DNA-Sequenzierung. Technologien & Geräte

Size: px
Start display at page:

Download "DNA-Sequenzierung. Technologien & Geräte"

Transcription

1 DNA-Sequenzierung Technologien & Geräte

2 Genome analysis DNA sequencing platforms ABI 3730xl 4/2004 & 6/ Mb/day, 850 nt reads 2 Mb/day, 550 nt reads Roche/454 GS FLX 12/ Mb/7h, 350 nt reads 800 Gb/23h, 800 nt reads Illumina/Solexa GAIIx 12/2008 & 11/ Gb/14d, 2x150 nt reads HiSeq /2010 2x150 Gb/10d, 2x100 nt reads 2x300 Gb/10d, 2x100 nt reads

3 Moore s law Next Generation Sequencing - a game changer

4 NGS Terminology 2 nd generation = massively parallel 3 rd generation = true single-molecule

5 1 st Generation Maxam-Gilbert. Sanger. Pyro

6 Maxam-Gilbert sequencing Chemical modifications, radioactive *1977

7 Maxam-Gilbert sequencing Reactions Maniatis, 1989

8 Sanger sequencing Dideoxy chain termination, radioactive *1977 Fred Sanger Nobel prices 1958, 1980

9 Sanger sequencing Fluorescence labeling

10 Sanger sequencing Dye primer

11 Sanger sequencing Dye terminator

12 Sanger sequencing Dye primer vs. terminator DP DT

13 Sanger sequencing Engineered polymerase Thermo-Sequenase = Taq polymerase Phe>Thy mutated Tabor & Richardson, PNAS 92:6339 (1995)

14 Sanger sequencing Cycle sequencing

15 Pyrosequencing PPi ATP

16 Pyrosequencing datp S is used in the pyrosequencing reaction Luciferase does not use datp S as substrate O O = P O O O = P O S O P O O O A datp S OH H

17 Pyro-Sequenzierung Demo

18 2 nd Generation 454/Roche. Solexa/Illumina. Solid Ion Torrent. Complete Genomics

19 454 Genome Sequencer GS20/FLX/FLX+ A Revolutionary Method for Rapid Whole Genome Sequencing and Assembly And more..

20 454 Nature, July

21 454 Nature, July Mb 99% accuracy 4h de novo assembly Mycoplasma genitalium (0.58 Mb): 96% coverage, 99,96% accuracy 100x currant Sanger technology

22 454 Workflow

23 454 Preparation of A/B-fragments for sequencing dsdna fragments P Bio A P Ligation B Bio Fill in Bio Bio Bio Capture on SA-Beads & Wash Alkaline Elution A B

24 454 empcr

25 454 Sample loading

26 454 Flowgram

27 454 No cloning bias green reads red - Sanger reads black - GC content G+C % GC poor low-cloned coverage GC normal high-cloned coverage

28 454 Deep sequencing rare mutation detection T only C to T ratio: 1/500 Mutation Freq. Mutation Freq. Primer sequence Background subtracted 0.16% Coverage Coverage Primer sequence

29 Roche/454 Read length

30 Roche/454 Read length

31 Advanced genetic analysis one billion bases at a time

32 Solexa Technology Clonal Singe Molecule Array TM Sequencing By Synthesis (SBS) reversible fluorescent labels reversible 3 OH blocking

33 Solexa Linker ligation

34 Solexa Solid-phase clonal single molecule PCR Bridge amplification

35 Solexa Solid-phase clonal single molecule PCR 100μm colony of 1000 singlestranded DNA templates Single well of 454 Life Sciences PicoTiterPlate TM (to same scale)

36 Solexa Sequencing by synthesis (SBS) * removal of fluorescent labels & 3 OH blocking

37 Solexa Sequencing by synthesis (SBS) μm colony of 1000 singlestranded DNA templates

38 Solexa Assembly - Mapping read length: nt

39 Illumina/Solexa Paired ends & Mate pairs

40 Illumina/Solexa Multiplexing

41 Illumina/Solexa Applications Re-sequencing RNA-seq DigiTag-seq mirna-seq ChIP-seq Ribosome-footprinting

42 Illumina/Solexa Data output

43 ABI Agencourt SOLID

44 SOLID Bead deposition

45 SOLID Probes

46 SOLID 2-base encoding 16 dinucleotides / 4 dyes = 4 dinucleotides/dye

47 SOLID 4-color ligation

48 SOLID 4-color ligation

49 SOLID Detection

50 SOLID Cleavage

51 SOLID 2 nd cycle ligation

52 SOLID 2 nd cycle detection

53 SOLID 2 nd cycle cleavage + additional 3 ligation cyles

54 SOLID Reset after 5 th cycle

55 SOLID 6 th cycle ligation

56 SOLID Cycling scheme

57 SOLID 2-base encoding

58 SOLID Paired ends two sequences

59 SOLID Performance

60

61 Complete Genomics In-house technology self-assembling DNA nanoballs (DNB) patterned nanoarrays combinatorial probe anchor ligation (cpal) Drmanac et al. Science 327:78 (2009)

62 Complete Genomics Performance launched by mid : 2011: ~600 human genomes ~4,000 genomes end 2011: genomes/month mid 2012: new machines with 6 genomes/day end 2012: <3,000 $/genome

63 PGM - Personal Genome Machine

64 Ion Torrent The chip is the machine ionogram

65 Ion Torrent Read length

66 Ion Torrent Data output

67 Ion Torrent Post-light sequencing of Gordon Moore Nature 475:348 (2011)

68 3 rd Generation Helicos. Pacific Biosciences VisigGen. Nanopore(s)

