INTRODUCTION TO NEXT-GENERATION SEQUENCING

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "INTRODUCTION TO NEXT-GENERATION SEQUENCING"

Transcription

1 INTRODUCTION TO NEXT-GENERATION SEQUENCING Louis Letourneau, eng. and Mathieu Bourgey, Ph.D CAGEKID Cancer Genomics Workshop March 18 th - 21 st

2 CAGEKID M12 Meeting - 6 May 2011 My work Many facets of genomic and proteomic Technology development on new instruments Cancer Analysis ATRT (Atypical Teratoid Rhabdoid Tumor), pediatric DIPG (Diffuse Intrinsic Pontine Glioma), pediatric Clear Cell Renal Cancer (CageKid) Tool, pipeline development

3 Outline 1. The technology 2. Base calling 3. Mapping vs. assembly 4. SNV calling 5. Conclusion

4 Four Major Players Roche: 454 Life technology: SOLiD / ion torrent Illumina: Genome Analyzer / Hiseq / Miseq Pacific Biosciences: PacBio

5 A Pyrosequencing method. System Workflow: One Fragment = One Bead = One Read Four main steps: Generation of a single-stranded template DNA library Emulsion-based clonal amplification of the library Data generation via sequencing-by-synthesis Data analysis using different bioinformatics tools

6 The Roche 454/GS FLX Sequencing Technology 1. Samples consisting of longer sequences are first sheared into a random library of base-pair long fragments. 2. Adaptors essential for purification, amplification and sequencing are added to both ends of the fragments

7 3. Using the adaptors, individual fragments are captured on own unique beads. 4. The empcr amplifies each fragment several million times The entire fragment collection is amplified in parallel.

8 5. The PicoTiterPlate is loaded with one fragment carrying bead per well and smaller beads with the enzymes necessary for sequencing. 6. Sequencing is accomplished by synthesizing the complementary strands of the bead attached templates. The incorporation of a new base is associated with the release of inorganic pyrophosphate starting a chemical cascade. This results in the generation of a light signal which is captured by a CCD camera

9 Signal saturation CAGEKID M12 Meeting - 6 May 2011

10 SOLiD Sequencing Sequencing by Ligation method via emulsion PCR

11 SOLiD Sequencing 1. Ligation of 3bp specific primer 2. Primer detection 3. Protection of unextended fragments 4. Cleaving extended fragments 5. Repeat N times steps 1-4 in order to complete the fragment ligation 6. Removing the primer and ligate a n-1 primer 7. Repeat steps Repeat steps 6-7 with primer n-2, n-3 and n-4

12

13 Ion Torrent CAGEKID M12 Meeting - 6 May 2011

14 Ion Torrent CAGEKID M12 Meeting - 6 May 2011

15 CAGEKID M12 Meeting - 6 May 2011 Ion Torrent Homopolymers

16 Bridge Sequencing Flow cells

17

18

19

20 Different type of sequencing libraries From Glenn TC, Mol Ecol Resour adatped for 2013

21 CAGEKID M12 Meeting - 6 May 2011 Pacbio RS: Build template

22 Pacbio RS: Bind bells CAGEKID M12 Meeting - 6 May 2011

23 Bases CAGEKID M12 Meeting - 6 May 2011 Pacbio RS: What you get 15% error rate ~30k-60k reads (depends on movie setup) ~2kb median C2 chemistry 60,000,000 50,000,000 40,000,000 1 cell 16,000 14,000 12,000 10,000 30,000,000 20,000,000 10,000,000 8,000 6,000 4,000 2,000 bases filtered reads Readlength

24 Sample Preparation two sequencing modes LS long sequencing reads Standard Large insert sizes (2kb-10kb) Generates one pass on each molecule sequenced CCS high quality sequencing reads Circular Consensus Small insert sizes 500bp Generates multiple passes on each molecule sequenced

25 CAGEKID M12 Meeting - 6 May 2011 Pacbio RS: Methylation/Kinetics

26 CAGEKID M12 Meeting - 6 May 2011 Pacbio RS: Methylation/Kinetics

27 CAGEKID M12 Meeting - 6 May 2011 Oxford Nanopore Talked about in AGBT 2012, silence in AGBT 2013 Mentioned Error rate of ~4% (Q14) Said they would wait for <1% 2 types, GridION, MinION

28 Technology comparison instrument Pacbio Ion Torrent 454 Illumina SOLiD Method Single-molecule in real-time Ion semiconductor Pyrosequencing synthesis Ligation Read length 3kb average 200 bp 700 bp 50 to 250 bp or bp Error type indel indel indel substitution A-T bias single-pass Error rate % 13 ~1 ~0.1 ~0.1 ~0.1 Reads per run up to 4M 1M up to 3.2G 1.2 to 1.4G Time per run Cost per 1 million bases (in US$) Advantages Disadvantages 30 minutes to 2 hours 2 hours 24 hours 1 to 10 days, 1 to 2 weeks $2 $1 $10 $0.05 to $0.15 $0.13 Longest read length. Fast. Low yield at high accuracy. Equipment can be very expensive. Less expensive equipment. Fast. Homopolymer errors. Long read size. Fast. Runs are expensive. Homopolymer errors. high sequence yield, cost, accuracy Equipment can be very expensive. Low cost per base. Slower than other methods, read length, longevity of the plateform

