Biochemistry 412. New Strategies & Technologies For DNA Sequencing. 2 February 2007

Transcription

1 Biochemistry 412 New Strategies & Technologies For DNA Sequencing 2 February 2007

2 Note: Scale is wrong!! (at least for sequences) 10 6 In 1980, the sequencing cost per finished bp $1.00 In 2003, the sequencing cost per finished bp $0.01 >>> a 100-fold reduction in years Corrected Shendure et al (2004) Nature Rev. Genetics 5, 335.

3 Today, the cost of sequencing each additional human genome ( resequencing ) is estimated to be about $10 million. Q1: Can that cost be dropped by two orders of magnitude (i.e, cost $100K per genome)? Q2: If the answer to Q1 is yes, what new technologies will be needed to achieve this?

4 Even more ambitious: Note: this was modeled on the Ansari X Prize for the first privately-financed human spaceflight, which was recently won by SpaceShipOne (at right -built by Mojave Aerospace Ventures). A $10 million prize for the first group that demonstrates the sequencing of 100 human genomes in 10 days or less!

5 Several companies are pursuing massively parallel (= cheaper) new DNA sequencing strategies, including some that involve single molecule analyses. Some of the main players are given below: 454 Life Sciences ( Solexa (now part of Illumina) ( Helicos BioSciences ( VisiGen Biotechnologies (

6 Classic Sanger Sequencing Church, Sci. American, Jan. 2006, p. 47.

7 For a primer on how large scale genomic sequencing is currently done, please see the educational link below at the U. S. Department of Energy Joint Genome Institute.

8 Shendure et al (2004) Nature Rev. Genetics 5, 335.

9 Note: Re-sequencing, doing the n th genome, or part of a genome, from an organism where at least one example of the complete genome is already known in the same (or a related) species, is almost always easier and cheaper than doing the de novo sequencing to get the first example of a genome in that species. Do you know why??

10 A sample of some of the approaches that are being tried. Shendure et al (2004) Nature Rev. Genetics 5, 335.

11 Some more technological approaches (some of which really work!) Sequencing by hybridization (annealing) Sequencing by ligase-edited annealing Pyrosequencing Note: there are also higher tech versions of classic Sanger sequencing in the works (see

12 Sequencing by Hybridization * *Note re nomenclature: hybridization originally referred to duplexes between complementary strands of RNA and DNA, i. e., hybrid duplexes. But in the conventional sense that the term is now used, hybridization also often refers to the formation of DNA-DNA duplexes, particular when one half of the duplex is a so-called probe molecule and the other is the target. A more general term describing in vitro formation of nucleic acid duplexes stabilized by complementary base-pairing -- whether DNA-DNA, RNA-DNA, or RNA-RNA -- is annealing (but you will almost never hear this term used instead of hybridization ).

13 For sequencing by hybridization, you typically need to have a fluorescently-labeled copy of your target DNA. Lockhart & Winzeler (2000) Nature 405, 827.

14 Sequencing by hybridization (Affymetrix chip) Cutler et al (2001) Genome Res. 11, 1913.

15 Sequencing by Ligation Shendure et al (2005) Science 309, Supplementary material

16 Pyrosequencing Ronaghi (2001) Genome Res. 11, 3.

17 Four enzyme pyrosequencing Use of an apyrase wash to destroy residual nucleotides Note: in the 454 variant of this technology, an apyrase wash separates each addition of a dntp. Ronaghi (2001) Genome Res. 11, 3.

18 Pyrograms Ronaghi (2001) Genome Res. 11, 3.

19 Other ways to reduce costs: do things in parallel (rather than in series) reduce volumes (= reduced reagent costs) A cool idea: micro-emulsion PCR

20 Microemulsions as tiny discrete reaction vessels for producting clonal populations of PCR-amplified DNA from single molecules Dressman et al (2003) Proc. Natl. Acad. Sci. USA 100, 8817.

21 Dressman et al (2003) Proc. Natl. Acad. Sci. USA 100, 8817.

22 Historical note: Bert Vogelstein and his colleagues at Johns Hopkins Medical School developed this technique in order to detect mutations in tumor suppressor genes (in cells shed from precancerous polyps) against a large background of unmutated genes (from shedding of normal cells) in urine samples, sputum samples, stool samples, etc. It has been estimated that half of all precancerous growths might be detected at an early enough stage by this approach to enable their surgical removal before they progressed to become malignant.

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24 Cost savings by using massively parallel pico-liter scale sequencing (454 Life Sciences Corp.) Rogers & Venter (2005) Nature 437, 376.

25 Design of 454 s sequencing scheme Margulies et al (2005) Nature 427, 376.

26 454 s Sequencing Instrument Margulies et al (2005) Nature 427, 376.

27 Actual sequencing data See note below Note Margulies et al (2005) Nature 427, 376.

28 Resequencing of a small bacterial genome (size = 580 kbp) in a single instrument run Margulies et al (2005) Nature 427, 376.

29 Note: conventional Sanger sequencing is still the gold standard for de novo sequencing of a never-before-sequenced genome. These new, rapid methods of sequencing will probably be most useful for cheaply re-sequencing genomes of different individuals (or strains) of the same species.

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31 Amplifying and sequencing total DNA from an autopsy sample can cause you to miss things. >>>Note: it s not really a failure of Sanger sequencing. Their approach works due to the fact that sequencing lots and lots of clonal DNA isolates (as opposed to a mixture) gives you a more sensitive means of detecting rare sequence variations. Thomas et al (2006) Nature Medicine 12, 853.

32 Sensitive detection of a tumor mutation causing drug resistance and patient relapse Resistance mutation (frequency 2% in sample) wt allele (frequency 98% in total DNA sample) Thomas et al (2006) Nature Medicine 12, 853.

33 One last item: An exciting developing area of genomics is..metagenomics!

34 Metagenomics entails the direct cloning and sequencing of genomes from organisms with unknown or impractical cultivation conditions. Examples of some sources of DNA for metagenomic studies: Obligate pathogens or symbionts Mixed microbial populations in environmental samples Extinct organisms (paleogenomics)

35 Tringe & Rubin (2005) Nature Rev. Genet. 6, 805.

36 Tringe & Rubin (2005) Nature Rev. Genet. 6, 805.