69

70 Helicos First true single molecule sequencing (tsms)

71 Helicos Performance

72 Helicos DRS Nature 461:814 (2009)

73

74 Pacific Biosciences Technologogies

75 Pacific Biosciences Fluoreszensmarkierung

76 Pacific Biosciences Fluoreszensmarkierung

77 Pacific Biosciences Hintergrund-Rauschen

78 Pacific Biosciences Kleinstes Detektionsvolumen

79 Pacific Biosciences Immobilisierte Polymerase

80 Pacific Biosciences Immobilisierte Polymerase lange Sequenzen

81 Pacific Biosciences Template

82 Pacific Biosciences Error rate Tex

83 Pacific Biosciences Read length

84 Pacific Biosciences Real-time DNA methylation detection Tex Nature Methods 7:461 (2010)

85 Pacific Biosciences Epigenetics

86 Pacific Biosciences Direct RNA sequencing

87 Pacific Biosciences Translation

88 VisiGen Fluoreszens-Resonanz-Energie-Transfer (FRET) F-Donor : F-Akzeptor: Polymerase -Phosphat des dntp 1Mb/s >1 humanes Genom/Tag visigenbio.com

89 Nanopore Ion current Messwert Strom von K + -Ionen, die der DNA beim Porendurchtritt entgegen fließen

90 Nanopore Protein pore & exonuclease Clarke et al., Nature Nanotechnology 4:265(2009)

91 IBM Waver pore

92 genome.fli-leibniz.de Teaching Lectures

DNA-Sequencing. Technologies & Devices

DNA-Sequencing. Technologies & Devices DNA-Sequencing Technologies & Devices Genome analysis DNA sequencing platforms ABI 3730xl 4/2004 & 6/2006 1 Mb/day, 850 nt reads 2 Mb/day, 550 nt reads Roche/454 GS FLX 12/2006 800 Mb/23h, 800 nt reads

More information

DNA-Sequencing. Technologies & Devices

DNA-Sequencing. Technologies & Devices DNA-Sequencing Technologies & Devices Genome analysis DNA sequencing platforms ABI 3730xl 4/2004 & 6/2006 1 Mb/day, 850 nt reads 2 Mb/day, 550 nt reads Roche/454 GS FLX 12/2006 800 Mb/23h, 800 nt reads

More information

DNA-Sequencing. Technologies & Devices. Matthias Platzer. Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

DNA-Sequencing. Technologies & Devices. Matthias Platzer. Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) DNA-Sequencing Technologies & Devices Matthias Platzer Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Genome analysis DNA sequencing platforms ABI 3730xl 4/2004 & 6/2006 1 Mb/day,

More information

DNA-Sequencing. Technologies & Devices. Matthias Platzer. Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

DNA-Sequencing. Technologies & Devices. Matthias Platzer. Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) DNA-Sequencing Technologies & Devices Matthias Platzer Genome Analysis Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Genome analysis DNA sequencing platforms ABI 3730xl 4/2004 & 6/2006 1 Mb/day,

More information

Next Generation Sequencing (NGS)

Next Generation Sequencing (NGS) Next Generation Sequencing (NGS) Fernando Alvarez Sección Biomatemática, Facultad de Ciencias, UdelaR 1 Uruguay Montevide o 3 TANGO World Champ 1930 1950 (Maraca 4 Next Generation Sequencing module Next

More information

Matthew Tinning Australian Genome Research Facility. July 2012

Matthew Tinning Australian Genome Research Facility. July 2012 Next-Generation Sequencing: an overview of technologies and applications Matthew Tinning Australian Genome Research Facility July 2012 History of Sequencing Where have we been? 1869 Discovery of DNA 1909

More information

Overview of Next Generation Sequencing technologies. Céline Keime

Overview of Next Generation Sequencing technologies. Céline Keime Overview of Next Generation Sequencing technologies Céline Keime keime@igbmc.fr Next Generation Sequencing < Second generation sequencing < General principle < Sequencing by synthesis - Illumina < Sequencing

More information

Human genome sequence

Human genome sequence NGS: the basics Human genome sequence June 26th 2000: official announcement of the completion of the draft of the human genome sequence (truly finished in 2004) Francis Collins Craig Venter HGP: 3 billion

More information

Third Generation Sequencing

Third Generation Sequencing Third Generation Sequencing By Mohammad Hasan Samiee Aref Medical Genetics Laboratory of Dr. Zeinali History of DNA sequencing 1953 : Discovery of DNA structure by Watson and Crick 1973 : First sequence

More information

Next Generation Sequencing. Jeroen Van Houdt - Leuven 13/10/2017

Next Generation Sequencing. Jeroen Van Houdt - Leuven 13/10/2017 Next Generation Sequencing Jeroen Van Houdt - Leuven 13/10/2017 Landmarks in DNA sequencing 1953 Discovery of DNA double helix structure 1977 A Maxam and W Gilbert "DNA seq by chemical degradation" F Sanger"DNA

More information

Next generation sequencing techniques" Toma Tebaldi Centre for Integrative Biology University of Trento

Next generation sequencing techniques Toma Tebaldi Centre for Integrative Biology University of Trento Next generation sequencing techniques" Toma Tebaldi Centre for Integrative Biology University of Trento Mattarello September 28, 2009 Sequencing Fundamental task in modern biology read the information

More information

The Journey of DNA Sequencing. Chromosomes. What is a genome? Genome size. H. Sunny Sun

