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The History of DNA Sequencing Technology. ARC Biotechnology Platform Dr Jasper Rees

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Presentation on theme: "The History of DNA Sequencing Technology. ARC Biotechnology Platform Dr Jasper Rees"— Presentation transcript:

1 The History of DNA Sequencing Technology

2 ARC Biotechnology Platform Dr Jasper Rees

3 ARC Biotechnology Platform In 2010, the ARC set out to create a new single integrated platform for advanced high throughput, next generation technologies Dr Jasper Rees

4 Vision To create a world class biotechnology platform to lead research in agriculture in Africa

5 Mission To provide excellent biotechnology research and service platforms to enhance food security and promote agriculture in Africa To provide biotechnology tools in support of all areas of research and development within the mission of the ARC To create a world class research and innovation environment to attract the best researchers and students To train the next generation of specialist researchers in cutting edge biotechnologies

6 The Objectives To create Service, Development and Research structures in support of and in collaboration with all ARC Institutes and external partners To address the needs of commercial and emerging agriculture nationally and continentally To train new researchers and postgraduates at the highest level To compete at the top level internationally To have the “best in class” resources for modern biotechnology To raise funds external funding, nationally and internationally

7 Service and Research Facilities Model Core Services Development group Research teams within platform Unit Research teams at Institutes Technology Focus of Unit Key technologies being performed with the sub-platform as services to research groups and pipelines with the ARC and to outside clients Each sub-platform to have a development group responsible for introducing new technology and applications into the core services Internal Research teams, lead by SR, SpR, PR level scientists. With MSc, PhD and PD level students as the major part of each team. Primarily externally funded with competitive grants External Research teams, led by SR, SpR, PR level scientists. MSc, PhD and PD level students are the major part of each team. Primarily externally funded with competitive grants

8 Biotech Platform Phase I – 2010/11 DNA Isolation Next Gen Sequencing Genotyping Genetic Mapping DNA Isolation Next Gen Sequencing Genotyping Genetic Mapping Development group Research teams within platform Genomics Sample Preparation 2D PAGE MALDI-MS LC/GC-MS-MS Sample Preparation 2D PAGE MALDI-MS LC/GC-MS-MS Development group Research teams within platform Proteomics Databases Annotation Assembly Expression Analysis Databases Annotation Assembly Expression Analysis Development group Research teams within platform Bioinformatics Tissue Culture Construct development Transformation Regeneration Tissue Culture Construct development Transformation Regeneration Development group Research teams within platform Plant Transformation

9 Biotech Platform Phase II/III: Reverse Genetics Gene identification Vector Development Construct development Reverse Genetics Gene identification Vector Development Construct development Functional Genomics Robotic platform High throughput DNA Isolation Genotyping Informatics Mutation Breeding Robotic platform High throughput DNA Isolation Genotyping Informatics Mutation Breeding Marker Assisted Breeding Robotic platform High throughput imaging and sensing GC MS/MS Informatics Robotic platform High throughput imaging and sensing GC MS/MS Informatics Plant Phenotyping Gene Silencing Zinc Finger Nucleases Gene targeting Male Sterile Technology Targeted Mutagenesis Gene Silencing Zinc Finger Nucleases Gene targeting Male Sterile Technology Targeted Mutagenesis Genome Engineering

10 Platforms and Programs Drought Tolerant Sorghum Apple Breeding Vaccine Development Animal Reproductive Biotechnologies Diagnostics Genomics11121 Proteomics12221 Bioinformatics11121 Plant Transformation 23 Functional Genomics 233 Genome Engineering 343 Imaging12 NanoBiotechnology2 Protein Expression22

11 ARC Biotech Platform Implementation 2010/11 Staff recruitment – 6 researchers team leaders in genomics, proteomics, bioinformatics; 3 more posts in 2011, more in the future. >25 postgraduate and postdoctoral researchers already Capital equipment procurement: >R10m to date Sites in Pretoria and Stellenbosch Building renovations in progress Operational start: Jan 2011

12 ARC Biotech Platform Implementation 2010/11 Staff recruitment – 6 researchers team leaders in genomics, proteomics, bioinformatics; 3 more posts in 2011 Jasper Rees: Genomics and Bioinformatics: Fruit Bongani Ndimba: Proteomics: Cereals and Fruit Damaris Odeny; Genetics, Genomics: Vegetables Joseph Mafofo: Genomics, plant pathogens: Fruit Dirk Swanevelder: Genomics: Plant Pests, Cereals Farai Muchadeyi: Genotyping: Animal Genetics

13 Genomics Applications Sequencing applications Genomes, De novo and re-sequencing SNPs and CNV calling Transcriptomes, De novo and re-sequencing SNPs and splicing variation Expression profiling Small RNA discovery and expression analysis SNP applications GWAS Association Genetics SNP validation Candidate Genes Diversity studies

14 14 Platform Synergy for Agrigenomics Research HiSeq 2000 iScan/HiScan SQ BeadXpress InterrogateValidate/ScreenDiscover ► De novo Genome Sequencing ► mRNA Sequencing & Gene Expression ► SNP Discovery ► DNA Methylation, Targeted Resequencing Applications Platform ► Genome-wide marker / phenotype association ► Focused marker / phenotype association ► Genetic Identity Confirmation ► QTL Mapping Disease Screening ► Marker Assisted Selection ► Parentage / Lineage ► Genetic Purity Screening ► >10 9 Discovery Focused Research/Validation Screening Whole Genome Single Marker

