Greg Phillips Veterinary Microbiology gregory@iastate.edu.

Slides:

Advertisements

Similar presentations

High throughput sequencing Barbera van Schaik

Advertisements

Schulich School of Medicine & Dentistry The University of Western Ontario London Regional Genomics Centre Next Generation Sequencing Meeting April 1, 2010.

The Past, Present, and Future of DNA Sequencing

The Good, Bad, and Ugly of Next-Gen Sequencing

 Sequencing technology › Roche/454 GS-FLX (‘454’) › Illumina  Prokaryotic profiling › De novo genome sequencing › Metagenomics › SNP profiling › Species.

Next–generation DNA sequencing technologies – theory & practice

High-Throughput Sequencing Technologies

Next-generation sequencing

The 454 and Ion PGM at the Genomics Core Facility Dr. Deborah Grove, Director for Genetic Analysis Genomics Core Facility Huck Institutes of the Life Sciences.

Next-generation sequencing – the informatics angle Gabor T. Marth Boston College Biology Department AGBT 2008 Marco Island, FL. February

What Is Genomics? Genomics is the study of how the entire genome of a species functions as a unit and evolves over time. It is the study of life’s blueprint,

Reference books: Molecular Biology of the Cell, 4th edition, by B. Alberts et al., Molecular Cell Biology, 5th edition, by H. Lodish et al., 2004.

Next-generation sequencing and PBRC. Next Generation Sequencer Applications DeNovo Sequencing Resequencing, Comparative Genomics Global SNP Analysis Gene.

Transcriptomics Jim Noonan GENE 760.

Next-generation sequencing: informatics & software aspects Gabor T. Marth Boston College Biology Department.

The SOLiD System: Next-Generation Sequencing Overview of the SOLiD System –  Scalable  Accurate Ultra High Throughput  Flexible  Mate Pairs.

CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Quality of assemblies—mouse N50 contig length Terminology: N50 contig length If we sort.

Next-generation sequencing: informatics & software aspects Gabor T. Marth Boston College Biology Department.

$399 Personal Genome Service $2,500 Health Compass service $985 deCODEme (November 2007) (April 2008) $350,000 Whole-genome sequencing (November 2007)

CS273a Lecture 1, Autumn 10, Batzoglou DNA Sequencing.

BME 130 – Genomes Lecture 4 Sequencing technology II Next generation sequencing.

Informatics for next-generation sequence analysis – SNP calling Gabor T. Marth Boston College Biology Department PSB 2008 January

High Throughput Sequencing

RNA-Seq Sebastian Groß  Why transcriptomics?  RNA-Seq: a revolutionary tool for transcriptomics  RNA-Seq benefits and comparison with other.

Department of Bioinformatics and Computational Biology

CS 6293 Advanced Topics: Current Bioinformatics

Next Generation DNA Sequencing Platforms: Evolving Tools for

GENOME SEQUENCING. I. Genome sequencing The Sanger Method (1977) Denaturation +priming Polymerization.

Next generation sequencing platforms Applications

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

Next Now-Generation Genomics: methods and applications for modern disease research Aaron J. Mackey, Ph.D. Center for Public Health.

High-Throughput Sequencing Technologies

Introduction to Next-Generation Sequencing

Sequencing Technologies

Mapping protein-DNA interactions by ChIP-seq Zsolt Szilagyi Institute of Biomedicine.

Molecular Microbial Ecology

The virochip (UCSF) is a spotted microarray. Hybridization of a clinical RNA (cDNA) sample can identify specific viral expression.

H = -Σp i log 2 p i. SCOPI Each one of the many microbial communities has its own structure and ecosystem, depending on the body environment it exists.

Introduction to next generation sequencing Rolf Sommer Kaas.

Genomics and High Throughput Sequencing Technologies: Applications Jim Noonan Department of Genetics.

Next Generation Sequencing and its data analysis challenges Background Alignment and Assembly Applications Genome Epigenome Transcriptome.

High throughput sequencing: informatics & software aspects Gabor T. Marth Boston College Biology Department BI543 Fall 2013 January 29, 2013.

Chromatin Immunoprecipitation DNA Sequencing (ChIP-seq)

I519 Introduction to Bioinformatics, Fall, 2012

Stratton Nature 45: 719, 2009 Evolution of DNA sequencing technologies to present day DNA SEQUENCING & ASSEMBLY.

How will new sequencing technologies enable the HMP? Elaine Mardis, Ph.D. Associate Professor of Genetics Co-Director, Genome Sequencing Center Washington.

SEQUENCING – THE BENCHTOPS. Roche 454 Junior Same technology as 454 FLX Read length: 400 bases Paired-end 100,000 reads 12 hours (instrument time) Output.

Anna Shcherbina Bioinformatics Challenge Day 01/10/2013 De novo assembly from clinical sample This work is sponsored by the Defense Threat Reduction Agency.

GigAssembler. Genome Assembly: A big picture

Lecture-5 ChIP-chip and ChIP-seq

Next-generation sequencing: the informatics angle

Next-generation sequencing: the informatics angle Gabor T. Marth Boston College Biology Department CHI Next-Generation Data Analysis meeting Providence,

Next Generation Sequencing Lenka Veselovská Laboratory of Developmental Biology and Genomics.