The Journey of DNA Sequencing. Chromosomes. What is a genome? Genome size. H. Sunny Sun The Journey of DNA Sequencing H. Sunny Sun What is a genome? Genome is the total genetic complement of a living organism. The nuclear genome comprises approximately 3.2 * 10 9 nucleotides of DNA, divided

More information

Introduction to Next Generation Sequencing (NGS)

Introduction to Next Generation Sequencing (NGS) Introduction to Next eneration Sequencing (NS) Simon Rasmussen Assistant Professor enter for Biological Sequence analysis Technical University of Denmark 2012 Today 9.00-9.45: Introduction to NS, How it

More information

Aaron Liston, Oregon State University Botany 2012 Intro to Next Generation Sequencing Workshop

Aaron Liston, Oregon State University Botany 2012 Intro to Next Generation Sequencing Workshop Output (bp) Aaron Liston, Oregon State University Growth in Next-Gen Sequencing Capacity 3.5E+11 2002 2004 2006 2008 2010 3.0E+11 2.5E+11 2.0E+11 1.5E+11 1.0E+11 Adapted from Mardis, 2011, Nature 5.0E+10

More information

Next Generation Sequencing Lecture Saarbrücken, 19. March Sequencing Platforms

Next Generation Sequencing Lecture Saarbrücken, 19. March Sequencing Platforms Next Generation Sequencing Lecture Saarbrücken, 19. March 2012 Sequencing Platforms Contents Introduction Sequencing Workflow Platforms Roche 454 ABI SOLiD Illumina Genome Anlayzer / HiSeq Problems Quality

More information

Genome Sequencing. I: Methods. MMG 835, SPRING 2016 Eukaryotic Molecular Genetics. George I. Mias

Genome Sequencing. I: Methods. MMG 835, SPRING 2016 Eukaryotic Molecular Genetics. George I. Mias Genome Sequencing I: Methods MMG 835, SPRING 2016 Eukaryotic Molecular Genetics George I. Mias Department of Biochemistry and Molecular Biology gmias@msu.edu Sequencing Methods Cost of Sequencing Wetterstrand

More information

Next Generation Sequencing. Simon Rasmussen Assistant Professor Center for Biological Sequence analysis Technical University of Denmark

Next Generation Sequencing. Simon Rasmussen Assistant Professor Center for Biological Sequence analysis Technical University of Denmark Next eneration Sequencing Simon Rasmussen Assistant Professor enter for Biological Sequence analysis Technical University of Denmark DNA Sequencing DNA sequencing Reading the order of bases in DNA fragments

More information

Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis

Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis 1 Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype

More information

Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis

Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis 1 Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype

More information

Opportunities offered by new sequencing technologies

Opportunities offered by new sequencing technologies Opportunities offered by new sequencing technologies Pierre Taberlet Laboratoire d'ecologie Alpine CNRS UMR 5553 Université Joseph Fourier, Grenoble, France Nature Biotechnology, October 2008: special

More information

Next-generation sequencing Technology Overview

Next-generation sequencing Technology Overview Next-generation sequencing Technology Overview UQ Winter School 2018 Christopher Noune, PhD AGRF Melbourne christopher.noune@agrf.org.au What is NGS? Ion Torrent PGM (Thermo-Fisher) MiSeq (Illumina) High-Throughput

More information

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Monday June 16, 2014

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Monday June 16, 2014 High Throughput Sequencing Technologies J Fass UCD Genome Center Bioinformatics Core Monday June 16, 2014 Sequencing Explosion www.genome.gov/sequencingcosts http://t.co/ka5cvghdqo Sequencing Explosion

More information

Sequencing technologies

Sequencing technologies Sequencing technologies part of High-Throughput Analyzes of Genome Sequenzes Computational EvoDevo University of Leipzig Leipzig, WS 2014/15 Sanger Sequencing (Chain Termination Method) Sequencing of one

More information

Concepts and methods in sequencing and genome assembly

Concepts and methods in sequencing and genome assembly BCM-2002 Concepts and methods in sequencing and genome assembly http://megasun.bch.umontreal.ca/papers/bcm-2002/sequencing-bcm2002-nov2015.pdf B. Franz LANG, Département de Biochimie Bureau: H307-15 Courrier

More information

Chapter 7. DNA Microarrays

Chapter 7. DNA Microarrays Bioinformatics III Structural Bioinformatics and Genome Analysis Chapter 7. DNA Microarrays 7.9 Next Generation Sequencing 454 Sequencing Solexa Illumina Solid TM System Sequencing Process of determining

More information

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Monday September 15, 2014

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Monday September 15, 2014 High Throughput Sequencing Technologies J Fass UCD Genome Center Bioinformatics Core Monday September 15, 2014 Sequencing Explosion www.genome.gov/sequencingcosts http://t.co/ka5cvghdqo Sequencing Explosion

More information

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

Functional Genomics Research Stream. Research Meetings: November 2 & 3, 2009 Next Generation Sequencing Functional Genomics Research Stream Research Meetings: November 2 & 3, 2009 Next Generation Sequencing Current Issues Research Meetings: Meet with me this Thursday or Friday. (bring laboratory notebook

More information

CSC Assignment1SequencingReview- 1109_Su N_NEXT_GENERATION_SEQUENCING.docx By Anonymous. Similarity Index