29 Applications Equipment 454 Genome Quebec number 3 (1) Ion Torrent 1 Illumina MiSeq 1 SOLiD 0 Current Applications Small de novo genome sequencing Amplicon sequencing Metagenomics Small de novo genome sequencing Amplicon sequencing Metagenomics Validation Small de novo genome sequencing Amplicon sequencing Metagenomics Validation Transcriptome sequencing (RNA-Seq) Whole Exome Sequencing Whole Genome Sequencing Illumina HiSeq 2000/2500 Pacific Biosciences 12 1 Transcriptome sequencing (RNA-Seq) Whole Exome Sequencing Whole Genome Sequencing Small genomes, Long haplotype sequencing, Epigenomics

30 What the NGS problem is about? Strings of 100 (to 1kb) letters Puzzle of 3,000,000,000 letters Usually have 120,000,000,000 letters you need to fit Many pieces don t fit : sequencing error/snp/structural variant Many pieces fit in many places: Low complexity region/microsatellite/repeat

31 outline 1. The technology 2. Base calling 3. Mapping vs. assembly 4. SNV calling 5. Conclusion

32 Basecalling How do we translate the machine readouts to base calls? How do we estimate and represent sequencing errors?

33 33 Base quality and Phred scores Q_sanger = -10 log_10 (p) Q_illumina = -10 log_10 (p / (1-p)) Where Q is the quality and p is the probability of the base being incorrect.

34 From MICHAEL STRÖMBERG

35 CAGEKID M12 Meeting - 6 May 2011 Illumina: Pre-phasing & Phasing

36 Base qualities usage: Trimming Will generate input sequence data of various size!! low qualtity bases can bias subsequent anlaysis (i.e, SNP and SV calling, )

37 Outline 1. The technology 2. Base calling 3. Mapping vs. Assembling 4. SNV calling 5. Conclusion

38 Assembling vs Mapping contig1 contig2 assembly all vs all reads mapping all vs reference Reference

39 Genome/deNovo assembly One of the most important tasks in genome biology is to obtain a complete genome sequence Without a good reference genome several genetic analysis are not doable With the decreasing cost of sequencing the demand for genome/transcriptome assembly is increasing

40 De Novo assembly metrics There is no perfect metrics yet: Total amount of sequence assembled: Should fit the specie estimate Contig size distribution: Useful in transcriptome assembly N50: the largest number L such that the combined length of all contigs of length L is at least 50% of the total length of all contigs Note that these most popular metrics emphasize only size and poorly capture the contig quality

41 Assembling vs Mapping Mapping: useful for interrogating the known genome SNP detection (targeted and whole-genome) SV detection (sometimes) RNA sequencing ChIP sequencing Methyl-seq Assembly: Essential if no genome sequence Whole genome analysis Transcriptome analysis unbiased ascertainment of variation in known genome SV detection

42 Mapping chalenges Find the TRUE/BEST location of a read in the reference genome: There may be several, equally likely places in the reference sequence. If we were only looking for perfect matches to the reference, we would never see any variation. Any sequencing technology produces its own type of errors. We need to do that for each of the millions of reads in our sequencing data

43 Mapping quality Algorithms use a mapping quality score: Quantify the probability that a read is misplaced and report it in a phred score (bwa example) SUM_BASE_Q(best) : sum of base quality scores at mismatched bases for the alignment SUM_BASE_Q(i) same, but for each other possible alignment Li H, Ruan J, Durbin R. (2008). Genome Research

44 Illumina AB SOLiD Roche 454 gapped all alignments multithreaded BFAST X X X X X X Bowtie X X X X BWA aln X X X X BWA bwasw X X X X X ELANDv2 X X GenomeMapper X X X X gnumap X X X X karma X X X * MAQ X X MOSAIK X X X X X X MrFAST X X X MrsFAST X X Novoalign X X X X * RMAP X X SeqMap X X X SHRiMP X X X X X Slider X X SOAP2 X X X SSAHA2 X X X X SOCS X X SXOligoSearch X X X X Zoom X X * X

45 INDEL Cleaning

46 INDEL Cleaning

47 Outline 1. The technology 2. Base calling 3. Mapping vs. assembly 4. SNV calling 5. Conclusion

48 SNPs Modified from Bionformatics.ca

49 SNP Discovery: Goal sequencing errors SNP An accurate SNP dicovery is closely linked with a good base quality and a suffisent depth of coverage Modified from Bionformatics.ca

