The impact of next-generation sequencing technology of genetics Elaine R. Mardis – 11 February Washington School of Medicine, Genome Sequencing Center. Presented by Jacob Juhn

“If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up.” -Elaine R. Mardis

Overview Next Generation Instruments -Roche (454) GS FLX sequencer -Illumina genome analyzer -Applied Biosystems SOLiD sequencer Mutation Discover Sequencing clinical isolates in strain-to-reference sequences Enabling metagenomics Regulatory protein binding

Overview Exploring chromatic packaging Future Challenges Concluding Remarks

Preface Dideoxynucloetide sequencing of DNA major changes Cost per reaction of DNA sequencing Fallen / Moore’s Law (Especially over last 5 years) High-throughput DNA sequencing performed by “handful” of sites :

Preface – next generation instruments New sequencing instruments revolutionizing genetics. Process millions of sequence reads in parallel rather than 96 at a time. Fragment libraries not subject to vector-based cloning and Escherichia coli-based amplification stages The workflow to produce next-generation sequence- ready libraries is straight foward

Preface – next generation instruments Relatively little input DNA needed for library Produce shorter read lengths (*35-250bp) compared to capillary sequencers ( bp) Accuracy of their sequencings and quality values not understood Labs underway to benchmark relative to capillary electrophoresis *Depending on platform

Roche (454) GS FLX sequencer

Introduced in 2004 ‘Pyrosequencing’ – pyrophosphate molecule released on nucleotide incorporation by DNA polymerase Reactions produce light from cleavage of oxyluciferin by luciferase DNA strands amplified en masse by emulsion PCR

Roche (454) GS FLX sequencer Emulsion PCR use mixed oil/aqueos mixture to isolate agarose beads Has unique DNA fragment, aqueous micelles contain PCR reactants Pipetting micelles in microtiter plate / performing temperature cycle, >1,000,000 sequence 454 beads produced in matter of hours! Several thousands added to 454 picotiter plate Picotiter plate placed in genomic sequencer

Roche (454) GS FLX sequencer

Single nucleotide pattern match sequences of four nucleotide, enables 454 software calibrate light emitted. Signals recorded during the run for each reporting bead position on PTP are translated into a sequence Several quality-checking steps remove poor quality sequences

Roche (454) GS FLX sequencer

Illumina genome analyzer Introduced in 2006 Concept of ‘sequencing by synthesis’ (SBS) Produce ~32-40bp from tens of millions of surface amplified DNA fragments

Illumina genome analyzer

Applied Biosystems SOLiD sequencer

Commercial release in October 2007 Unique sequencing catalyzed by DNA ligase Sequencing by Oligo Ligation and Detection ~5 days to run / produces 3-4Gb Average read length of 25-35bp

Applied Biosystems SOLiD sequencer

Comparison

Mutation Discovery Old ways used PCR to amplify genomic regions Roche sequencer detect rare variants / alleviate noisy capillary sequence data 10,000 human exons using primers / parallel approach Significantly faster and less expensive Single Illumina run found Caenorhabditis elegans

Clinical Isolates DNA sequence library from single genomic fragment Conventional method long process HIV clinical isolate Campylobacter jejuni Mycobacterium tuberculosis

Enabling metagenomics Sequencing DNA from uncultured, unpurified microbial and/or viral population “Who’s there?” Cost too high with conventional capillary platforms Symbiotic microbes ‘human microbiome’ characterize with next- generation sequencing Roche used in process

Regulatory protein binding Chromatin immunoprecipitation (ChIP) Old method replaced by next-generation Both methods complementary in application ChIP likely to contribute significantly to how protein binding sites are regulated

Exploring chromatin packaging How genomic DNA packaged into histones 454-based study for C. elegans genome ChIP-seq w/Solexa technology Combining techniques to further explore possibilties

Future challenges Human genome / Hap-MAP Little known below phenotype level Re-sequence using next-generation ChIP-seq / ncRNA increase knowledge of genome variability

Concluding remarks Sequence-based genomes relatively young pursuit Fundamental knowledge being enhanced Time and ingenuity will determine boundaries