Objectives. The Evolution of Sequencing. The How and Why of Next Generation Sequencing in Personalized Medicine 10/2/2016. Whole Genome Sequencing

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1 The How and Why of Next Generation Sequencing in Personalized Medicine Pat Tille Ph.D. MLS(ASCP) FACSc SDSU Program Director ASCLS Region V Director This is a printable version, that does not contain presentation color graphics. Objectives Describe the overall application of NGS to predictive and personalized medicine List strengths and weaknesses of NGS Describe the overall difference of NGS in comparison to the traditional implementation of a laboratory test Whole Genome Sequencing Whole genome sequencing provides information about coding and noncoding parts of a genome. To identify important pathways. For evolutionary studies and species comparison. For more effective personalized medicine (why a drug works for person X and not for Y). Disease-susceptibility prediction based on gene sequence variation. The Evolution of Sequencing Maxim-Gilbert Sequencing Sanger Dideoxy Sequencing Slab-gel electrophoresis Capillary electrophoresis Shot gun sequencing High-through put sequencing 1

2 The History of Sequencing Allan Maxim and Walter Gilbert developed an important method of DNA sequencing in This method of chemical modification of DNA was technically complex and used extensive hazardous chemicals. Difficulties with scale-up. Sanger Sequencing Sanger developed the chain-termination method of DNA sequencing in Method was used for fairly short strands (100 to 1000 base pairs) and longer sequences were subdivided into smaller fragments. The small fragments were then subsequently re-assembled into the overall sequence Shotgun Sequencing Shotgun sequencing was developed for sequencing of large fragments of DNA in DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method producing short reads. Shotgun sequencing led to full genome sequencing. Technical Challenges Removal of artifacts Genome assembly Annotation and validation of assembled genome 2

3 Next Generation Sequencing Technique Ion torrent Roche s 454 Illumina ABI s SOLiD Sequence full genome of an organism in a few days at a very low cost. Produce high throughput data in the form of short reads. Data (Mb per run) Time per run 1.5 Hrs 7 Hrs 9 Days 9 Days Read length 200 bp 400 bp 150 bp 75 bp Cost per Mb 5 $ $ 0.03 $ 0.04 $ NGS Implementation Bacteriophage fx174, was the first genome to be sequenced, a viral genome with only 5,368 base pairs (bp). First bacterial genome sequenced was Haemophilus influenza. The first nearly complete human genomes sequenced were J. Craig Venter's, James Watson's, a Han Chinese, a Yoruban from Nigeria, a female leukemia patient, and Seong- Jin Kim. Genome Annotation A process of attaching biological information to sequences (contigs or chromosomes). Consists of two main steps: - Identifying elements on genome a process called gene prediction (Structural annotation). Attaching biological information to these elements (Functional annotation). 3

4 Genome Annotation Structural annotation ORFs and their localization Gene structure Coding regions Location of regulatory motifs Functional annotation Biochemical function Biological function Involved regulation and interactions Expression EMULSION PCR Semi-conductor Sequencing Ion Torent LIBRARY PREPARATION Pyro Sequencing 454 POLONY PCR ON A SLIDE Sequencing by Ligation SOLiD Reversible Terminator Sequencing Illumina Technical Challenges High Complexity Errors in Amplification Contamination G-C Base Pair Bias Is every gene or target present in library (unampifiable) Secondary structures-read through Low quality DNA- extraction or other types of samples (Forensic, archealogical) Information Processing (supercomputing) Technical and Application Advantages Rapid sequencing Information available Pharmacogenomics Exome Sequencing Transcriptome Sequencing Applications beyond basic knowledge of sequences Third Generation Sequencing has no GC Bias, no library development, sequence RNA directly 4

5 Medical and Diagnostic Applications Genome Sequencing Denovo sequencing Resequencing Targeted resequencing Mitochondrial sequencing Mutation detection Amplicon sequencing Amplicon panels Transcript Expression Profiling RNA sequencing mirna sequencing Transcription Factor Binding Structural Variations Metagenomics Sequencing to the Laboratory Can next generation solve the problem or diagnostic questions? What application is needed? (Denovo versus exome or transcriptome or structural) What is the best platform? Technical differences? Do I need more than one? What about data analysis? Bioinformatics? Software? Free or purchase? Coverage? Implementation Coverage? How much of the genome is actually included? Multiple comparisons to result (1X versus 3X) Garbage in and Garbage out Contamination Sample degradation Mixed samples Control material Biobanks Statistical Accuracy 5

6 Quality Initiatives Next Generation Sequencing- Standardization of Clinical Testing (Nex- StoCT) Genetic Testing Reference Materials Coordination Program (GeT-RM) Quality Control Proficiency Testing Test Development and Validation Molecular Oncology Infectious Disease Inherited Diseases Pharmacogenetics 454 Sequencing / Roche GS Junior System GS FLX+ System Illumina (Solexa) HiSeq System Genome analyzer IIx MySeq Applied Biosystems - Life Technologies SOLiD5500 System SOLiD5500xl System Ion Torrent - Life Technologies Personal Genome Machine (PGM) Proton Helicos Helicos Genetic Analysis System Pacific Biosciences PacBio RS Oxford Nanopore Technologies GridION System MinION Laboratory Medicine is quickly evolving into the era of METAGENOMIC MEDICINE! 6