CSC Assignment1SequencingReview- 1109_Su N_NEXT_GENERATION_SEQUENCING.docx By Anonymous. Similarity Index Page 1 of 6 Document Viewer TurnitinUK Originality Report Processed on: 05-Dec-20 10:49 AM GMT ID: 13 Word Count: 1587 Submitted: 1 CSC8313-201 - Assignment1SequencingReview- 1109_Su N_NEXT_GENERATION_SEQUENCING.docx

More information

Research school methods seminar Genomics and Transcriptomics

Research school methods seminar Genomics and Transcriptomics Research school methods seminar Genomics and Transcriptomics Stephan Klee 19.11.2014 2 3 4 5 Genetics, Genomics what are we talking about? Genetics and Genomics Study of genes Role of genes in inheritence

More information

Outline. General principles of clonal sequencing Analysis principles Applications CNV analysis Genome architecture

Outline. General principles of clonal sequencing Analysis principles Applications CNV analysis Genome architecture The use of new sequencing technologies for genome analysis Chris Mattocks National Genetics Reference Laboratory (Wessex) NGRL (Wessex) 2008 Outline General principles of clonal sequencing Analysis principles

More information

DNA Sequencing by Ion Torrent. Marc Lavergne CHEM 4590

DNA Sequencing by Ion Torrent. Marc Lavergne CHEM 4590 DNA Sequencing by Ion Torrent Marc Lavergne CHEM 4590 OVERVIEW History DNA Synthesis and First-Gen Sequencing Technology Sequencing Signal Detection Advantages/Disadvantages Applications Current Research

More information

DNA and genome sequencing. Matthew Hudson Dept of Crop Sciences University of Illinois

DNA and genome sequencing. Matthew Hudson Dept of Crop Sciences University of Illinois DNA and genome sequencing Matthew Hudson Dept of Crop Sciences University of Illinois Genome projects 2,424 ongoing genome projects 696 for eukaryotes 520 completed genomes 47 from eukaryotes Almost every

More information

Ultrasequencing: methods and applications of the new generation sequencing platforms

Ultrasequencing: methods and applications of the new generation sequencing platforms Ultrasequencing: methods and applications of the new generation sequencing platforms Nuria Tubío Santamaría Course: Genomics Universitat Autònoma de Barcelona 1 Introduction Clasical methods of sequencing:

More information

NGS technologies: a user s guide. Karim Gharbi & Mark Blaxter

NGS technologies: a user s guide. Karim Gharbi & Mark Blaxter NGS technologies: a user s guide Karim Gharbi & Mark Blaxter genepool-manager@ed.ac.uk Natural history of sequencing 2 Brief history of sequencing 100s bp throughput 100 Gb 1977 1986 1995 1999 2005 2007

More information

THE SEQUENCING TECNOLOGY (R)EVOLUTION

THE SEQUENCING TECNOLOGY (R)EVOLUTION THE SEQUENCING TECNOLOGY (R)EVOLUTION TIM STAKENORG IMEC MB&C meeting May 16, 2013 IMEC 2013 HISTORY OF SEQUENCING 384-322 BC - Aristotle told his students that all inheritance comes from the father 1977

More information

High throughput sequencing technologies

High throughput sequencing technologies High throughput sequencing technologies and NGS applications Mei-yeh Lu 呂美曄 High Throughput Sequencing Core Manager g g p q g g Academia Sinica 6/30/2011 Outlines Evolution of sequencing technologies Sanger

More information

Next Gen Sequencing. Expansion of sequencing technology. Contents

Next Gen Sequencing. Expansion of sequencing technology. Contents Next Gen Sequencing Contents 1 Expansion of sequencing technology 2 The Next Generation of Sequencing: High-Throughput Technologies 3 High Throughput Sequencing Applied to Genome Sequencing (TEDed CC BY-NC-ND

More information

Potential for Diagnostic Application of New Sequencing Technologies. Chris Mattocks National Genetics Reference Laboratory (Wessex)

Potential for Diagnostic Application of New Sequencing Technologies. Chris Mattocks National Genetics Reference Laboratory (Wessex) Potential for Diagnostic Application of New Sequencing Technologies Chris Mattocks National Genetics Reference Laboratory (Wessex) Overview Technologies and platforms Applications Issues for diagnostic

More information

Nuts and bolts of phage genome sequencing. the 5 5 and 5 8 perspective. Allison Johnson & Anneke Padolina

Nuts and bolts of phage genome sequencing. the 5 5 and 5 8 perspective. Allison Johnson & Anneke Padolina Nuts and bolts of phage genome sequencing the 5 5 and 5 8 perspective Allison Johnson & Anneke Padolina Our role in DNA sequencing Rachel, do you want to get on the bus and take your sample to the sequencing

More information

A Crash Course in NGS for GI Pathologists. Sandra O Toole

A Crash Course in NGS for GI Pathologists. Sandra O Toole A Crash Course in NGS for GI Pathologists Sandra O Toole The Sanger Technique First generation sequencing Uses dideoxynucleotides (dideoxyadenine, dideoxyguanine, etc) These are molecules that resemble

More information

2/5/16. Honeypot Ants. DNA sequencing, Transcriptomics and Genomics. Gene sequence changes? And/or gene expression changes?