50 Modified from Nielsen et al June 2011 SNP and genotype calling workflow Bayesian approachs MLE approachs Bayesian, threshold or t-test approachs

51 Handling Trios Take advantage of duplicate data Mendelian segregation of alleles De novo mutation rate Modified from Bionformatics.ca

52 outline 1. The technology 2. Base calling 3. Mapping vs. assembly 4. SNV calling 5. Conclusion

53 Concluding remarks NGS offers a variety of technologies and methods There is no one size fits all. NGS is still an open fields where many area are under constructs NGS analyses requires both mathematics and informatics skills The major challenge is actually link to the compute and storage capacities

54 Lincoln Stein (http://goo.gl/td4te)

55 About DNA and computers We ll hit the $1000 genome probably in 2013, then need to go for the $100 genome The doubling time of sequencing is 5-6 months. The doubling time of storage and network bandwidth is 12 months. The doubling time of CPU speed is 18 months The cost of sequencing a base pair will equal the cost of storing a base pair by 2018

56 Acknowledgments This lecture uses material from : Guillaume Bourque Mathieu Bourgey

Next Generation Sequencing

Next Generation Sequencing Next Generation Sequencing Technology and applications 10/1/2015 Jeroen Van Houdt - Genomics Core - KU Leuven - UZ Leuven 1 Landmarks in DNA sequencing 1953 Discovery of DNA double helix structure 1977

More information

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

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

Next generation DNA sequencing technologies. theory & prac-ce

Next generation DNA sequencing technologies. theory & prac-ce Next generation DNA sequencing technologies theory & prac-ce Outline Next- Genera-on sequencing (NGS) technologies overview NGS applica-ons NGS workflow: data collec-on and processing the exome sequencing

More information

Introduction to NGS data analysis

Introduction to NGS data analysis Introduction to NGS data analysis Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Sequencing Illumina platforms Characteristics: High

More information

Introduction to next-generation sequencing data

Introduction to next-generation sequencing data Introduction to next-generation sequencing data David Simpson Centre for Experimental Medicine Queens University Belfast http://www.qub.ac.uk/research-centres/cem/ Outline History of DNA sequencing NGS

More information

NGS data analysis. Bernardo J. Clavijo

NGS data analysis. Bernardo J. Clavijo NGS data analysis Bernardo J. Clavijo 1 A brief history of DNA sequencing 1953 double helix structure, Watson & Crick! 1977 rapid DNA sequencing, Sanger! 1977 first full (5k) genome bacteriophage Phi X!

More information

INTRODUCTION TO NGS VARIANT CALLING ANALYSIS

INTRODUCTION TO NGS VARIANT CALLING ANALYSIS Hospital Universitari Vall d Hebron Institut de Recerca - VHIR Institut d Investigació Sanitària de l Instituto de Salud Carlos III (ISCIII) INTRODUCTION TO NGS VARIANT CALLING ANALYSIS Bioinformàtica

More information

The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics

The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long

More information

Overview of Next Generation Sequencing platform technologies

Overview of Next Generation Sequencing platform technologies Overview of Next Generation Sequencing platform technologies Dr. Bernd Timmermann Next Generation Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin, Germany Outline 1. Technologies

More information

Nazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office

Nazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office 2013 Laboratory Accreditation Program Audioconferences and Webinars Implementing Next Generation Sequencing (NGS) as a Clinical Tool in the Laboratory Nazneen Aziz, PhD Director, Molecular Medicine Transformation

More information

Data Analysis for Ion Torrent Sequencing

Data Analysis for Ion Torrent Sequencing IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page

More information

How is genome sequencing done?

How is genome sequencing done? How is genome sequencing done? Using 454 Sequencing on the Genome Sequencer FLX System, DNA from a genome is converted into sequence data through four primary steps: Step One DNA sample preparation; Step

More information

Ion Torrent Amplicon Sequencing

Ion Torrent Amplicon Sequencing APPLICATION NOTE Amplicon Sequencing Ion Torrent Amplicon Sequencing Introduction The ability to sequence a genome or a portion of a genome has enabled researchers to begin to understand how the genetic

More information

July 7th 2009 DNA sequencing

July 7th 2009 DNA sequencing July 7th 2009 DNA sequencing Overview Sequencing technologies Sequencing strategies Sample preparation Sequencing instruments at MPI EVA 2 x 5 x ABI 3730/3730xl 454 FLX Titanium Illumina Genome Analyzer

More information

Introduction to NGS Technologies

Introduction to NGS Technologies Introduction to NGS Technologies Ignacio Medina im411@cam.ac.uk Head of Computational Biology Lab HPC Service, University of Cambridge, UK EMBL-EBI Scientific collaborator Genome Campus, Hinxton, Cambridge,

