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FIND MEANING IN COMPLEXITY © Copyright 2013 by Pacific Biosciences of California, Inc. All rights reserved. Kevin Corcoran, SVP Market Development PacBio.

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Presentation on theme: "FIND MEANING IN COMPLEXITY © Copyright 2013 by Pacific Biosciences of California, Inc. All rights reserved. Kevin Corcoran, SVP Market Development PacBio."— Presentation transcript:

1 FIND MEANING IN COMPLEXITY © Copyright 2013 by Pacific Biosciences of California, Inc. All rights reserved. Kevin Corcoran, SVP Market Development PacBio User Group Meeting September 18, 2013

2 PacBio User Meeting Welcome West Coast User Group Meeting Welcome West Coast User Group Meeting 2

3 Thank You! Your Success Is Our Success More than 50 customer publications

4 Special Thanks to our Reception Sponsors 4

5 Latest Advances – Last 9 Months 5

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7 Finishing Genomes Using Only PacBio ® Reads Utilizes all PacBio data from single, long-insert library –Longest reads for continuity –All reads for high consensus accuracy Hierarchical Genome Assembly Process (HGAP)

8 Quiver: A New Consensus Caller for PacBio ® Data Can achieve accuracy >Q50 (i.e. > %) using only PacBio reads How Quiver works –Takes multiple reads of a given DNA template, outputs best guess of template’s identity –QV-aware hidden Markov model to account for sequencing errors; a greedy algorithm to find the maximum likelihood template –Similar underlying algorithm as currently used for CCS generation Links: –www.pacbiodevnet.com/quiverwww.pacbiodevnet.com/quiver –https://github.com/PacificBiosciences/GenomicConsensushttps://github.com/PacificBiosciences/GenomicConsensus 8

9 SMRT ® Sequencing Accuracy % (QV 70) % (QV 60) % (QV 50) 99.99% (QV 40) 99.9% (QV 30) 99% (QV 20) 90% (QV 10) Data generated with P4-C2 chemistry on PacBio ® RS II; Analyzed using Quiver with SMRT ® Analysis E. coli R. palustris S. aureus Perfect consensus

10 Latest Advances – Last 9 Months 10

11 PacBio ® RS II

12 Pre- and Post-PacBio ® RS II Upgrade Throughput effectively doubles with no significant changes to other sequencing metrics OrganismChem Insert Size System Model Filtered Reads Filtered Bases (Mb) Mapped Subreads Avg Subread Length Avg Read Length 95 th % Read Length Max Read Length Single Pass Accuracy B. subtilisC2/C210 kbRS II68, ,0712,0002,7297,21521, % R. palustrisC2/C210 kbRS II63, ,9982,1042,7847,45719, % E. coliC2/C210 kbRS II73, ,5202,1723,2348,44620, % E. coliC2/C210 kbRS32, ,8941,9382,7847,23719, %

13 Latest Advances – Last 9 Months

14 Berman, A.J. et al., EMBO J. (2007) 26(14): Phi29 DNA Polymerase

15 P4 Polymerase Performance Performance summary of current chemistries Key Points –P4 polymerase shows similar consensus accuracy as C2 polymerase –P4 polymerase shows similar read lengths as XL polymerase *E. coli 10 kb library, PacBio ® RS II, Stage Start, 120 minute movies EnzymeSequence Chemistry QV50 Coverage Mean Mapped Read Length P4C232x3,995 C2 32x3,235 XLC270x4,012

16 Typical Results: Accuracy with P4 Polymerase Consensus Accuracy XL-C2 C2-C2 P4-C2 Coverage QV *E. coli 10 kb library, PacBio ® RS II, Stage Start, 120 min movies, C2 sequencing chemistry, SMRT ® Analysis Key Points –P4 polymerase shows similar consensus accuracy as C2 –P4 polymerase outperforms XL

17 Increased Read Length Beyond P4 Enzyme Photodamage Impacts Read Length

18 Pol Protecting Scaffold Dye Pol Polymerase surface that dye can access Dye cannot access polymerase surface Photodamage Mitigation: Photo-Protected Analogs A large macromolecule scaffold can prevent the dye from touching the polymerase Dye

19 19 Coming Soon P5-C3 Chemistry: Photo-Protected Analogs Protective scaffold prevents the dye from damaging the polymerase Dye Protective scaffold Polymerase

20 Early PacBio chemistries LPR FCR ECR2 C2–C2 P4–C2 P5–C3 8,500 bp Read Length (bp) P5-C3 Chemistry Average Read Lengths Throughput: ~ Mb

21 New Products and Features

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26 Social Media Policy Talks are ‘tweetable’ unless speakers says otherwise Use #PacBioUGM for hashtag Follow Subscribe to our Blog at:

27 Morning Agenda TimeAgenda 9:00 – 9:15 a.m.Opening Remarks Kevin Corcoran, Senior Vice President, Market Development, Pacific Biosciences 9:15 – 9:35 a.m.Overview of JGI’s Microbial and Fungal Reference Assembly Pipeline Alex Copeland, DOE - Joint Genome Institute 9:35 – 9:55 a.m.The Epigenomic Landscape of Bacteria Matthew Blow, Ph.D., DOE - Joint Genome Institute 9:55 – 10:20 a.m.Population Genomics & Molecular Diagnostics: 100K Pathogen Genomes Bart Weimer, Ph.D., UC Davis - School of Veterinary Medicine 10:20 – 10:45 a.m.Population Genomic and Epigenomic Study of Arabidopsis thaliana with SMRT Sequencing Chongyuan Luo, Ph.D., Salk Institute for Biological Studies 10:45 – 11:20 a.m.Coffee Break 11:20 – 11:45 a.m.A Comparison of 454 and PacBio RS in the Context of Characterizing HIV-1 Intra-host Diversity Lance Hepler, Ph,D.,Center for AIDS Research, UC San Diego 11:45 – 12:10 p.m.PacBio Meets the Microbiome George Weinstock, Ph.D., Washington University St. Louis 12:10 – 12:35 p.m.Genomic Architecture of the KIR and MHC-B and -C Regions in Orangutan Lisbeth Guethlein, Ph.D., Stanford University School of Medicine

28 Afternoon Agenda TimeAgenda 12:35 – 1:55 p.m.Lunch 1:55 – 2:20 p.m.Reconstructing Complex Regions of Genomes Using Long-read Sequencing Technology John Huddleston, M.S., University of Washington 2:20 – 2:45 p.m.Taking Advantage of Long RNA-Seq Reads Vince Magrini, Ph.D., Washington University St. Louis 2:45 – 3:10 p.m.Chicken in Awesome Sauce: A Recipe for New Transcript Identification Alisha K. Holloway, Ph.D., Gladstone Institutes 3:10 – 3:45 p.m.Break 3:45 – 4:10 p.m.Gene Isoform Identification by Error-corrected PacBio Data Kin Fai Au, Ph.D., Stanford University 4:10 – 4:35 p.m.Optimizing BluePippin Size Selection for Increased Subread Lengths on the PacBio RS II Bobby Sebra, Ph.D., Mt. Sinai School of Medicine 4:35 – 5:00 p.m.Looking Ahead: Improving Workflows for SMRT Sequencing Jonas Korlach, Ph.D., Pacific Biosciences 5:00 – 6:30 p.m.Reception - Sponsored by Sage Science

29 Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, and SMRTbell are trademarks of Pacific Biosciences in the United States and/or other countries. All other trademarks are the sole property of their respective owners.


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