Gregory A. Buck, Ph.D. Director, Center for the Study of Biological Complexity

1. Introduction to DNA Sequencing TechnologiesAdvanced Genetic Epidemiology and Statistical Molecular Genetics WorkshopOctober 22, 2010 Gregory A. Buck, Ph.D. Director, Center for the Study of Biological Complexity Professor, Microbiology and Immunology Virginia Commonwealth University

2. Holy Grail: the Human Genome Complexity (number of bases per haploid genome) of the human genome: - 3x109 base pairs (nucleotides)

3. Human Genome How much does it cost to sequence? • First genome: $3-5 billion - James Watson: ~$300,000 - Today: $5,000 - $100,000 - Goal: $1000 (soon < $100?)

4. Human Genome How much time to sequence? - First genome sequenced (2004): . Estimated - 15 years (1990’s) . Actual - 13 years (capillary sequencing) • James Watson (2008): ~ 2 months . So-called ‘next generation’ sequencing • Now: two weeks? • Goal: tricorder (Star Trek)

5. X Prize: $10 million award is set for faster DNA maps (2006) By Nicholas Wade Published: THURSDAY, OCTOBER 5, 2006 A $10 million prize for cheap and rapid sequencing of the human genome was announced by the X Prize Foundation of Santa Monica, California. The terms of the prize require competitors to sequence 100 human genomes of their choice within 10 days, and within six months, those of a further 100 people chosen by the foundation. http://www.iht.com/articles/2006/10/05/news/genome.php

6. NHGRI Grants Support for 'Revolutionary' Sequencing for $1,000 GenomeAugust 5, 2008 By a GenomeWeb staff reporter Under one program, NHGRI may grant as much as $5 million in fiscal 2009 to between two and seven awardees. Applicants for these funds may seek up to $1.5 million per year for a period of up to five years.   A parallel grant program would give up to $2 million over three years to between two and seven grantees, for direct costs of up to $200,000 per year.   A Small Business Innovation Research Grant from NHGRI will grant between four and six small businesses up to a total of $3.6 million in fiscal 2009 to propose novel technologies to bring down the cost of sequencing. Phase I of this program will give up to $250,000 of total costs per year for up to two years, and Phase II applicants may seek up to $1.5 million total costs per year for up to three years.   A parallel Small Business Technology Transfer program will spend up to $2 million in fiscal 2009 to support between two and five awards to small businesses investigating the development of new sequencing methods. This program will award up to $250,000 total costs per year for up to two years for Phase I programs, and it will support up to $1.5 million in total costs per year for up to three years for Phase II programs.

7. Sequencing Technologies 1977: Fred Sanger (Cambridge, England) and Walter Gilbert (Harvard University) • Chemical sequencing (Gilbert) • Dideoxy Nucleotide Triphosphate chain termination sequencing (Sanger) • Both used for 8-10 years (different strengths/drawbacks) Chain termination sequencing proves most versatile, robust • Applicable to automation • First automated sequencers commercially available ~1985

8. Sanger or di-deoxy- method of sequencing

9. Sequencing Technologies Commercially available (1985): • Dideoxy- (Sanger, enzymatic, termination method) • Applied Biosystems, Inc., uses fluorescent primers • Requires four primers (four dyes) per sequence read • Requires four reactions (one for each primer) • Works, but expensive, laborious • DuPont: Genesis 1000 DNA Sequencer • Fluorescent chain termination sequencing • One primer, four terminators (one for each base, A, G, C, T) • One reaction per sequence read • Very efficient • Sells IP to ABI……….

10. Fluorescent chain termination sequencing See video

11. High Throughput Genome Sequencing: The main player... The PE/ABI 3700 Prism: - automated, easy to use - capillaries (not slab gel) - 10 runs per day - 96 sequences per run - ~1000 sequences/day - >300,000 sequences/ year - >150 million bases/ year - $300,000 per machine First truly automated high throughput sequencing Sequenced the first human genome…..

12. Output from Fluorescent Chain Termination Sequencing

13. Fluorescent chain termination sequencing: dominates market until ~ 2005: Next Generation (NextGen) Sequencing First out of the blocks: Roche 454 FLX Genome Sequencer

14. www.roche-applied-science.com Genome Sequencer FLX System Customer Training Technical Overview 400 million bases/ day (5th floor, Sanger Hall) (equal to 2 years output from cap sequencer!!)