More information

Next Generation Sequencing: Technology, Mapping, and Analysis

Next Generation Sequencing: Technology, Mapping, and Analysis Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took

More information

History of DNA Sequencing & Current Applications

History of DNA Sequencing & Current Applications History of DNA Sequencing & Current Applications Christopher McLeod President & CEO, 454 Life Sciences, A Roche Company IMPORTANT NOTICE Intended Use Unless explicitly stated otherwise, all Roche Applied

More information

New generation sequencing: current limits and future perspectives. Giorgio Valle CRIBI - Università di Padova

New generation sequencing: current limits and future perspectives. Giorgio Valle CRIBI - Università di Padova New generation sequencing: current limits and future perspectives Giorgio Valle CRIBI Università di Padova Around 2004 the Race for the 1000$ Genome started A few questions... When? How? Why? Standard

More information

Illumina Sequencing Technology

Illumina Sequencing Technology Illumina Sequencing Technology Highest data accuracy, simple workflow, and a broad range of applications. Introduction Figure 1: Illumina Flow Cell Illumina sequencing technology leverages clonal array

More information

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) A typical RNA Seq experiment Library construction Protocol variations Fragmentation methods RNA: nebulization,

More information

G E N OM I C S S E RV I C ES

G E N OM I C S S E RV I C ES GENOMICS SERVICES THE NEW YORK GENOME CENTER NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases. capabilities. N E X T- G E

More information

Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center

Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center Computational Challenges in Storage, Analysis and Interpretation of Next-Generation Sequencing Data Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center Next Generation Sequencing

More information

Concepts and methods in sequencing and genome assembly

Concepts and methods in sequencing and genome assembly BCM-2004 Concepts and methods in sequencing and genome assembly B. Franz LANG, Département de Biochimie Bureau: H307-15 Courrier électronique: Franz.Lang@Umontreal.ca Outline 1. Concepts in DNA and RNA

More information

SEQUENCING. From Sample to Sequence-Ready

SEQUENCING. From Sample to Sequence-Ready SEQUENCING From Sample to Sequence-Ready ACCESS ARRAY SYSTEM HIGH-QUALITY LIBRARIES, NOT ONCE, BUT EVERY TIME The highest-quality amplicons more sensitive, accurate, and specific Full support for all major

More information

MiSeq: Imaging and Base Calling

MiSeq: Imaging and Base Calling MiSeq: Imaging and Page Welcome Navigation Presenter Introduction MiSeq Sequencing Workflow Narration Welcome to MiSeq: Imaging and. This course takes 35 minutes to complete. Click Next to continue. Please

More information

Genome Sequencer System. Amplicon Sequencing. Application Note No. 5 / February 2007. www.roche-applied-science.com

Genome Sequencer System. Amplicon Sequencing. Application Note No. 5 / February 2007. www.roche-applied-science.com Genome Sequencer System Application Note No. 5 / February 2007 Amplicon Sequencing www.roche-applied-science.com 1 Amplicon Sequencing Corresponding author: Tom Jarvie, 454 Life Sciences Corporation, Branford,

More information

Genotyping by sequencing and data analysis. Ross Whetten North Carolina State University

Genotyping by sequencing and data analysis. Ross Whetten North Carolina State University Genotyping by sequencing and data analysis Ross Whetten North Carolina State University Stein (2010) Genome Biology 11:207 More New Technology on the Horizon Genotyping By Sequencing Timeline 2007 Complexity

More information

3 rd Generation Sequencing Technologies. Roger E. Bumgarner

3 rd Generation Sequencing Technologies. Roger E. Bumgarner 3 rd Generation Sequencing Technologies Roger E. Bumgarner rogerb@uw.edu Brief review First generation sequencing technologies Sanger and Maxim Gilbert methods Used either chemical or enzymatic methods

More information

Computational Genomics. Next generation sequencing (NGS)

Computational Genomics. Next generation sequencing (NGS) Computational Genomics Next generation sequencing (NGS) Sequencing technology defies Moore s law Nature Methods 2011 Log 10 (price) Sequencing the Human Genome 2001: Human Genome Project 2.7G$, 11 years

More information

Next Generation Sequencing for DUMMIES

Next Generation Sequencing for DUMMIES Next Generation Sequencing for DUMMIES Looking at a presentation without the explanation from the author is sometimes difficult to understand. This document contains extra information for some slides that

More information

Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms

Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms Introduction Mate pair sequencing enables the generation of libraries with insert sizes in the range of several kilobases (Kb).