2/5/16. Honeypot Ants. DNA sequencing, Transcriptomics and Genomics. Gene sequence changes? And/or gene expression changes? 2/5/16 DNA sequencing, Transcriptomics and Genomics Honeypot Ants "nequacatl" BY2208, Mani Lecture 3 Gene sequence changes? And/or gene expression changes? gene expression differences DNA sequencing, Transcriptomics

More information

Sequence Assembly and Next Generation Sequencing Informatics CBPS7711

Sequence Assembly and Next Generation Sequencing Informatics CBPS7711 Sequence Assembly and Next Generation Sequencing Informatics CBPS7711 Oct 5, 2010 Sonia Leach, PhD Assistant Professor National Jewish Health sonia.leach@gmail.com Next Generation Sequencing Increasing

More information

BIOINFORMATICS 1 SEQUENCING TECHNOLOGY. DNA story. DNA story. Sequencing: infancy. Sequencing: beginnings 26/10/16. bioinformatic challenges

BIOINFORMATICS 1 SEQUENCING TECHNOLOGY. DNA story. DNA story. Sequencing: infancy. Sequencing: beginnings 26/10/16. bioinformatic challenges BIOINFORMATICS 1 or why biologists need computers SEQUENCING TECHNOLOGY bioinformatic challenges http://www.bioinformatics.uni-muenster.de/teaching/courses-2012/bioinf1/index.hbi Prof. Dr. Wojciech Makałowski"

More information

Next-Generation Sequencing. Technologies

Next-Generation Sequencing. Technologies Next-Generation Next-Generation Sequencing Technologies Sequencing Technologies Nicholas E. Navin, Ph.D. MD Anderson Cancer Center Dept. Genetics Dept. Bioinformatics Introduction to Bioinformatics GS011062

More information

Deep Sequencing technologies

Deep Sequencing technologies Deep Sequencing technologies Gabriela Salinas 30 October 2017 Transcriptome and Genome Analysis Laboratory http://www.uni-bc.gwdg.de/index.php?id=709 Microarray and Deep-Sequencing Core Facility University

More information

Next Generation Sequencing Technologies

Next Generation Sequencing Technologies Next Generation Sequencing Technologies What is first generation? Sanger Sequencing DNA Polymerase Base-adding reaction +H + http://chemwiki.ucdavis.edu/organic_chemistry/organic_chemistry_with_a_biological_emphasis/chapter_10%3a_phosphoryl_transfer_reactions/section_10.4%3a_phosphate_diesters

More information

Contact us for more information and a quotation

Contact us for more information and a quotation GenePool Information Sheet #1 Installed Sequencing Technologies in the GenePool The GenePool offers sequencing service on three platforms: Sanger (dideoxy) sequencing on ABI 3730 instruments Illumina SOLEXA

More information

Genome 373: High- Throughput DNA Sequencing. Doug Fowler

Genome 373: High- Throughput DNA Sequencing. Doug Fowler Genome 373: High- Throughput DNA Sequencing Doug Fowler Tasks give ML unity We learned about three tasks that are commonly encountered in ML Models/Algorithms Give ML Diversity Classification Regression

More information

Design. Construction. Characterization

Design. Construction. Characterization Design Construction Characterization DNA mrna (messenger) A C C transcription translation C A C protein His A T G C T A C G Plasmids replicon copy number incompatibility selection marker origin of replication

More information

Chapter 6 - Molecular Genetic Techniques

Chapter 6 - Molecular Genetic Techniques Chapter 6 - Molecular Genetic Techniques Two objects of molecular & genetic technologies For analysis For generation Molecular genetic technologies! For analysis DNA gel electrophoresis Southern blotting

More information

Executive Summary. Technologies

Executive Summary. Technologies First-generation DNA sequencing, dominated by the Sanger method, reached its peak with the introduction of automated capillary electrophoresis-based instruments, which facilitated the timely completion

More information

High throughput DNA Sequencing. An Equal Opportunity University!

High throughput DNA Sequencing. An Equal Opportunity University! High throughput DNA Sequencing An Equal Opportunity University! irst Generation DNA sequencing utilize chain terminator technologies (adaptation of Sanger sequencing) Adapt fluorescence chemistry, high-resolution

More information

Bio(tech) Interlude. 3 Nobel Prizes: PCR: Kary Mullis, 1993 Electrophoresis: A.W.K. Tiselius, 1948 DNA Sequencing: Frederick Sanger, 1980

Bio(tech) Interlude. 3 Nobel Prizes: PCR: Kary Mullis, 1993 Electrophoresis: A.W.K. Tiselius, 1948 DNA Sequencing: Frederick Sanger, 1980 Bio(tech) Interlude 3 Nobel Prizes: PCR: Kary Mullis, 1993 Electrophoresis: A.W.K. Tiselius, 1948 DNA Sequencing: Frederick Sanger, 1980 PCR 1: 25ºC G 2: 95ºC A 3: 60ºC T 5 3 A A G 3 G T C 5 T T T 6: 72ºC

More information

Welcome to the NGS webinar series

Welcome to the NGS webinar series Welcome to the NGS webinar series Webinar 1 NGS: Introduction to technology, and applications NGS Technology Webinar 2 Targeted NGS for Cancer Research NGS in cancer Webinar 3 NGS: Data analysis for genetic

More information

Sequencing techniques and applications

Sequencing techniques and applications I519 Introduction to Bioinformatics Sequencing techniques and applications Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Contents Sequencing techniques Sanger sequencing Next generation

More information

Application of NGS (next-generation sequencing) for studying RNA regulation

Application of NGS (next-generation sequencing) for studying RNA regulation Application of NGS (next-generation sequencing) for studying RNA regulation SAIHST, SKKU Sung Wook Chi In this lecturre Intro: Sequencing Technology NGS (Next-Generation Sequencing) Sequencing of RNAs