DNA Sequencing Technology and its Applications in Evolution Research Julie Urban, Ph.D. Assistant Director, Genomics & Microbiology Laboratory NC Museum.

Third Generation Sequencing. Today Illumina – Solexa sequencing technology 454 Life sciences – 454 sequencer Applied Biosystem – SOLiD system Tomorrow.

Introduction to Illumina Sequencing

BME 130 – Genomes Lecture 4 Sequencing technology II Next generation sequencing.

Next-generation sequencing technology

Next generation sequencing

Dr. Christoph W. Sensen und Dr. Jung Soh Trieste Course 2017

Analysis of genomes and transcriptomes using ChIP-seq and RNA-seq

Next-generation sequencing technology

High-throughput sequencing techniques

H = -Σpi log2 pi.

ULTRASEQUENCING. Next Generation Sequencing: methods and applications.

Sequencing techniques

Next-generation DNA sequencing

Introduction to Sequencing

General overview of the bioinformatic pipelines for the 16S rRNA gene microbial profiling and shotgun metagenomics. General overview of the bioinformatic.

Presentation transcript:

Greg Phillips Veterinary Microbiology gregory@iastate.edu

Next Generation DNA Sequencing Review of DNA sequencing technology 3 Next Gen platforms-technology (and advertising) New applications of Next Gen technology Next Next Gen technology $1,000 genome

The First Generation- Sanger DNA Sequencing

Sanger DNA Sequencing by Capillary Electrophoresis & Fluorescent Detection Long read length >1000 bp)

Traditional Applications of DNA Sequencing Gene sequencing New gene discovery Mutations (natural variants & synthetic) Genome sequencing New genomes (microbial to human) Comparative genomics Metagenomics Environmental samples of mixed populations

Shotgun Sequencing Approach

Next-Generation DNA Sequencing: 3 Platforms 454 (Roche) Pyrosequencing Medium read length (~500 bp) Illumina (Solexa) Sequencing by synthesis Short read sequencing (up to 100 bp) SOLiD (Applied Biosystems) Sequencing by ligations Short read sequencing (~35 bp)

Next-Generation DNA Sequencing Advantages/Disadvantages Depth of coverage of genome sequencing Sanger: 4-5x 454: >20x Illumina, SOLiD: up to 100x Library preparation less laborious Methods unique to each platform Lower cost VS. Shorter read lengths De novo sequence assembly difficult Lower accuracy in homopolymer tracts Large amount of data generated

454 Sequencing Technology Pyrosequencing Library Preparation Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

454 Sequencing Technology Amplification Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

454 Sequencing Technology Sequencing Reaction Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

454 Sequencing Technology Detection

Roche/454 DNA Sequencing Pyrosequencing

Illumina Sequencing Technology Sequencing by Synthesis Library Preparation Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

Illumina Sequencing Technology Bridge Amplification Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

Illumina Sequencing Technology Detection Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

Illumina Sequencing Technology

ABI/SOLiD DNA Sequencing Technology Sequencing by ligation Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

ABI/SOLiD DNA Sequencing Technology Sequencing by ligation Mardis. 2008. Annu. Rev. Genomics Human Genet. 9:387.

ABI/SOLiD DNA Sequencing Technology

Characteristics of New DNA Sequencing Technology Rothberg &Leamon. 2008. Nat. Biotechnol. 26:1117

New DNA Sequencing Technology is Well-Suited for Microbial Genomes

Next-Generation DNA Sequencing- Applications Genome sequencing Short read de novo assembly requires new bioinformatic tools Genome resequencing of mutants Metagenomics …the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species -Chen, K; Pachter L (2005). . PLoS Comp Biol 1: 24.

Next Gen Sequencing & Metagenomics • Microbial communities in a natural environment Seawater Soil • Host-associated microbial communities Human microbiome Gut Oral cavity • Microbial communities in a “managed-environment” Sewage treatment plant Aquaculture facility

Next-Generation DNA Sequencing- More Applications RNA-seq Transcriptional profiling Consensus sequencing ChIP sequencing Chromatin immunoprecipitation Identification of protein binding sites Small RNA-seq Epigenetics

Next-Generation DNA Sequencing RNA-seq Marguerat, et al. 2008. Biochem. Soc. Trans. 36: 1091–1096.

Next-Generation DNA Sequencing ChIP-seq Chromatin immunoprecipitation

Next-Generation DNA Sequencing Small RNA-seq Animals/Plants/Bacteria encode small, non-coding RNAs that function in: Gene regulation Antiviral defense mechanisms Development Unknown functions

Next-Generation DNA Sequencing Epigenetics

The Next-Next Generation- Helicos Single Molecule DNA Sequencing

The Next-Next Generation- Helicos Single Molecule DNA Sequencing

Single Molecule DNA Sequencing- Pacific Biosciences http://www.pacificbiosciences.com/video_lg.html Eid et al. 2009 Science

Nanopore DNA Sequencing http://www.nanoporetech.com/sequences/index/34

What do YOU think?