 24/04/

22 SOLiD sequencing: sequencing by ligation n = random A C T or G z = base that fits all Next gen Sequencing technologies 24/04/

23 SOLiD sequencing: sequencing by ligation Next gen Sequencing technologies 24/04/

24 SOLiD sequencing: sequencing by ligation Next gen Sequencing technologies 24/04/

25 SOLiD sequencing: sequencing by ligation Next gen Sequencing technologies 24/04/

26 Roche Pyrosequencing Next gen Sequencing technologies 24/04/

27 Roche Pyrosequencing Next gen Sequencing technologies 24/04/

28 Roche Pyrosequencing Next gen Sequencing technologies 24/04/

29 Roche Pyrosequencing Next gen Sequencing technologies 24/04/

30 Roche Pyrosequencing Next gen Sequencing technologies 24/04/

31 Ion Torrent Semiconductor detection of H+ Detection of clonally amplified sequences on beads (emulsion PCR) Next gen Sequencing technologies 24/04/

32 Ion Torrent Next gen Sequencing technologies 24/04/

33 Ion Torrent Next gen Sequencing technologies 24/04/

34 Single molecule sequencers ( 3rd gen) Helicos PacBio Oxford Nanopore Next gen Sequencing technologies 24/04/

35 Helicos Next gen Sequencing technologies 24/04/

36 Helicos Sampleprep Helicos: Disadvantage Helicos: Next gen Sequencing technologies 24/04/

37 PacBio (Pacific Biosystems) Next gen Sequencing technologies 24/04/

38 PacBio Next gen Sequencing technologies 24/04/

39 PacBio SMRTbell Next gen Sequencing technologies 24/04/

40 Pac Bio SMRTbell sequencing strategies Next gen Sequencing technologies 24/04/

41 Oxford Nanopore (NO PRODUCT YET AVAILABLE) Next gen Sequencing technologies 24/04/

42 Comparison of sequencing methods method Pac Bio Ion torrent Pyroseq Seq by synthesis Seq by ligation Company Pac Bio Life tech Roche Illumina Applied bio Sanger Read length 2900 bp 200 bp 700 bp 150 bp 50 bp 800 bp Reads/run 75 * * * * ,2 * Time /run 2 hours 2 hours 24 hours 10 days 14 days 2 hours $ 1*10 6 bases $2 $1 $10 $0.1 $0.13 $2400 Next gen Sequencing technologies 24/04/

43 Read length Next gen Sequencing technologies 24/04/

44 Sequencing aproaches: barcoding Next gen Sequencing technologies 24/04/

45 Sequencing aproaches: Paired end Next gen Sequencing technologies 24/04/

46 Sequencing aproaches: mate paired For large structural variations Next gen Sequencing technologies 24/04/

47 NGS Topics not covered in this presentation De novo seq Sequencing and building a new genome Resequencing looking for structural and functional mutations cdna seq RNA expression and mutations and splice variants MiRNA seq seq of 20-25bp non coding regulating RNA s ChIP seq Chromatin Immunoprecipitation, discover regulation sequences Methylation sequencing Epigenetic DNA regulation Metagenomics sequencing of a pool of organisms (bacteria/virussus) Targeted sequencing Fish out a pool of sequences you like to sequence NGS data analysis Next gen Sequencing technologies 24/04/

48 acknowledgements All speakers of the Next gen sequencing short course. Next gen Sequencing technologies 24/04/

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