Functional Genomics Research Stream. Research Meetings: November 2 & 3, 2009 Next Generation Sequencing

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1 Functional Genomics Research Stream Research Meetings: November 2 & 3, 2009 Next Generation Sequencing

2 Current Issues Research Meetings: Meet with me this Thursday or Friday. (bring laboratory notebook - updated) RT Protocol Changes: Print and use new protocol. Cell Synchrony: Alpha factor mostly functional. Issues?

3 Recommended: Next Generation Reviews Shendure and Ji. Next-generation DNA sequencing. Nat Biotechnol (2008) vol. 26 (10) pp Mardis. Next-generation DNA sequencing methods. Annual review of genomics and human genetics (2008) vol. 9 pp Ansorge. Next-generation DNA sequencing techniques. N Biotechnol (2009) vol. 25 (4) pp Important: will need significant background in final report.

4 History: Sanger Sequencing With high-throughput shotgun Sanger sequencing, genomic DNA is fragmented, then cloned to a plasmid vector and used to transform E. coli. For each sequencing reaction, a single bacterial colony is picked and plasmid DNA isolated. Each cycle sequencing reaction takes place within a microliter-scale volume, generating a ladder of ddntp-terminated, dye-labeled products, which are subjected to high-resolution electrophoretic separation within one of 96 or 384 capillaries in one run of a sequencing instrument. As fluorescently labeled fragments of discrete sizes pass a detector, the four-channel emission spectrum is used to generate a sequencing trace. Shendure and Ji. Next-generation DNA sequencing. Nat Biotechnol (2008) vol. 26 (10) pp

5 Current: Cyclic Array Methods In shotgun sequencing with cyclic-array methods, common adaptors are ligated to fragmented genomic DNA, which is then subjected to one of several protocols that results in an array of millions of spatially immobilized PCR colonies or polonies. Each polony consists of many copies of a single shotgun library fragment. As all polonies are tethered to a planar array, a single microliter-scale reagent volume (e.g., for primer hybridization and then for enzymatic extension reactions) can be applied to manipulate all array features in parallel. Similarly, imaging-based detection of fluorescent labels incorporated with each extension can be used to acquire sequencing data on all features in parallel. Successive iterations of enzymatic interrogation and imaging are used to build up a contiguous sequencing read for each array feature. Shendure and Ji. Next-generation DNA sequencing. Nat Biotechnol (2008) vol. 26 (10) pp

6 Advantages In vitro construction of a sequencing library, followed by in vitro clonal amplification to generate sequencing features (as compared to in vivo Sanger methods). Enables a much higher degree of parallelism than conventional capillary-based sequencing. Enzymatic manipulation by a single reagent volume. Lower cost per base-pair of sequence. Disadvantages Read length (much shorter). Raw accuracy (1/10th).

7 Three Major Platforms Roche/454 FLX Illumina/Solexa Genome Analyzer Applied Biosystems (ABI) SOLiD System (next week)

8 Roche/454 FLX Utilizes pyrosequencing and emulsion PCR: Each incorporation of a nucleotide by DNA polymerase results in the release of pyrophosphate, which initiates a series of downstream reactions that ultimately produce light by the firefly enzyme luciferase. Mardis. Next-generation DNA sequencing methods. Annual review of genomics and human genetics (2008) vol. 9 pp

9 Pyrosequencing sheds light on DNA sequencing. Genome Res Jan;11(1):3-11.

10 The method used by the Roche/454 sequencer to amplify singlestranded DNA copies from a fragment library on agarose beads. A mixture of DNA fragments with agarose beads containing complementary oligonucleotides to the adapters at the fragment ends are mixed in an approximately 1:1 ratio. The mixture is encapsulated by vigorous vortexing into aqueous micelles that contain PCR reactants surrounded by oil, and pipetted into a 96-well microtiter plate for PCR amplification. The resulting beads are decorated with approximately 1 million copies of the original single-stranded fragment, which provides sufficient signal strength during the pyrosequencing reaction that follows to detect and record nucleotide incorporation events. sstdna = single-stranded template DNA. Mardis. Next-generation DNA sequencing methods. Annual review of genomics and human genetics (2008) vol. 9 pp

11

12 Sequencing is performed in picotiter plate (PTP). Enzyme containing beads surround template bead. Each well acts as a flow cell with nucleotide addition, imaging and wash steps.

13 Roche/454 FLX Strengths & Weaknesses Weakness: Homopolymers: (consecutive instances of the same base) The length of all homopolymers must be inferred from the signal intensity. Strength: Read Length: 200 to 300 base-pairs. Weakness: Cost per base-pair much higher. Shendure and Ji. Next-generation DNA sequencing. Nat Biotechnol (2008) vol. 26 (10) pp

14 Illumina/Solexa Genome Analyzer The Illumina sequencing-by-synthesis approach. Cluster strands created by bridge amplification are primed and all four fluorescently labeled, 3 -OH blocked nucleotides are added to the flow cell with DNA polymerase. The cluster strands are extended by one nucleotide. Following the incorporation step, the unused nucleotides and DNA polymerase molecules are washed away, a scan buffer is added to the flow cell, and the optics system scans each lane of the flow cell by imaging units called tiles. Once imaging is completed, chemicals that effect cleavage of the fluorescent labels and the 3 -OH blocking groups are added to the flow cell, which prepares the cluster strands for another round of fluorescent nucleotide incorporation. Mardis. Next-generation DNA sequencing methods. Annual review of genomics and human genetics (2008) vol. 9 pp

15 Mardis. Next-generation DNA sequencing methods. Annual review of genomics and human genetics (2008) vol. 9 pp

16 Illumina Genome Analyzer Workflow: Similar fragmentation and adapter ligation steps take place (I), before applying the library onto the solid surface of a flow cell. Attached DNA fragments form ʻbridgeʼ molecules which are subsequently amplified via an isothermal amplification process, leading to a cluster of identical fragments that are subsequently denatured for sequencing primer annealing (II). Amplified DNA fragments are subjected to sequencing-by-synthesis using 30 blocked labelled nucleotides (III). Weakness: Read Length Ansorge. Next-generation DNA sequencing techniques. N Biotechnol (2009) vol. 25 (4) pp

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