The SOLiD 3 System ™

Enabling the Next Generation of Science
Revolutionary Technology
SOLID Platform




Applied Biosystems has been the leader in sequence             Imagine the sci...
Compute cluster for real-time data analysis   SOLiD 3 System                    Side and bottom reagent storage for walk a...
SOLiD™ System Chemistry | SOLID INSIDE AND OUT

A. LIBrArY PrEPArATIOn

The SOLiD 3 System uses two types of
libraries—fra...
P1 Adapter            TA    Template Sequence                                            TA




               2. Image   ...
Your Science Deserves
a SOLID Foundation
The SOLiD™ 3 System is revolutionary in terms of throughput, and differentiates i...
System Scalability                                                                                       Superior Accuracy...
SOLID Science
SOLID Applications


Increase your research productivity with the maximum flexibility, superior accuracy and...
Complete solutions for your experimental workflow.

DESIGN                 ISOLATE            PREPARE LIBRARY             ...
SOLID Software. Your Analysis Solution.

Large scale science requires solid analysis                      SOLID Data Acqui...
Join the SOLiD Software Community
The SOLiD Software Community provides a resource to those seeking application-specific t...
The Future Is SOLID
The ability to increase both data output and sample throughput will be a key driver for
pushing the bo...
Increasing Future Data Output and Throughput                                                               Bead Density — ...
Your Success Depends on SOLID Support

             Global Service & Support
             With more than 2,000 field perso...
Applied Biosystems
850 Lincoln Centre Drive
Foster City, CA 94404
USA

For Research Use Only. Not for use in diagnostic pr...
SOLiD SYSTEM
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SOLiD SYSTEM

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Next Generation Sequencing with SOLiD System