More information

Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe

Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe Go where the biology takes you. To published results faster With proven scalability To the forefront of discovery To limitless applications

More information

Next Generation Sequencing

Next Generation Sequencing Next Generation Sequencing DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection Over the past three years, massively

More information

PreciseTM Whitepaper

PreciseTM Whitepaper Precise TM Whitepaper Introduction LIMITATIONS OF EXISTING RNA-SEQ METHODS Correctly designed gene expression studies require large numbers of samples, accurate results and low analysis costs. Analysis

More information

TruSeq Custom Amplicon v1.5

TruSeq Custom Amplicon v1.5 Data Sheet: Targeted Resequencing TruSeq Custom Amplicon v1.5 A new and improved amplicon sequencing solution for interrogating custom regions of interest. Highlights Figure 1: TruSeq Custom Amplicon Workflow

More information

Automated DNA sequencing 20/12/2009. Next Generation Sequencing

Automated DNA sequencing 20/12/2009. Next Generation Sequencing DNA sequencing the beginnings Ghent University (Fiers et al) pioneers sequencing first complete gene (1972) first complete genome (1976) Next Generation Sequencing Fred Sanger develops dideoxy sequencing

More information

Focusing on results not data comprehensive data analysis for targeted next generation sequencing

Focusing on results not data comprehensive data analysis for targeted next generation sequencing Focusing on results not data comprehensive data analysis for targeted next generation sequencing Daniel Swan, Jolyon Holdstock, Angela Matchan, Richard Stark, John Shovelton, Duarte Mohla and Simon Hughes

More information

Sequencing power for every scale. Systems for every application, for every lab.

Sequencing power for every scale. Systems for every application, for every lab. Sequencing power for every scale. Systems for every application, for every lab. Proven sequencing technology. Accelerate your research. Achieve your next breakthrough. What started as novel Illumina chemistry,

More information

Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation

Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation PN 100-9879 A1 TECHNICAL NOTE Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation Introduction Cancer is a dynamic evolutionary process of which intratumor genetic and phenotypic

More information

PLNT2530 Unit 6e DNA Sequencing

PLNT2530 Unit 6e DNA Sequencing PLNT2530 Unit 6e DNA Sequencing Unless otherwise cited or referenced, all content of this presenataion is licensed under the Creative Commons License Attribution Share-Alike 2.5 Canada 1 High-throughput

More information

DNA Sequencing & The Human Genome Project

DNA Sequencing & The Human Genome Project DNA Sequencing & The Human Genome Project An Endeavor Revolutionizing Modern Biology Jutta Marzillier, Ph.D Lehigh University Biological Sciences November 13 th, 2013 Guess, who turned 60 earlier this

More information

Analysis of NGS Data

Analysis of NGS Data Analysis of NGS Data Introduction and Basics Folie: 1 Overview of Analysis Workflow Images Basecalling Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference

More information

BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls?

BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls? BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls? Giovanni Luca Scaglione, PhD ------------------------ Laboratory of Clinical Molecular Diagnostics and Personalized Medicine, Institute

More information

DNA Sequence Analysis

DNA Sequence Analysis DNA Sequence Analysis Two general kinds of analysis Screen for one of a set of known sequences Determine the sequence even if it is novel Screening for a known sequence usually involves an oligonucleotide

More information

Welcome to Pacific Biosciences' Introduction to SMRTbell Template Preparation.

Welcome to Pacific Biosciences' Introduction to SMRTbell Template Preparation. Introduction to SMRTbell Template Preparation 100 338 500 01 1. SMRTbell Template Preparation 1.1 Introduction to SMRTbell Template Preparation Welcome to Pacific Biosciences' Introduction to SMRTbell

More information

Ankyrin 3 Genetic Association Studies of Bipolar Disorders

Ankyrin 3 Genetic Association Studies of Bipolar Disorders Ankyrin 3 Genetic Association Studies of Bipolar Disorders Wade Berrettini, MD, PhD The Karl E. Rickels Professor of Psychiatry and Director of the Center for Neurobiology and Behavior, Department of Psychiatry

More information

How Sequencing Experiments Fail

How Sequencing Experiments Fail How Sequencing Experiments Fail v1.0 Simon Andrews simon.andrews@babraham.ac.uk Classes of Failure Technical Tracking Library Contamination Biological Interpretation Something went wrong with a machine

More information

Public Health Laboratory Workforce Development Bioinformatics

Public Health Laboratory Workforce Development Bioinformatics Public Health Laboratory Workforce Development Bioinformatics Templates for Course Development Contents Overview... 1 Going Beyond the Introductory Courses... 1 Course Templates... 3 Template 1: Introduction

More information

The author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report:

The author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report: The author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report: Document Title: Author(s): Resolution of DNA Mixtures and Analysis of Degraded

More information

An example of bioinformatics application on plant breeding projects in Rijk Zwaan

An example of bioinformatics application on plant breeding projects in Rijk Zwaan An example of bioinformatics application on plant breeding projects in Rijk Zwaan Xiangyu Rao 17-08-2012 Introduction of RZ Rijk Zwaan is active worldwide as a vegetable breeding company that focuses on

More information

Next generation sequencing (NGS)