More information

Thema Gentechnologie. Erwin R. Schmidt Institut für Molekulargenetik Vorlesung #

Thema Gentechnologie. Erwin R. Schmidt Institut für Molekulargenetik Vorlesung # Thema Gentechnologie Erwin R. Schmidt Institut für Molekulargenetik Vorlesung #10 01. 07. 2014 Pyrosequenzierung The Pyrosequencing technology is a relatively new DNA sequencing method originally

More information

SEQUENCING TARU SINGH UCMS&GTBH

SEQUENCING TARU SINGH UCMS&GTBH SEQUENCING TARU SINGH UCMS&GTBH What is Sequencing???? Sequencing is a method for determining the order of the nucleotide bases Adenine, Guanine, cytosine, & thymine in a molecule of DNA. What is the purpose

More information

Introduction to NGS. Josef K Vogt Slides by: Simon Rasmussen Next Generation Sequencing Analysis

Introduction to NGS. Josef K Vogt Slides by: Simon Rasmussen Next Generation Sequencing Analysis Introduction to NGS Josef K Vogt Slides by: Simon Rasmussen 2017 Life science data deluge Massive unstructured data from several areas DNA, patient journals, proteomics, imaging,... Impacts Industry, Environment,

More information

Next Generation Sequencing. Josef K Vogt Slides by: Simon Rasmussen

Next Generation Sequencing. Josef K Vogt Slides by: Simon Rasmussen Next eneration Sequencing Josef K Vogt Slides by: Simon Rasmussen 2017 Second generation sequencing 454 Illumina 10 6-10 9 90% market share SOLiD Ion Torrent (PM) Library preparation 1.reate library molecules

More information

The Expanded Illumina Sequencing Portfolio New Sample Prep Solutions and Workflow

The Expanded Illumina Sequencing Portfolio New Sample Prep Solutions and Workflow The Expanded Illumina Sequencing Portfolio New Sample Prep Solutions and Workflow Marcus Hausch, Ph.D. 2010 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life, Oligator,

More information

INTRODUCCIÓ A LES TECNOLOGIES DE 'NEXT GENERATION SEQUENCING'

INTRODUCCIÓ A LES TECNOLOGIES DE 'NEXT GENERATION SEQUENCING' INTRODUCCIÓ A LES TECNOLOGIES DE 'NEXT GENERATION SEQUENCING' Bioinformàtica per a la Recerca Biomèdica Ricardo Gonzalo Sanz ricardo.gonzalo@vhir.org 14/12/2016 1. Introduction to NGS 2. First Generation

More information

Biochemistry 412. New Strategies, Technologies, & Applications For DNA Sequencing. 12 February 2008

Biochemistry 412. New Strategies, Technologies, & Applications For DNA Sequencing. 12 February 2008 Biochemistry 412 New Strategies, Technologies, & Applications For DNA Sequencing 12 February 2008 Note: Scale is wrong!! (at least for sequences) 10 6 In 1980, the sequencing cost per finished bp $1.00

More information

Application of NGS (nextgeneration. for studying RNA regulation. Sung Wook Chi. Sungkyunkwan University (SKKU) Samsung Medical Center (SMC)

Application of NGS (nextgeneration. for studying RNA regulation. Sung Wook Chi. Sungkyunkwan University (SKKU) Samsung Medical Center (SMC) Application of NGS (nextgeneration sequencing) for studying RNA regulation Samsung Advanced Institute of Heath Sciences and Technology (SAIHST) Sungkyunkwan University (SKKU) Samsung Research Institute

More information

Outline General NGS background and terms 11/14/2016 CONFLICT OF INTEREST. HLA region targeted enrichment. NGS library preparation methodologies

Outline General NGS background and terms 11/14/2016 CONFLICT OF INTEREST. HLA region targeted enrichment. NGS library preparation methodologies Eric T. Weimer, PhD, D(ABMLI) Assistant Professor, Pathology & Laboratory Medicine, UNC School of Medicine Director, Molecular Immunology Associate Director, Clinical Flow Cytometry, HLA, and Immunology

More information

The New Genome Analyzer IIx Delivering more data, faster, and easier than ever before. Jeremy Preston, PhD Marketing Manager, Sequencing

The New Genome Analyzer IIx Delivering more data, faster, and easier than ever before. Jeremy Preston, PhD Marketing Manager, Sequencing The New Genome Analyzer IIx Delivering more data, faster, and easier than ever before Jeremy Preston, PhD Marketing Manager, Sequencing Illumina Genome Analyzer: a Paradigm Shift 2000x gain in efficiency

More information

APPLICATION OF MOLECULAR TECHNICS FOR DIAGNOSIS OF VIRAL INFECTIONS

APPLICATION OF MOLECULAR TECHNICS FOR DIAGNOSIS OF VIRAL INFECTIONS APPLICATION OF MOLECULAR TECHNICS FOR DIAGNOSIS OF VIRAL INFECTIONS Hossein Keyvani Basic Diagnostic Methods in Virology Immunology and serology techniques (Antigen-Antibody Reactions) 1 ELISA ( Enzyme

More information

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es Sequencing technologies Jose Blanca COMAV institute bioinf.comav.upv.es Outline Sequencing technologies: Sanger 2nd generation sequencing: 3er generation sequencing: 454 Illumina SOLiD Ion Torrent PacBio

More information

Human Genome Sequencing Over the Decades The capacity to sequence all 3.2 billion bases of the human genome (at 30X coverage) has increased

Human Genome Sequencing Over the Decades The capacity to sequence all 3.2 billion bases of the human genome (at 30X coverage) has increased Human Genome Sequencing Over the Decades The capacity to sequence all 3.2 billion bases of the human genome (at 30X coverage) has increased exponentially since the 1990s. In 2005, with the introduction

More information

NPTEL VIDEO COURSE PROTEOMICS PROF. SANJEEVA SRIVASTAVA

NPTEL VIDEO COURSE PROTEOMICS PROF. SANJEEVA SRIVASTAVA LECTURE-03 GENOMICS AND TRANSCRIPTOMICS: WHY PROTEOMICS? TRANSCRIPT Welcome to the proteomics course. Today, we will talk about Genomics and Transcriptomics and then we will talk about why to study proteomics?

