Next Generation Sequencing (NGS)

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1 Next Generation Sequencing (NGS) Fernando Alvarez Sección Biomatemática, Facultad de Ciencias, UdelaR 1

2 Uruguay Montevide o

3 3

4 TANGO World Champ (Maraca 4

5 Next Generation Sequencing module Next Generation Sequencing technologies. Monday morning Genome Sequencing and Assembling. Monday afternoom Assembling Practical Monday afternoom RNA seq Theoretical and Practical. Tuesday morning Chiptser (Data analysis platform for microarray, proteomics and NGS data) Tuesday afternoom 5

6 Agenda 1- Sanger Sequencing 2- Next Generation Sequencing Deep sequencing Sanger sequencing Technologies Genome sequencers- Ultra high throughput sequencers Roche - Solexa illumina Description of the different technologies, comparison of their throughput, limitations 3- Next-next generation sequencers (single molecule sequencers) -Pacific Biosciences -Helicos 6

7 7

8 DNA Sequencing 1977 Sanger enzymatic method dd(nucleotides) 8

9 DNA Sequencing Requirements: Template (to be sequenced) Primer dntp s ddntp s 4 independent reactions 9

10 DNA Sequencing Result: Fragments of different size according to where the ddntp has been incorporated Gel denaturing Gel separate the fragments to 10

11 DNA Sequencing Sequenced segment: = bases

12 12

13 Parallelization in the lab 13

14 Fluorometry and Sequencing 1986: contribution of fluorometry. Use of ddntp s linked to fluorescent labels Requeriments: Template Primer dntp s ddntp s (each one linked to a different Dye) Only 1 reaction Automatic Sequencing Nature 321, (12 June 1986) 14

15 15

16 Last 90 Applied Biosystems ABI 3730XL 96 capilaries 800 nt per read 1 Mb / days 16

17 Capillary sequencers (Sanger Centre, 2000) 17

18 Agenda 1- Sanger Sequencing 2- Next Generation Sequencing Deep sequencing Sanger sequencing Technologies Genome sequencers- Ultra high throughput sequencers Roche - Solexa illumina Description of the different technologies, comparison of their throughput, limitations 3- Next-next generation sequencers (single molecule sequencers) -Pacific Biosciences -Helicos 18

19 ROCHE Sequencing is a massively-parallel pyrosequencing system capable of sequencing roughly 20 megabases of raw DNA per 7-hour (GS20). The GSFLX is able to sequence 100 Mb. The system relies on fixing nebulized and adapter-ligated DNA fragments to small DNA-capture beads in a water-in-oil emulsion. The DNA fixed to these beads is then amplified by PCR. Finally, each DNA-bound bead is placed into a ~44 μm well on a PicoTiterPlate, a fiber optic chip. A mix of enzymes such as polymerase, ATP sulfurylase, and luciferase are also packed 19

20 454 sequencer ROCHE 20

21 Amplification empcr (Emulsion PCR) 1 DNA fragment 1 bead 1 microreactor 21 One Fragment = One Bead (limiting concentration)

22 1,6 millones de secuenciadores 22

23 Pyrosequencing 23 23

24 Colección de Datos 24

25 Pyrogram 1st cycle 2nd cycle AGGGG TGGC 25

26 26

27 Some Data 27

28 Some Data 2011: Genome Sequencer FLX System GS Junior System 28

29 Some throughput Data Genome Sequencer FLX System 29

30 Solexa Technology (200 Gb sequencer) 30

31 Deep sequencing 31

32 250 millions of clusters, 1000 copies each 32

33 33 Cesped de primers

34 34

35 35

36 Illumina 2011: 36

37 Illumina HiSeq

38 Illumina miseq 38

39 Comparison of the technologies Technology Read Length Number of Reads Total throughput Capillary (Sanger) 800 nt 96 <80 kb millions Roche (from 300 to 500) Solexa Solid 76 (100) Mb Aprox 100 millions 10 Gb (x2) (x2) (today 200 GB ) 500 millions 16 GB 39

40 Agenda 1- Sanger Sequencing 2- Next Generation Sequencing Deep sequencing Sanger sequencing Technologies Genome sequencers- Ultra high throughput sequencers Roche - Solexa illumina Description of the different technologies, comparison of their throughput, limitations 3- Next-next generation sequencers (single molecule sequencers) -Pacific Biosciences -Helicos 40

41 Next-Next Generation Sequencers Sequencing without amplification Oxford Nanopore 41

42 PACBIO HELICOS 42

43 Secuenciación : J. Rothberg 43

44 44

45 Ion Torrent 2011 PGM: 45

46 Ion Torrent 2011 PGM: 46

47 Secuenciación 2011 PGM: 47

48 Oxford Nanopore Tech: Oxford Nanopore Tech: 48

49 Oxford Nanopore α-hemolysin Staphylococcus aureus exonuclease 49

50 50

51 Huma sequencing project (finished) 13 years, 3 dólares months, 60 k dolar, Today, 1 week 10 k dolars In the neext few years Few hours or minutes, less than 1000 dolars -Genome sequencing will become a routine clinical technique This is allowing and will allow even more, to pose questions that were unthinkable few years ago -Eg. what is the genetic basis of longevity, hypertension, or whatever trait with a very complex genetic basis 51

52 52

53 53

54 54

55 Many things can be done, and many more will be possible in the future, 55

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