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SOLiD SYSTEM

  1. 1. The SOLiD 3 System ™ Enabling the Next Generation of Science
  2. 2. Revolutionary Technology SOLID Platform Applied Biosystems has been the leader in sequence Imagine the scientific discoveries that can be achieved with the power of the SOLiD 3 System: analysis for more than 20 years and has revolutionized the industry by developing innovative chemistries and robust, • The power to view the whole transcriptome — without any holes. automated instrumentation. The SOLiD™ 3 System is • The ability to distinguish strand specific expression patterns — for the first time. Applied Biosystems latest revolutionary step forward in • The accuracy to detect SNPs at low coverage — with a low false positive rate. sequence analysis technology. The throughput capability • The capacity to globally assess DNA-protein binding interactions — across multiple samples and unrivaled accuracy inherent in the SOLiD 3 System, in a single run. coupled with broad application flexibility, provide a unique • The sensitivity to discover novel transcripts and splice variation — without the bias of microarrays. system for advancing your research like never before. • The resolution to characterize structural rearrangements — including balanced translocations.
  3. 3. Compute cluster for real-time data analysis SOLiD 3 System Side and bottom reagent storage for walk away operations Pre-filled reagent strip tubes Dual independent flow cells APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 2
  4. 4. SOLiD™ System Chemistry | SOLID INSIDE AND OUT A. LIBrArY PrEPArATIOn The SOLiD 3 System uses two types of libraries—fragment or mate-paired. The type LIBRARY PREPARATION of library used depends on the application and information required. A. B. EMuLSIOn PCr/BEAD EnrIChMEnT Clonal bead populations are prepared in microreactors containing template, PCr reaction components, beads and primers. After PCr, the templates are denatured and bead enrichment is performed to select beads with extended templates. The template on the selected beads undergoes a 3’ modification to allow covalent bonding to the slide. B. C. BEAD DEPOSITIOn 3’ modified beads are deposited onto a glass slide. Deposition chambers offer the ability to segment a slide into one, four or eight chambers during the bead loading process. A key advantage of the system is the ability to accommodate increasing densities of beads per slide, which will result in a higher level of throughput from the same system. C. 3 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  5. 5. P1 Adapter TA Template Sequence TA 2. Image 5. Repeat steps 1-4 to Extend Sequence Excite Fluorescence Ligation cycle 1 2 3 4 5 6 7 ... (n cycles) AT TT CT GT TT CA GC D. SEquEnCInG BY LIGATIOn 3’ TA AA GA CA AA GT CG D. TA 3’ Primers hybridize to the P1 adaptor sequence within the library template. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing 3. Cap Unextended Strands 6. Primer Reset primer. Specificity of the di-base probe is achieved by interrogating every 1st Phosphatase and 2nd base in each ligation reaction. PO4 Universal seq primer (n-1) Multiple cycles of ligation, detection and 3’ 2. Primer reset 1. Melt off extended cleavage are performed with the number sequence 1 m of cycles determining the eventual read 3’ bead 3’ length. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a 7. Repeat steps 1-5 with new primer second round of ligation cycles. 1 base shift PRIMER ROUND 2 -1 Universal seq primer (n-1) AA CA CG TC AA TA CC 3’ 1 m bead 3’ T GT GC AG TT AT GG E. PrIMEr rESET E. 8. Repeat Reset with , n-2, n-3, n-4 primers Five rounds of primer reset are completed Read Position 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 for each sequence tag. Through the primer DUAL INTERROGATION OF EACH BASE Universal seq primer (n) reset process, each base is interrogated 1 3’ in two independent ligation reactions Universal seq primer (n-1) by two different primers. For example, 2 3’ Primer Round the base at read position 5 is assayed by 3 Universal seq primer (n-2) primer number 2 in ligation cycle 2 and by 3’ primer number 3 in ligation cycle 1. This 4 Universal seq primer (n-3) dual interrogation is fundamental to the 3’ unmatched accuracy characterized by the 5 Universal seq primer (n-4) 3’ SOLiD System. Indicates positions of interrogation Ligation Cycle 1 2 3 4 5 6 7 To view an animation of the SOLiD System, visit solid.appliedbiosystems.com. APPLIED BIOSYSTEMS | ThE FuTurE IS SOLiD 3 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 4
  6. 6. Your Science Deserves a SOLID Foundation The SOLiD™ 3 System is revolutionary in terms of throughput, and differentiates itself from other next-generation platforms with unparalleled accuracy, system robustness and scalability. Walk away automation and enhanced data analysis tools significantly reduce hands on time and expedite your time to results. With longer read lengths and sample multiplexing capabilities, the SOLiD 3 System provides the most cost effective analysis for a wide range of genomic, transcriptomic and epigenomic applications. 5 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  7. 