Revolutionize Genomics with SMRT Sequencing. Single Molecule, Real-Time Technology

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1 Revolutionize Genomics with SMRT Sequencing Single Molecule, Real-Time Technology

2 Resolve to Master Complexity Despite large investments in population studies, the heritability of the majority of Mendelian and complex diseases remains unclear, limiting development of diagnostics and treatments. Shedding light on the complete spectrum of sequence variant types with chromosome-level phasing across genomes unique to a population, disease or individual may provide a holistic view of human genetics to resolve missing heritability linkages. The complex genomes of plants and animals, with their multi-gigabase sizes, polyploidy, and difficult-to-sequence repetitive regions, hold the key to resolving agricultural and environmental challenges like drought and disease. With a complete view of genomes and transcriptomes of crops, livestock, and associated microbes, scientists can finally unlock the genetic diversity required to advance breeding, precision engineer genes, develop novel treatments and natural growth enhancers, and secure a global food supply. Infectious diseases are responsible for more than 23% of global deaths, including 50% of child mortality. Antibiotic drug resistance is a major threat to global health security, extending far beyond the human health sector, and globalization has created vast opportunities for novel diseases to emerge, spread, and kill. Only comprehensive characterization of these pathogens including their mobile elements will lead to the discovery and design of better vaccines, treatments, and outcomes.

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4 Accelerate your research with the most comprehensive view of genomes, transcriptomes and epigenomes Sequel System The Leader in Long-Read Sequencing pacb.com/sequel

5 A SMRT Foundation Single Molecule, Real-Time (SMRT ) technology is built upon two key innovations that overcome major challenges in the field of sequencing. Zero-Mode Waveguides (ZMWs) allow light to illuminate only the bottom of a well in which a DNA polymerase/template complex is immobilized. Phospholinked nucleotides allow observation of the immobilized complex as the DNA polymerase produces a completely natural DNA strand. Primer Polymerase Zero-Mode Waveguides Template Phospholinked Nucleotides Up to a million ZMWs per SMRT Cell SMRT Cells containing up to a million ZMWs are processed on PacBio Systems which simultaneously monitor each of the waveguides in real time. The SMRT Sequencing advantage: Long Read Lengths High Consensus Accuracy Uniform Coverage Simultaneous Epigenetic Characterization

6 SMRT Sequencing Achieves Long Read Lengths Half of data in reads: >30 kb Data per SMRT Cell: Up to 10 Gb High Consensus Accuracy Free of systematic errors Achieves >99.999% (QV50) 30, ,000 Half of data in reads: >30 kb 50 20,000 Top 5% of reads: >50 kb 40 Reads 15,000 Longest read lengths: >90 kb QV 30 10,000 5, ,000 20,000 30,000 40,000 50,000 60,000 70,000 80,000 90,000 Read Length Read length data shown above from a 35 kb size-selected E. coli library using the SMRTbell Express Template Prep Kit on a Sequel System (2.1 Chemistry, Sequel System Software v5.1, 10-hour movie). Sequel System SMRT Cells typically generate ~400,000 reads each. Read lengths, reads/data per SMRT Cell and other sequencing performance results vary based on sample quality/type and insert size among other factors Coverage Consensus accuracy is a function of coverage and chemistry. The data above is based on a bacterial genome run on the Sequel System with 2.1 chemistry and 5.1 Sequel Software. Single-molecule accuracy has similar coverage requirements. Uniform Coverage No amplification required Even coverage across GC content Simultaneous Epigenetic Characterization Directly detect DNA modifications using polymerase kinetics 60 Sequence coverage Polymerase Dynamics 6m 6m Forward Strand Reverse Strand Percent GC content Mean coverage per GC window across a human sample. Kinetic analysis of DNA base incorporation during sequencing can distinguish modified versus unmodified bases. This information is automatically generated and processed during every run.

7 Comprehensive Genomics Unobstructed Views Sequence low-complexity regions, like trinucleotide repeats Access all variant types, including structural variants, Indels and SNVs Allele-specific phasing of haplotypes in targeted regions or between chromosomes GRCh38 chr9 71,654,000 71,655,000 71,656,000 heterozygous 280 bp deletion A heterozygous deletion structural variant downstream of the gene TMEM2 is supported by half of the PacBio reads that map to the locus. Sequence data is from the human sample HG002. PacBio coverage Haplotype 1 Haplotype 2 Structural Variants Confident Discoveries Directly detect full-length transcripts without assembly Characterize gene-isoform expression within targeted genes, or across an entire transcriptome Full length isoform sequences from brain tissue of Anna s hummingbird (red transcript models) identify two additional non-coding 5 exons (purple arrows and inset) and extend 3 UTRs (green arrow) while also capturing all five known splice variants (blue transcript models). Complete Knowledge Affordably generate gold-standard microbial genomes Detect and resolve plasmids, mobile elements, and structural variation including gene duplication and inversion Simultaneously analyze genome-wide methylation with single-base resolution Complete genome assembly and methylome (red spikes) of an E. coli strain with six plasmids (not to scale). pacb.com/publications

8 Flexible Design and Analytics Express template preparation in as few as 3 hrs Accepts a variety of sample types and insert sizes Low-template options available from ng Size-selection options to enrich for longest inserts Multiplexing and barcoding solutions available Sequel System Flexible run time less than a day Serially process up to 12 SMRT Cells in a single run Walk away time up to 4 days Variety of analysis methods available through SMRT Link and PacBio DevNet community Open source software Advanced data visualization and mining Comprehensive de novo assemblies Target all types of variants across relevant genomic regions Full-length isoform transcripts Resolution of complex populations Methylation profiles

9 Headquarters 1305 O Brien Drive Menlo Park, CA United States Phone: Singapore Office 20 Science Park Road #01-22 TeleTech Park Singapore Phone: Customer Service Phone: PACB (7222) option 1 Fax: orders@pacb.com Technical Support Phone: PACB (7222) option 2 support@pacb.com PacBio Sequencing Providers Inquiries North America: nasales@pacb.com South America: sasales@pacb.com Europe/Middle East/ Africa: emea@pacb.com Asia Pacific: apsales@pacb.com For Research Use Only. Not for use in diagnostic procedures. Copyright 2018, Pacific Biosciences of California, Inc. All rights reserved. Information in this document is subject to change without notice. Pacific Biosciences assumes no responsibility for any errors or omissions in this document. Certain notices, terms, conditions and/ or use restrictions may pertain to your use of Pacific Biosciences products and/or third party products. Please refer to the applicable Pacific Biosciences Terms and Conditions of Sale and to the applicable license terms at Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, SMRTbell, Iso-Seq, and Sequel are trademarks of Pacific Biosciences. BluePippin and SageELF are trademarks of Sage Science. NGS-go and NGSengine are trademarks of GenDx. FEMTO Pulse and Fragment Analyzer are trademarks of Advanced Analytical Technologies. All other trademarks are the sole property of their respective owners. PN: BR

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