15. Based on Pyrosequencing…..

16. Roche 454 Flx Technologies • Based on Pyrosequencing – • Pyrosequencing video • Roche 454 FLX workflow video

17. Pyrosequencing – 454/Roche http://454.com/products-solutions/how-it-works/sequencing-chemistry.asp

18. Roche 454 FLX Output: • Based on Pyrosequencing – • Currently: • ~400 base maximum read length • ~1 X 106 reads • ~ 400 X 106 bases per run • 1 run ~ 8 hours (1 day) • [compare to 200 X 106 / year for capillary sequencing] • Good for de novo sequencing, assembly • Cost: $10,000 per run

19. Solexa/Illumina Current Market Leader: Illumina Genome Analyzer

20. Reversible Terminator Chemistry OH X O O HN HN 5’ cleavage site fluor O O N N DNA O O O PPP 3’ 3’ block Incorporation Detection Deblock; fluor removal free 3’ end Next cycle Solexa/Illumina • All 4 labeled nucleotides in 1 reaction

21. 3’ 5’ A A A A A A A A T T T T T T T T G G G G G G G C C C C C C C C C 5’ Solexa/Illumina Cycle 1: Add sequencing reagents First base incorporated Remove unincorporated bases Detect signal Cycle 2-n: Add sequencing reagents and repeat • All four labelled nucleotides in one reaction • High accuracy • Base-by-base sequencing • No problems with homopolymer repeats

22. 5 1 2 3 4 TGCTACGAT … 6 8 9 7 T T T T T T TGT … Solexa/Illumina Base Calling The identity of each base of a cluster is read off from sequential images (sequencing genomes with the Illumina video)

23. Illumina/Solexa Technologies • Based on Sequencing by Synthesis (bridge PCR) – • Currently: • ~100 base maximum read length • ~ 500 X 106 reads/run • ~ 50 X 109 bases per run (100 X 109in paired end reads) • 1 run ~ 10 days • Good for re-sequencing, CHiP Seq, RNA seq • Cost: $10 – 20,000 per run New Illumina HiSeq2000: 200 X 109bases/run - ~ 10 X 1012bases/year - 100,000 fold increase over fluor. chain termination seq - >3,000 human genomes!

24. Applied Biosystems: Solid 4/HQ Sequencing by Ligation…

25. See video….. http://marketing.appliedbiosystems.com/images/Product_Microsites/Solid_Knowledge_MS/video/SOLiD_video_final.wmv

26. SOLiD Sequencing Technology Currently: • 50 base reads (75?) • Up to 400 Giga bases (billion bases) per run • >20 X 1012 bases per year (~2X Illumina) • Reduced costs (<50%/base cost) Best for applications where short reads are sufficient: CHiP seq, RNA Seq…. (not de novo sequencing)

27. Single Molecule Technologies Holy Grail: • No bias (due to replication, amplification) • Should work with limiting amounts of template • Long reads: for de novo sequencing Contenders: • true Single-Molecule Sequencing (tSMS) – Helicos • SMRT (Single Molecule, Real Time Sequencing) – Pacific BioSciences see videos

28. Single Molecule Technologies Advantages: • No amplification, cloning biases • Use small quantities of substrate (DNA) • Fast (rate of replication) Challenges • Signal to noise ratios • Sensitivity • Error rates To date: still largely experimental: • Short reads (Helioscope) • Low output; e.g., < 100,000 reads/run (Pac Bio)

29. Other Technologies Looming: • Ion Torrent: based on release of H+ ions • requires emulsion PCR • Inherent biases • Current read length < 100 bp; high error rate • Oxford Nanopore Technologies: passage of bases through a nanopore in a lipid bilayer • No data available • Others coming

30. http://www.iontorrent.com/technology/

31. http://www.iontorrent.com/technology/

32. Nanopore http://www.nanoporetech.com/sections/first/14

34. Wish list: • Longer reads • Today: 25 - 800 bases • Looming: 1 – 20 Kbases? • Ideal: entire chromosome [metagenomics] • Low amounts DNA required • No amplification bias • No replication bias • Can sequence hard to get DNA • High accuracy and fidelity • Rapid (currently over a week per run) • Lower cost ($100/human genome?)

35. Thank you!