More information

BENG 183 Trey Ideker The next generation

BENG 183 Trey Ideker The next generation BENG 183 Trey Ideker The next generation Sequencing topics to be covered in today s lecture (1) Devils in the details: DNA preparation prior to sequencing Amplification: vectors or cycle sequencing PAGE

More information

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es Sequencing technologies Jose Blanca COMAV institute bioinf.comav.upv.es Outline Sequencing technologies: Sanger 2nd generation sequencing: 3er generation sequencing: 454 Illumina SOLiD Ion Torrent PacBio

More information

Jonathan A. Eisen. University of California, Davis

Jonathan A. Eisen. University of California, Davis The Now Generation Sequencing: The Now Generation Bodega Bay Applied Phylogenetics Jonathan A. Eisen University of California, Davis Sequencing Technology Key Issues Cost / bp Read length Paired end Ease

More information

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es

Sequencing technologies. Jose Blanca COMAV institute bioinf.comav.upv.es Sequencing technologies Jose Blanca COMAV institute bioinf.comav.upv.es Outline Sequencing technologies: Sanger 2nd generation sequencing: 3er generation sequencing: 454 Illumina SOLiD Ion Torrent PacBio

More information

Lecture 8: Sequencing and SNP. Sept 15, 2006

Lecture 8: Sequencing and SNP. Sept 15, 2006 Lecture 8: Sequencing and SNP Sept 15, 2006 Announcements Random questioning during literature discussion sessions starts next week for real! Schedule changes Moved QTL lecture up Removed landscape genetics

More information

Next Generation Sequencing. Tobias Österlund

Next Generation Sequencing. Tobias Österlund Next Generation Sequencing Tobias Österlund tobiaso@chalmers.se NGS part of the course Week 4 Friday 13/2 15.15-17.00 NGS lecture 1: Introduction to NGS, alignment, assembly Week 6 Thursday 26/2 08.00-09.45

More information

High Throughput Sequencing Technologies. UCD Genome Center Bioinformatics Core Monday 15 June 2015

High Throughput Sequencing Technologies. UCD Genome Center Bioinformatics Core Monday 15 June 2015 High Throughput Sequencing Technologies UCD Genome Center Bioinformatics Core Monday 15 June 2015 Sequencing Explosion www.genome.gov/sequencingcosts http://t.co/ka5cvghdqo Sequencing Explosion 2011 PacBio

More information

Molecular Cloning. Genomic DNA Library: Contains DNA fragments that represent an entire genome. cdna Library:

Molecular Cloning. Genomic DNA Library: Contains DNA fragments that represent an entire genome. cdna Library: Molecular Cloning Genomic DNA Library: Contains DNA fragments that represent an entire genome. cdna Library: Made from mrna, and represents only protein-coding genes expressed by a cell at a given time.

More information

CHEM 4420 Exam I Spring 2013 Page 1 of 6

CHEM 4420 Exam I Spring 2013 Page 1 of 6 CHEM 4420 Exam I Spring 2013 Page 1 of 6 Name Use complete sentences when requested. There are 100 possible points on this exam. The multiple choice questions are worth 2 points each. All other questions

More information

Get to Know Your DNA. Every Single Fragment.

Get to Know Your DNA. Every Single Fragment. HaloPlex HS NGS Target Enrichment System Get to Know Your DNA. Every Single Fragment. High sensitivity detection of rare variants using molecular barcodes How Does Molecular Barcoding Work? HaloPlex HS

More information

Gene Expression Technology

Gene Expression Technology Gene Expression Technology Bing Zhang Department of Biomedical Informatics Vanderbilt University bing.zhang@vanderbilt.edu Gene expression Gene expression is the process by which information from a gene

More information

TREE CODE PRODUCT BROCHURE

TREE CODE PRODUCT BROCHURE TREE CODE PRODUCT BROCHURE Single Molecule, Real-Time (SMRT) Sequencing technology offers: Long read sequencing ~10 Gb with 20 kb average read lengths for WGS ~20 Gb with 40 kb average read length for

More information

Galaxy Workshop

Galaxy Workshop Galaxy Workshop 1-8-13 Intros: Tom Bair thomas-bair@uiowa.edu Ann Black-Ziegelbein annblack@eng.uiowa.edu Srinivas Maddhi srinivas-maddhi@uiowa.edu What is galaxy good for Access to resources Documentation

More information

NEXT GENERATION SEQUENCING. Farhat Habib

NEXT GENERATION SEQUENCING. Farhat Habib NEXT GENERATION SEQUENCING HISTORY HISTORY Sanger Dominant for last ~30 years 1000bp longest read Based on primers so not good for repetitive or SNPs sites HISTORY Sanger Dominant for last ~30 years 1000bp

More information

Next-generation sequencing technologies

Next-generation sequencing technologies Next-generation sequencing technologies NGS applications Illumina sequencing workflow Overview Sequencing by ligation Short-read NGS Sequencing by synthesis Illumina NGS Single-molecule approach Long-read

More information

How is genome sequencing done?