7. System Scalability Superior Accuracy The SOLiD 3 System’s open slide format and flexible bead densities With system accuracy greater than 99.94%, due to 2 base encoding, enable increases in throughput with modest analysis and chemistry the SOLiD 3 System distinguishes itself by providing data that is optimizations. While competitive technologies are already near more accurate than alternative next-generation platforms for variation maximum throughput, detection. This unrivaled accuracy is inherent in the system and results the SOLiD 3 System is in lower false Superior Accuracy scalable to meet your positive rates. research needs today 40 40% 35 35% and tomorrow. MEASURED QUALITY VALUE 30 30% 25% ERROR RATE 25 20 20% 15 15% 10 10% 0 0% 0 5 10 15 20 25 30 35 40 POSITION IN READ BP Unmatched Throughput Maximum Flexibility The SOLiD 3 System can generate over 20 gigabases of mappable data The independent flow cells of the SOLiD 3 System enable users to run two and more than 400 million tags per run, which is more usable data than completely independent experiments on one SOLiD Analyzer – providing two any other next-generation instruments in one. system available Sample multiplexing Unsegmented Quad Octet Full Slide today. This throughput 50 with barcoding translates into 45 sequences provides AB R&D Individual efficient sequencing 40 CUSTOMER LAB additional flexibility Samples of multiple genomes 35 and dramatically 2 samples/run 8 samples/run 16 samples/run or cost effective 30 increases the cost- GB/RUN analysis of multiple 25 effectiveness of Multiplexed transcriptomes. 20 targeted resequencing, Samples (20 barcodes) 15 expression and ChIP ≤20 samples/slide ≤20 samples/segment ≤4 segments/slide ≤20 samples/segment ≤8 segments/slide 10 analyses. x 2 slides/run ≤ 40 samples/run x 2 slides/run ≤ 160 samples/run x 2 slides/run ≤ 320 samples/run 0 OCTOBER ‘07 FEBRUARY ‘08 MAY ‘08 OCTOBER ‘08 FEBRUARY ‘09 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 6
  8. 8. SOLID Science SOLID Applications Increase your research productivity with the maximum flexibility, superior accuracy and unmatched throughput of the SOLiD™ 3 System. Walk away automation and enhanced data analysis tools significantly reduce hands on time and expedite your time to results. With longer read lengths and sample multiplexing capabilities, the SOLiD 3 System provides the most cost effective analysis for a wide range of genomic, transcriptomic and epigenomic applications. Whole Transcriptome Analysis Whole Genome Resequencing Targeted Resequencing The SOLiD 3 System provides researchers The SOLiD 3 System enables a new level of whole The superior accuracy of the SOLiD 3 System with access to the entire transcriptome with a genome sequencing with massive throughput and provides a very low false positive rate that enables hypothesis generating, highly sensitive assay mate-paired technology. The system’s ultra high variation detection with less coverage than that preserves the strand information of the throughput results in high coverage levels and the alternative platforms. The inclusion of barcodes original RNA molecule. The combination of 400 M ability to sequence multiple genomes in a single for sample multiplexing dramatically lowers the sequence tags and sample multiplexing capabilities run. The combination of unmatched throughput and cost, time and labor involved in processing allow cost effective analysis of multiple samples superior accuracy dramatically reduces the time multiple samples. in a single run while maintaining the sensitivity to and cost to lower than that of other technologies. discover molecules present at low levels. 7 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  9. 9. Complete solutions for your experimental workflow. DESIGN ISOLATE PREPARE LIBRARY AMPLIFY & ANALYZE DATA VALIDATE EXPERIMENT N NUCLEIC ACID SEQUENCE RESULTS 20 10 5 0 0 5 10 20 0 0 5 5 01 01 02 02 0 5 01 02 TNEMIREPXE N DICA CIELCUN ECNEUQES STLUSER NGISED YRARBIL ERAPERP ATAD EZYLANA ETALOSI & YFILPMA ETADILAV Small RNA Analysis into a scaffold that can then be filled in with the SOLiD System’s flexible slide format and The SOLiD Small RNA Solution is a robust method capillary electrophoresis-based sequencing. multiplexing capability allows researchers to for hypothesis-generating, whole genome analysis analyze multiple samples in a single run. of expression patterns that enable discovery of Gene Expression Profiling novel RNA without the probe bias of microarrays. The massive amount of sequence tags generated Methylation Analysis Using the SOLiD Small RNA Expression Kit, you in a single run can be used to identify and quantify The SOLiD 3 System provides a high throughput can convert total RNA into a library suitable for exon sequences associated with alternative method for analyzing genome-wide DNA emulsion PCR using five easy steps with a single splicing and promoter usage. Simple tag counting methylation with a much higher level of resolution purification. This simplified protocol conserves allows for digital readout of expression levels and than traditional methods. the strand information of the original molecule the ability to detect lowly expressed genes with and enables one to decipher strand-specific greater sensitivity. expression patterns. Chromatin Immunoprecipitation (ChIP) ChIP-Sequencing (ChIP-Seq) with the SOLiD 3 De Novo Sequencing System combines a chromatin immunoprecipitation The longer read lengths and new data analysis (ChIP) assay with massively parallel DNA software of the SOLiD 3 System enable the de sequencing, offering a highly sensitive method novo assembly of small organisms. Researchers to accurately characterize the protein-DNA have demonstrated the assembly of 50 bp reads interactions of an entire genome. Additionally, APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 8