Next generation sequencing (NGS) Next generation sequencing (NGS) Vijayachitra Modhukur BIIT modhukur@ut.ee 1 Bioinformatics course 11/13/12 Sequencing 2 Bioinformatics course 11/13/12 Microarrays vs NGS Sequences do not need to be known

More information

Structural Variations

Structural Variations Analysis of Structural Variants using 3 rd generation Sequencing Michael Schatz Analysis of Structural Variants using 3 rd generation Sequencing Michael Schatz January 12, 2016 Bioinformatics / PAG XXIV

More information

Targeted. sequencing solutions. Accurate, scalable, fast TARGETED

Targeted. sequencing solutions. Accurate, scalable, fast TARGETED Targeted TARGETED Sequencing sequencing solutions Accurate, scalable, fast Sequencing for every lab, every budget, every application Ion Torrent semiconductor sequencing Ion Torrent technology has pioneered

More information

KAPA HYPER PLUS: A single-tube NGS library prep workflow integrating enzymatic fragmentation results in high yields and low sequencing bias.

KAPA HYPER PLUS: A single-tube NGS library prep workflow integrating enzymatic fragmentation results in high yields and low sequencing bias. Poster Note As presented at AGBT 215, Marco Island, FL KAPA HYPER PLUS: A single-tube NGS library prep workflow integrating enzymatic fragmentation results in high yields and low sequencing bias. Authors

More information

Single-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples

Single-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples DATA Sheet Single-Cell DNA Sequencing with the C 1 Single-Cell Auto Prep System Reveal hidden populations and genetic diversity within complex samples Single-cell sensitivity Discover and detect SNPs,

More information

Version 5.0 Release Notes

Version 5.0 Release Notes Version 5.0 Release Notes 2011 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) +1.734.769.7249 (elsewhere) +1.734.769.7074 (fax) www.genecodes.com

More information

Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage

Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research March 17, 2011 Rendez-Vous Séquençage Presentation Overview Core Technology Review Sequence Enrichment Application

More information

RNAseq / ChipSeq / Methylseq and personalized genomics

RNAseq / ChipSeq / Methylseq and personalized genomics RNAseq / ChipSeq / Methylseq and personalized genomics 7711 Lecture Subhajyo) De, PhD Division of Biomedical Informa)cs and Personalized Biomedicine, Department of Medicine University of Colorado School

More information

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes:

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes: SMRT Analysis v2.2.0 Overview 100 338 400 01 1. SMRT Analysis v2.2.0 1.1 SMRT Analysis v2.2.0 Overview Welcome to Pacific Biosciences' SMRT Analysis v2.2.0 Overview 1.2 Contents This module will introduce

More information

Analysis of DNA methylation: bisulfite libraries and SOLiD sequencing

Analysis of DNA methylation: bisulfite libraries and SOLiD sequencing Analysis of DNA methylation: bisulfite libraries and SOLiD sequencing An easy view of the bisulfite approach CH3 genome TAGTACGTTGAT TAGTACGTTGAT read TAGTACGTTGAT TAGTATGTTGAT Three main problems 1.

More information

Bioruptor NGS: Unbiased DNA shearing for Next-Generation Sequencing

Bioruptor NGS: Unbiased DNA shearing for Next-Generation Sequencing STGAAC STGAACT GTGCACT GTGAACT STGAAC STGAACT GTGCACT GTGAACT STGAAC STGAAC GTGCAC GTGAAC Wouter Coppieters Head of the genomics core facility GIGA center, University of Liège Bioruptor NGS: Unbiased DNA

More information

14/12/2012. HLA typing - problem #1. Applications for NGS. HLA typing - problem #1 HLA typing - problem #2

14/12/2012. HLA typing - problem #1. Applications for NGS. HLA typing - problem #1 HLA typing - problem #2 www.medical-genetics.de Routine HLA typing by Next Generation Sequencing Kaimo Hirv Center for Human Genetics and Laboratory Medicine Dr. Klein & Dr. Rost Lochhamer Str. 9 D-8 Martinsried Tel: 0800-GENETIK

More information

Third Generation Sequencing

Third Generation Sequencing March 2012 Third Generation Sequencing Barbara Hutter Division of Theoretical Bioinformatics (B080) Computational Oncology group The Next Next Generation http://seqanswers.com/forums/showthread.php?t=6263

More information

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment Tutorial for Windows and Macintosh Preparing Your Data for NGS Alignment 2015 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) 1.734.769.7249

More information

Copy Number Variation: available tools

Copy Number Variation: available tools Copy Number Variation: available tools Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Introduction A literature review of available

More information

NSilico Life Science Introductory Bioinformatics Course

NSilico Life Science Introductory Bioinformatics Course NSilico Life Science Introductory Bioinformatics Course INTRODUCTORY BIOINFORMATICS COURSE A public course delivered over three days on the fundamentals of bioinformatics and illustrated with lectures,