How is genome sequencing done? Click here to view Roche 454 Sequencing Genome Sequence FLX available at www.ssllc.com>> How is genome sequencing done? Using 454 Sequencing on the Genome Sequencer FLX System, DNA from a genome is converted

More information

Next Generation Sequences & Chloroplast Assembly. 8 June, 2012 Jongsun Park

Next Generation Sequences & Chloroplast Assembly. 8 June, 2012 Jongsun Park Next Generation Sequences & Chloroplast Assembly 8 June, 2012 Jongsun Park Table of Contents 1 History of Sequencing Technologies 2 Genome Assembly Processes With NGS Sequences 3 How to Assembly Chloroplast

More information

Wheat CAP Gene Expression with RNA-Seq

Wheat CAP Gene Expression with RNA-Seq Wheat CAP Gene Expression with RNA-Seq July 9 th -13 th, 2018 Overview of the workshop, Alina Akhunova http://www.ksre.k-state.edu/igenomics/workshops/ RNA-Seq Workshop Activities Lectures Laboratory Molecular

More information

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Tuesday December 16, 2014

High Throughput Sequencing Technologies. J Fass UCD Genome Center Bioinformatics Core Tuesday December 16, 2014 High Throughput Sequencing Technologies J Fass UCD Genome Center Bioinformatics Core Tuesday December 16, 2014 Sequencing Explosion www.genome.gov/sequencingcosts http://t.co/ka5cvghdqo Sequencing Explosion

More information

Illumina Sequencing Overview

Illumina Sequencing Overview Illumina Sequencing Overview Part # 15045845_Rev.C 2013 Illumina, Inc. All rights reserved. Illumina, IlluminaDx, BaseSpace, BeadArray, BeadXpress, cbot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic

More information

1. Introduction Gene regulation Genomics and genome analyses

1. Introduction Gene regulation Genomics and genome analyses 1. Introduction Gene regulation Genomics and genome analyses 2. Gene regulation tools and methods Regulatory sequences and motif discovery TF binding sites Databases 3. Technologies Microarrays Deep sequencing

More information

Lecture 7. Next-generation sequencing technologies

Lecture 7. Next-generation sequencing technologies Lecture 7 Next-generation sequencing technologies Next-generation sequencing technologies General principles of short-read NGS Construct a library of fragments Generate clonal template populations Massively

More information

SMARTer for NGS. SMARTer Solutions 다카라코리아바이오메디칼

SMARTer for NGS. SMARTer Solutions 다카라코리아바이오메디칼 SMARTer for NGS SMARTer Solutions 다카라코리아바이오메디칼 Contents Next Generation Sequencing SMARTer Sequencing Kits Single Cell RNA-Seq & mrna-seq SMARTer Ultra Low Input RNA Kit for Sequencing -v3 SMARTer Ultra

More information

Introduction to NGS. Simon Rasmussen Associate Professor DTU Bioinformatics Technical University of Denmark 2018

Introduction to NGS. Simon Rasmussen Associate Professor DTU Bioinformatics Technical University of Denmark 2018 Introduction to NGS Simon Rasmussen Associate Professor DTU Bioinformatics Technical University of Denmark 2018 Life science data deluge Massive unstructured data from several areas DNA, patient journals,

More information

Bioinformatics Advice on Experimental Design

Bioinformatics Advice on Experimental Design Bioinformatics Advice on Experimental Design Where do I start? Please refer to the following guide to better plan your experiments for good statistical analysis, best suited for your research needs. Statistics

More information

Molecular Biology. DNA structure and function. Recombinant DNA technology. DNA amplification. DNA sequencing

Molecular Biology. DNA structure and function. Recombinant DNA technology. DNA amplification. DNA sequencing Molecular Biology DNA structure and function Recombinant DNA technology DNA amplification DNA sequencing Arthur Günzl, PhD Dept. of Genetics & Genome Sciences University of Connecticut Health Center Bioinformatics

More information

you can see that if if you look into the you know the capability kilobases per day, per machine kind of calculation if you do.

you can see that if if you look into the you know the capability kilobases per day, per machine kind of calculation if you do. Functional Genomics Professor S Ganesh Department of Biological Sciences & Bioengineering Indian Institute of Technology Kanpur Lecture No 11 DNA Sequencing Methods Part 2 So welcome back to this course

More information

Bioinformatics: A perspective

Bioinformatics: A perspective Bioinformatics: A perspective Dr. Matthew L. Settles Genome Center University of California, Davis settles@ucdavis.edu Outline The World we are presented with Advances in DNA Sequencing Bioinformatics

More information

Joint RuminOmics/Rumen Microbial Genomics Network Workshop

Joint RuminOmics/Rumen Microbial Genomics Network Workshop Joint RuminOmics/Rumen Microbial Genomics Network Workshop Microbiome analysis - Amplicon sequencing Dr. Sinéad Waters Animal and Bioscience Research Department, Teagasc Grange, Ireland Prof. Leluo Guan

More information

Advanced Technology in Phytoplasma Research

Advanced Technology in Phytoplasma Research Advanced Technology in Phytoplasma Research Sequencing and Phylogenetics Wednesday July 8 Pauline Wang pauline.wang@utoronto.ca Lethal Yellowing Disease Phytoplasma Healthy palm Lethal yellowing of palm

More information