15 15 Illumina HiScanSQ Platform Dual function system SNPs and Sequencing High throughput SNPs Infinium and GoldenGate technology 10k to 2.5M SNP chips Next Generation Sequencing Linear scanning optics 100 Gb of DNA sequence per run Paired end sequencing 400 M filtered clusters per flow cell 8 lanes per flow cell Sample Multiplexing

16 DNA ( ug) Single molecule array Sample preparation Cluster growth 5’ 3’ G T C A G T C A G T C A C A G T C A T C A C C T A G C G T A G T Image acquisition Base calling T G C T A C G A T … Sequencing Illumina Sequencing Technology

17 17 Unravel 20 whole transcriptomes In four days Profile 200 gene expression samples In less than two days Analyze two human methylomes In one week Sequence one cancer & one normal genome At 30x coverage What if, in one sequencing run you could… One Sequencing Run SIMULTANEOUSLY Run multiple applications requiring different read lengths Whole genome sequencing Targeted resequencing Gene expression Whole transcriptome ChIP-seq Metagenomics De novo Methylation

18 18 Focused Genotyping HumanCVD BeadChip BovineSNP50 BeadChip CanineSNP20 BeadChip CanineHD BeadChip EquineSNP50 BeadChip OvineSNP50 BeadChip PorcineSNP60 BeadChip MaizeSNP50 BeadChip iSelect Custom Panel Infinium BeadChips

19 19 Custom Genotyping Infinium iSelect HD Interrogate virtually any SNP for any species 24-sample format (3,000 to 68,000 attempted bead types) 12-sample format (68,001 to 200,000 attempted bead types) Custom GoldenGate Genotyping Panels Create assays tailored directly to their specific needs for targeted region genotyping or fine-mapping of candidate disease association regions. Interrogate 96, or from 384 to 1,536, SNP loci simultaneously GoldenGate Indexing v1 Kit Screen up to 16 times as many samples per reaction as the standard GoldenGate Assay Increase throughput from 288 samples per day to greater than 2000, while decreasing total reagent consumption. Current plexity ranges for GoldenGate Indexing include 96-plex, 192-plex, and 384- plex. The GoldenGate Indexing Assay is conveniently processed on the Universal-32 BeadChip

20 The Rosaceae – Fruits, Nuts and Flowers

21 Rosaceae BeadChips Roscaeae BeadChip – SA and NZ working in collaboration with RosBREED –Using around 9,000 SNPs per species –Apple, Peach, Cherry, Strawberry –SNPs are from founders of major breeding programs and novel cultivars –Optimised for cultivated populations as opposed to wild crosses –Available March 2011

22 22 Customize HiScanSQ To Meet Your Needs – Now or Later SPLs: Samples HumanOmniExpress 12 sample BeadChips. Throughput varies by BeadChip For illustration purposes only – consult your rep to discuss your expected sample throughput. Assumptions: 6 Gb/day sequencing output. Manual sample processing: 1 HiScan, 0 Autoloader2.x, 0 Tecan liquid handling robots, 5 day work week; 2 FTEs. Automated sample processing: 5 day work week; 24 hour scanning powered by 1 AutoLoader2.x, 1 Tecan liquid handling robot.

23 23 Predictions Cost per data point will continue dramatic reduction for both Arrays and Sequencing Sequencing output will scale quickly Array content and complexity will increase significantly Sample numbers for projects will grow Sequencing and array solutions will continue to co-exist and complement Cost, Complexity and Complementary Solutions

24 ARC Biotech Platform Implementation The First Genomes First genome sequencing: March 2011 Apple, pear, aphid, tick, amaranth, heartwater, avian paramyxovirus (15 apple genomes resequenced in 2010) First major genotyping experiments, from May 2011 Apple (RosBREED - USA) Peach (ARC) Cattle (ARC) Sheep (US, ARC)

25 Agric-Biotech Smart Tools Rapid characterization of novel genomes (plants, animals, pathogens) Gene expression and genotyping technologies Molecular Breeding for rapid crop and animal improvement: –Genome-wide selection –Marker assisted selection Tissue Culture and micro-propagation of plants Cis-genesis and Genome Engineering Reproductive biotechnologies Vaccines, therapeutic proteins, diagnostics

26 Impact on Agricultural Research and Development Faster, better, more selective and more sensitive: –Plant Breeding –Animal Breeding –Cultivar identification (PBR) –Pathogen identification –Diagnostics –Vaccine development –Vaccine quality control and safety Bringing better crops and animals to farmer at all scales Bringing novel, cash generating, sustainable products to the market Increasing food and income security

27 ARC: BP – the 5 year horizon By 2015, The ARC Biotech Centre will be a vibrant Agri- Biotech institution – a Centre of Excellence in research, training and services with National and International standing Regional integration of services and research Training of new generation of researchers and postgraduates Implementation of high throughput systems for applied and basic research Increased funding and collaborative opportunities

28 Thank you Dr Jasper Rees


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