More information

An Overview of DNA Sequencing

An Overview of DNA Sequencing An Overview of DNA Sequencing Prokaryotic DNA Plasmid http://en.wikipedia.org/wiki/image:prokaryote_cell_diagram.svg Eukaryotic DNA http://en.wikipedia.org/wiki/image:plant_cell_structure_svg.svg DNA Structure

More information

Data Analysis & Management of High-throughput Sequencing Data. Quoclinh Nguyen Research Informatics Genomics Core / Medical Research Institute

Data Analysis & Management of High-throughput Sequencing Data. Quoclinh Nguyen Research Informatics Genomics Core / Medical Research Institute Data Analysis & Management of High-throughput Sequencing Data Quoclinh Nguyen Research Informatics Genomics Core / Medical Research Institute Current Issues Current Issues The QSEQ file Number files per

More information

Recombinant DNA & Genetic Engineering. Tools for Genetic Manipulation

Recombinant DNA & Genetic Engineering. Tools for Genetic Manipulation Recombinant DNA & Genetic Engineering g Genetic Manipulation: Tools Kathleen Hill Associate Professor Department of Biology The University of Western Ontario Tools for Genetic Manipulation DNA, RNA, cdna

More information

New Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc.

New Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc. New Technologies for Sensitive, Low-Input RNA-Seq Clontech Laboratories, Inc. Outline Introduction Single-Cell-Capable mrna-seq Using SMART Technology SMARTer Ultra Low RNA Kit for the Fluidigm C 1 System

More information

1. Molecular computation uses molecules to represent information and molecular processes to implement information processing.

1. Molecular computation uses molecules to represent information and molecular processes to implement information processing. Chapter IV Molecular Computation These lecture notes are exclusively for the use of students in Prof. MacLennan s Unconventional Computation course. c 2013, B. J. MacLennan, EECS, University of Tennessee,

More information

Software Getting Started Guide

Software Getting Started Guide Software Getting Started Guide For Research Use Only. Not for use in diagnostic procedures. P/N 001-097-569-03 Copyright 2010-2013, Pacific Biosciences of California, Inc. All rights reserved. Information

More information

Q&A: Kevin Shianna on Ramping up Sequencing for the New York Genome Center

Q&A: Kevin Shianna on Ramping up Sequencing for the New York Genome Center Q&A: Kevin Shianna on Ramping up Sequencing for the New York Genome Center Name: Kevin Shianna Age: 39 Position: Senior vice president, sequencing operations, New York Genome Center, since July 2012 Experience

More information

Assuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice. Supplementary Guidelines

Assuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice. Supplementary Guidelines Assuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT) Workgroup Principles and Guidelines Supplementary

More information

A Primer of Genome Science THIRD

A Primer of Genome Science THIRD A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:

More information

Chapter 6 DNA Replication

Chapter 6 DNA Replication Chapter 6 DNA Replication Each strand of the DNA double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can therefore

More information

FOR REFERENCE PURPOSES

FOR REFERENCE PURPOSES BIOO LIFE SCIENCE PRODUCTS FOR REFERENCE PURPOSES This manual is for Reference Purposes Only. DO NOT use this protocol to run your assays. Periodically, optimizations and revisions are made to the kit

More information

An FPGA Acceleration of Short Read Human Genome Mapping

An FPGA Acceleration of Short Read Human Genome Mapping An FPGA Acceleration of Short Read Human Genome Mapping Corey Bruce Olson A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Electrical Engineering University

More information

2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99.

2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99. 1. True or False? A typical chromosome can contain several hundred to several thousand genes, arranged in linear order along the DNA molecule present in the chromosome. True 2. True or False? The sequence

More information

TGC AT YOUR SERVICE. Taking your research to the next generation

TGC AT YOUR SERVICE. Taking your research to the next generation TGC AT YOUR SERVICE Taking your research to the next generation 1. TGC At your service 2. Applications of Next Generation Sequencing 3. Experimental design 4. TGC workflow 5. Sample preparation 6. Illumina

More information

Complete Genomics Sequencing

Complete Genomics Sequencing TECHNOLOGY OVERVIEW Complete Genomics Sequencing Introduction With advances in nanotechnology, high-throughput instruments, and large-scale computing, it has become possible to sequence a complete human

More information

Challenges associated with analysis and storage of NGS data

Challenges associated with analysis and storage of NGS data Challenges associated with analysis and storage of NGS data Gabriella Rustici Research and training coordinator Functional Genomics Group gabry@ebi.ac.uk Next-generation sequencing Next-generation sequencing

More information

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University Egypt Interpretation of sequence results An overview on

More information

4. GS Reporter Application 65

4. GS Reporter Application 65 Data Processing B Table of Contents Part B: Data Processing 2. GS Sequencer (Output Only; Not a DataRig Application) 42 2.1 GS Sequencer Application Output...42 2.1.1 datarunparams.parse...43 2.1.2 imagelog.parse...44

