THE SEQUENCING TECNOLOGY (R)EVOLUTION

Transcription

1 THE SEQUENCING TECNOLOGY (R)EVOLUTION TIM STAKENORG IMEC MB&C meeting May 16, 2013 IMEC 2013

2 HISTORY OF SEQUENCING BC - Aristotle told his students that all inheritance comes from the father 1977 (2 indepent methods published in PNAS) - Maxam & Gilbert: chemical degradation method - Sanger: ddntp-mediated chain termination!! 1995 (Fleishmann et al., Science 269: 485) - Mycoplasma genitalium (first fully sequenced bacterial genome) 2001 (Science/Nature) - First human genome (13 years, 300 million USD) May 2005 (454 technology) - 6 month, >30 million USD IMEC

3 HISTORY OF SEQUENCING 1,E+09 Itanium 2 G80 RV770 AMD K10 transistor count (Moore's law) vs. sequenced kilo base pairs/day 1,E+08 1,E+07 1,E+06 1,E+05 1,E+04 1,E+03 1,E+02 1,E+01 Intel 4004 Intel 8088 Moore s law Intel 8080 Intel Intel Pentium II Intel ABI373 Pentium Pentium 4 AMD K5 ABI377 AMD K7 Pentium III ABI37000 Cell AMD K8 Barton Roche 454 Life Sciences ABI 3730XL Illumina HiSeq Atom Pacific Biosciences SMRT* 454 Titanium, ABI Solid3 First Solid manual slab gel 1,E date of introduction 3 rd generation 2 nd generation (sequence by synthesis) 1 st generation (capillary electrophoresis) (slab gels) Note: human genome = ~ bases IMEC

4 HISTORY OF SEQUENCING Still many challenges in post-processing of data Data handling Computational algorithms IMEC

5 THE FIRST GENERATION IMEC

6 FIRST GENERATION (SANGER) Cyclic sequencing (amplification) reaction - PCR products of different length - Last base is fluorescent (different color per base) - Separation by size Pros and Cons - Extensive sample prep (-) - High cost (-) - Low throughput (-) - Long read lengths (+) IMEC

7 DRAFT GENOME 1990 Human genome project started First draft in 2001, over 10 years and $3 billion later In 2003 (published 2004) finished human genome sequence February 2001 April 2011 IMEC

8 IMEC 2013

9 THE NUMBER OF GENES Human genome : ~3 Gbase (300,000 kbases) Average gene size: ~3kbases, but sizes vary greatly (largest is dystrophin: 2.4 Mbases) GENE SWEEP (Cold Spring Harbor Lab ) Rules: $1 in 2000, $5 in 2001 and $20 in bets Mean Lowest (Lee Rowen) Highest IMEC

10 THE HUMAN GENOME ~3 Gbase, 24 chromosomes: 1-22, X, Y 21,500-24,000 genes only 2% of the genome encodes genes about 46% of the genome is repetitive sequence => THERE IS A LOT OF GENOMIC DARK MATTER (or non coding RNA) IMEC

11 THE HUMAN GENOME IMEC

12 THE HUMAN GENOME Almost all (99.9%) nucleotide bases are exactly the same in all people (0.1%, difference which is 1 difference per 1,000 base pairs) - Humans ( %) - Chimpanzees ( %) - Drosophila simulans (2%) - E. coli (5%) - HIV-I (30%) SNPs (a single base change in more than 1% humans) - Harmless (e.g. change in phenotype) - Harmful (e.g. diabetes, cancer, heart disease, Huntington s) - Latent (e.g. susceptibility to lung cancer) IMEC 2013 Photos from UN photo gallery 12

13 THE SECOND GENERATION (NEXT GEN) IMEC

14 SECOND GENERATION Sequence by synthesis - Step-wise base addition & read-out - Washing steps between each step Pros and Cons - Extensive sample-prep (-) - Relative costly reagents/run (-) - Massively parallel sequencing (+) - Relatively short fragments (-) Examples: Roche 454 GS-FLX, Illuminia HiSeq, Applied Solid, IonTorrent, etc IMEC

15 2 ND GENERATION: SAMPLE PREP Extensive sample prep - Library generation (generation of fragments with adapters) - Clonal amplification - e.g. empcr (e.g. Roche GS-FLX, ABI Solid, etc) - e.g. bridge PCR (e.g. Solexa from Illumina) IMEC

16 FLUORESCENT READ-OUT e.g. Illumina, ABI Solid, (or Helicos on single molecule level) IMEC

17 BASE CALLING: NOISE FACTORS Phasing noise - Leading / Lagging Fading noise - Exponential decay in fluorescent signal Cycle-dependent change in fluorophore cross-talk IMEC 2013 Erlich et al. Nature Methods 5: (2008); 17

18 PYROSEQUENCING (OPTICAL) e.g. Roche GS FLX 454 IMEC 2013 Figure from OMICS Journals (doi: /jcsb ) and Nature Biotechnology (doi: /nbt1485) 18

19 PYROSEQUENCING (ELECTRICAL) e.g. IonTorrent (Life Technologies) IMEC

20 PYROSEQUENCING (ELECTRICAL) Making small sequencing tests available (e.g. DNA electronics/roche) IMEC

21 THE THIRD GENERATION (NEXT NEXT-GEN) IMEC

22 THIRD GENERATION Sequencing (by synthesis) - Single molecule sensitivity - Read-out during copying Pros and Cons - Potentially long fragments (+) - Large cost reduction per run (+) - Easier sample prep (+) - Enzyme necessary: speed limited (1-3 bases/second/pore) Examples: Pacific Biosciences, Oxford Nanopore, Visigen (now Life Tech), etc. IMEC

23 REAL-TIME SEQUENCING Zero mode waveguides (Pacific Biosciences) Single Molecule Real-Time (SMRT) sequencing 70nm - Polymerase is immobilized in 20 zl sized zeromode waveguides (ZMW) - Polymerase cleaves off the fluorescent tags - Fluorescent read-out - Diffusion time: microseconds - Incorporation time: milliseconds IMEC

24 MINATURIZING DNA SEQUENCING IMEC Molecular Biology and Cytometry Course - SCK CEN 24

25 IMEC

26 COMPARISON OF COMMERCIAL PRODUCTS Illumina: HiSeq 2000, began shipping in the third quarter of The instrument produces 2x150-base paired-end reads, which will increase to 2x250. That will give you around 300 gigabases in approximately 60 hours, Roche: GS FLX+ system, coupled with its newest software produces reads of up to 1,000 bp and beyond Life Technologies (Ion Torrent): Ion Proton can sequence a human exome in a few hours, Proton II is basically a 50x improvement of their first chip (120 Gb), but with a somewhat higher error rate than Illumina Pacific Biosciences: PacBio RS, the company s new XL chemistry produces reads averaging 5,000 bases a piece, though about 5% of those exceed 10,000 bases. IMEC

27 FUTURE FOURTH GENERATION IMEC

28 NANOPORE BASED SEQUENCING e.g. Oxford Nanopore IMEC

29 NANOPORE BASED SEQUENCING Hybridization assisted sequencing e.g. Nabsys - Short fragments are hybridized to DNA - Their distance is measured - In parallel for many fragments e.g. Noblegen - Replace bases by barcode - Hybridize molecular beacons - Unzip DNA fragments in pore - Read fluorescent signals IMEC

30 FOURTH GENERATION Direct read-out of DNA - Nanopore based sequencing - Electron microscopy Pros and Cons - In principle, simple sample prep - Limited or no reagent costs - Long read lengths - No enzymatic reaction needed - Ability to read RNA, DNA modifications, etc Examples: imec, IBM, Halycon, IMEC

31 NANOPORE BASED SEQUENCING IMEC 2013 Figures from Hao Liu, (Biodesign Institute) and 31

32 NANOPORE/NANOSLIT COMBINATION Controlled translocation through a solid-state nanopore Electrically induced translocation Mechanical confinement of a single DNA strand V SERS in a plasmonic nanoslit Vibrational fingerprinting Molecular information in the pore IMEC RESTRICTED

33 MOLECULAR SPECTROSCOPY BY SERS The normal Raman effect Inelastic scattering from light by molecules through the excitation of molecular vibrations Spectroscopy Weak process! Surface Enhanced Raman Scattering Hot spots near metal nanostructures (excitation of plasmons) Enhancement with E 4 Single molecule resolution IMEC RESTRICTED

34 SERS NANOSLIT λ=785 nm Au H 2 O Hot spot Generating a hot spot using top-down designed plasmonic nanocavities Large and highly localized field enhancement Raman enhancement: x (to single molecule levels) IMEC RESTRICTED