More information

Description: Molecular Biology Services and DNA Sequencing

Description: Molecular Biology Services and DNA Sequencing Description: Molecular Biology s and DNA Sequencing DNA Sequencing s Single Pass Sequencing Sequence data only, for plasmids or PCR products Plasmid DNA or PCR products Plasmid DNA: 20 100 ng/μl PCR Product:

More information

Introduction Bioo Scientific

Introduction Bioo Scientific Next Generation Sequencing Catalog 2014-2015 Introduction Bioo Scientific Bioo Scientific is a global life science company headquartered in Austin, TX, committed to providing innovative products and superior

More information

NGS Technologies for Genomics and Transcriptomics

NGS Technologies for Genomics and Transcriptomics NGS Technologies for Genomics and Transcriptomics Massimo Delledonne Department of Biotechnologies - University of Verona http://profs.sci.univr.it/delledonne 13 years and $3 billion required for the Human

More information

SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications

SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications Product Bulletin Sequencing Software SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications Comprehensive reference sequence handling Helps interpret the role of each

More information

Services. Updated 05/31/2016

Services. Updated 05/31/2016 Updated 05/31/2016 Services 1. Whole exome sequencing... 2 2. Whole Genome Sequencing (WGS)... 3 3. 16S rrna sequencing... 4 4. Customized gene panels... 5 5. RNA-Seq... 6 6. qpcr... 7 7. HLA typing...

More information

Vector NTI Advance 11 Quick Start Guide

Vector NTI Advance 11 Quick Start Guide Vector NTI Advance 11 Quick Start Guide Catalog no. 12605050, 12605099, 12605103 Version 11.0 December 15, 2008 12605022 Published by: Invitrogen Corporation 5791 Van Allen Way Carlsbad, CA 92008 U.S.A.

More information

Fishing for variants in the deep end of the gene pool: OGT s custom bait designs

Fishing for variants in the deep end of the gene pool: OGT s custom bait designs Fishing for variants in the deep end of the gene pool: OGT s custom bait designs Jolyon Holdstock, Simon Hughes and Daniel Swan Abstract Oxford Gene Technology (OGT) has extensive expertise in probe design

More information

Introduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director

Introduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director Introduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director Gene expression depends upon multiple factors Gene Transcription

More information

Deep Sequencing Data Analysis

Deep Sequencing Data Analysis Deep Sequencing Data Analysis Ross Whetten Professor Forestry & Environmental Resources Background Who am I, and why am I teaching this topic? I am not an expert in bioinformatics I started as a biologist

More information

RNA-Seq Tutorial 1. John Garbe Research Informatics Support Systems, MSI March 19, 2012

RNA-Seq Tutorial 1. John Garbe Research Informatics Support Systems, MSI March 19, 2012 RNA-Seq Tutorial 1 John Garbe Research Informatics Support Systems, MSI March 19, 2012 Tutorial 1 RNA-Seq Tutorials RNA-Seq experiment design and analysis Instruction on individual software will be provided

More information

The Digital Biology TM. Company. Targeted DNA Sequencing Solutions It Pays To Be On Target

The Digital Biology TM. Company. Targeted DNA Sequencing Solutions It Pays To Be On Target The Digital Biology TM Company Targeted DNA Sequencing Solutions It Pays To Be On Target Proven Platform RainDance TM Technologies is pioneering digital biology and powering ground-breaking human genetics

More information

Buyer s Guide: Next-Generation Sequencing Systems

Buyer s Guide: Next-Generation Sequencing Systems Buyer s Guide: Next-Generation Sequencing Systems Covering All the Bases: What to Consider Before Making Your NGS System Purchase. This is an exciting time for biological research. Meaningful discovery

More information

DNA Sequencing. Ben Langmead. Department of Computer Science

DNA Sequencing. Ben Langmead. Department of Computer Science DN Sequencing Ben Langmead Department of omputer Science You are free to use these slides. If you do, please sign the guestbook (www.langmead-lab.org/teaching-materials), or email me (ben.langmead@gmail.com)

More information

GS Junior System The power of next-generation sequencing in your hands

GS Junior System The power of next-generation sequencing in your hands GS Junior System The power of next-generation sequencing in your hands A Complete Sequencing Solution All on your benchtop The GS Junior System includes: GS Junior Instrument, high-performance desktop

More information

Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data

Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data The Illumina TopHat Alignment and Cufflinks Assembly and Differential Expression apps make RNA data analysis accessible to any user, regardless

More information

An Introduction to Next-Generation Sequencing Technology

An Introduction to Next-Generation Sequencing Technology n Introduction to Next-eneration Sequencing echnology Part II: n overview of DN Sequencing pplications Diverse pplications Next-generation sequencing (NS) platforms enable a wide variety of applications,

More information