35 NEXT-GENERATION SEQUENCING 1 st generation 2 nd generation 3 nd generation 4 th generation Basic principle Sanger sequencing with size separation of amplified fragments Site-selective amplification followed by iterative base-incorporation, Enzymatic reaction to continuously integrate and read-out bases. True single molecule Direct read-out of bases (without copying). True single molecule analysis read and wash steps analyses Sample preparation Extensive Extensive Moderate Almost none Speed/base/site Very low (<<1/sec) Low (<1/sec) Moderate (3/sec) Very fast (~1 ms) Throughput Low Very high Very high Very high Accuracy High Low Low (~80%) NA Read length Long (~1000) Short (~15-400) Moderate (~450) Very long (>1000) De novo sequencing Possible Not possible Difficult Easy Repeat regions Limited Highly limited Limited No intrinsic limit DNA/protein Indirectly Indirectly Indirectly Yes derivatives Reagent cost Very high Very high High None IMEC

36 Technology Generation On market Single molecule Nanopore (NP) / Enzymatic (E) Based Principle website Illumina HiSeq * 2 Yes No E Fluorescence, sequence by synthesis Roche (FLX Titanium) 2 Yes No E Light, sequence by synthesis Polonator 2 Yes? E Fluorescence/Polony Complete Genomics 2 Yes No E Fluorescence, sequence by synthesis Helicos (TSMS) 2 Yes Yes E Fluorescent, sequence by synthesis Life Tech (ABI Solid4 ) 2 Yes No E Fluorescence, sequence by synthesis Life Tech (IonTorrent) 2 (3) Yes No E Electrical, sequence by synthesis Intelligent Bio 2 No? E Fluorescence, sequence by synthesis GE Global 2 No Yes E Fluorescence, sequence by synthesis GnuBio 2 No No E Microdroplets, sequence by ligation Genizon Bioscience 2? No No E Light Speed 2? No?? Light interference, patent: US 2009/ Mobious Biosystems (Nexus) 2? No No E?? Pacific Biosciences (tsmrt) 3 Yes Yes E Fluorescence (SMRT), sequence by synthesis Oxford Nanopore 3 No Yes NP/E Electrical, enzymatic cutting of DNA Visigen 3 No? E FRET measurement using TIRF Cracker 3 No Yes E SMRT, read-out on chip IBM/Roche nanopore 4 No Yes NP/- Electrical, tunneling using NPs Nabsys 4 No Yes NP/- Electrical, hybridization assisted NP sequencing NobleGen Biosciences 4 No Yes NP/- Electrical, fluorescent after hybiridization (Meller) Electronic Bio 3 (4?) No Yes NP/- Electrical using biological NPs Reveo 4 No Yes -/- Electrical, tunneling using nano-knifes Base4 Innovation 4 No Yes?? Nanopore + optical? ZS Genetics 4? No Yes -/- Electronmicroscopy Halcyon Molecular 4? No Yes -/- Electronmicroscopy IMEC

37 MANY APPLICATIONS & PUBLICATIONS IMEC

38 APPLICATIONS OF NEXT-GEN SEQUENCING Whole-genome sequencing Comparative genomics Genome re-sequencing Structural variation analysis Polymorphism discovery Meta-genomics Environmental sequencing Gene expression profiling Genotyping Population genetics Migration studies Ancestry inference Relationship inference Genetic screening Drug targeting Forensics IMEC

39 HAS NGS A PROGNOSTIC VALUE IMEC 2013

40 IMEC and for personal health?

41 IMEC and for personal health?

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44 ... and for personal health? 2 virus infections during the test period (common cold and sinus infection) Diabetes developed during / after the 2 nd infection (Genetic risk had already been identified from whole genome sequencing) IMEC 2013

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46 HAS NGS A PROGNOSTIC VALUE Sequencing has gone through a revolution and has become affordable for some applications (e.g. exome sequencing) Personal genome sequencing is already possible, but the medical interpretation is still difficult Genome sequencing can predict disease risks Genome sequencing should be combined with other omics to monitor disease risk Integrated analysis are possible, but still need further improvement and understanding Regulatory information needs to be considered Every person is unique and longitudinally follow-up will provide further insight Longitudinal follow-up: case studies have proven value, but no good biomarkers yet IMEC 2013

47 IMEC 2013 THANK YOU FOR YOUR ATTENTION