  10. 10. SOLID Software. Your Analysis Solution. Large scale science requires solid analysis SOLID Data Acquisition SOLID Analysis SOLID Interpretation The SOLiD Instrument Control The SOLiD Analysis Tools The SOLiD Alignment Browser solutions. That’s why the SOLiD 3 System ™ Software (ICS) performs image (SAT) provide a powerful back (SAB) is an open-source acquisition and quality control. end engine for automated data platform to enable visualization is designed to deliver not only the computing The ICS provides an easy-to-use analysis that generates base space of sequences aligned to interface for walk away automation. results. The SOLiD Experimental a reference genome. This power, but the software solutions to support Tracking System (SETS) is a allows further visualization and web-based integrated application discrimination of experimental all of your next generation projects. From image for real-time remote monitoring results without the need for and report viewing. A custom additional computing power. acquisition to biological interpretation, the analysis pipeline can be integrated with SAT/SETS via SOLiD integration of the SOLiD Software Suite and Applications Interface (SAI). tools from the SOLiD Software Community support a broad range of application-specific analyses for your genomic, epigenomic or ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT transcriptomic research. ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT ACGT Data Acquisition Sequence Analysis Biological Interpretation Application-Specific Analyses SOLID Applications The SOLiD Applications Interface integrates application-specific tools from the SOLiD Software Community with the Applied Biosystems’ Software Suite for seamless analysis of your data. 9 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  11. 11. Join the SOLiD Software Community The SOLiD Software Community provides a resource to those seeking application-specific tools or in developing new tools for analysis of SOLiD System data. The goal of this program is to directly address the challenges associated with analyzing and managing the vast amounts of research data generated by this ultra high throughput sequencing technology. Resources available through the program provide SOLID researchers with solutions for all supported applications including whole genome and targeted resequencing, whole transcriptome, de novo sequencing, ChIP-Seq and methylation studies. Academic AB Open Partner Open Source Source Analysis Software Tools Tools Visit the community today at info.appliedbiosystems.com/solidsoftwarecommunity PUBLICATION APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 10
  12. 12. The Future Is SOLID The ability to increase both data output and sample throughput will be a key driver for pushing the boundaries of biological analysis in the years to come. The SOLiD™ 3 System’s open slide format is amenable to vastly increasing bead densities and increasing read length without sacrificing robustness or accuracy. Increases in bead density come with minor incremental costs and will drive significant reductions in the overall cost per run. These features will ensure that today’s system will meet the needs of future experiments by growing and expanding with your research. 11 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  13. 13. Increasing Future Data Output and Throughput Bead Density — Amount of beads that can be deposited on a slide and analyzed. The SOLiD 3 System’s ability to dramatically increase data output The unique open format of the SOLiD 3 System allows more beads to using the same platform is a function of the flexible and modular be deposited on a single slide, than with microtiter-based technologies, nature of the technology. Achieving higher levels of increased data without changing the system configuration. Advancements in the output is possible with modest improvements. algorithms for bead finding will further increase the number of beads that can be analyzed from a given slide. These combined improvements are anticipated to more than double the data output of the current system. 50 45 AB R&D 40 CUSTOMER LAB 35 30 GB/RUN 25 20 15 10 0 OCTOBER ‘07 FEBRUARY ‘08 MAY ‘08 OCTOBER ‘08 FEBRUARY ‘09 read Length— Measure of the number FrAGMEnT LIBrArY MATE-PAIrED LIBrArY of bases sequenced. using two full slides/run using two full slides/run Protocol and chemistry optimization will 2007 2008 2009 2010 2007 2008 2009 2010 increase the read length of the current read Length 35 35 50 100 25 35 50 100 system, while maintaining strict accuracy Total Output* ~2.5 GB ~4 GB ~10 GB >35 GB ~3.5 GB ~12 GB >20 GB >50 GB and consistency standards. * Mappable data from 2 slide run APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS 12
  14. 14. Your Success Depends on SOLID Support Global Service & Support With more than 2,000 field personnel, Applied Biosystems has the most extensive network of dedicated Field Application Specialists (FAS) and Support Engineers to work with you. With Applied Biosystems, you can feel confident that we will be there when and where you need us most. World Class Training Programs* Regionally located training facilities offer courses in Library prep, System Sequencing and Bioinformatics. Europe: 330 Field Sales 270 Field Service Asia Pacific: * Americas: 150 Supply Chain * 200 Field Sales Headquarters: 350 Field Sales H 200 Field Service 120 Direct * 300 Field Service 40 Supply Chain Global Support 210 Supply Chain 13 APPLIED BIOSYSTEMS | ThE SOLID GEnErATIOn DELIvErS
  15. 15. Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA For Research Use Only. Not for use in diagnostic procedures. © 2009 Applied Biosystems. Applera, Applied Biosystems, and AB (Design) are registered trademarks and SOLiD is a Research UseApplera Corporationdiagnostic procedures. US and/or certain other countries. For trademark of Only. Not for use in or its subsidiaries in the All2009 Applied Biosystems.sole property of their and AB (Design) are01/2009 trademarks and SOLiD is a trademark of Applied Biosystems or its subsidiaries © other trademarks are the Applied Biosystems, respective owners. registered in the US and/or certain other countries. All other trademarks are the sole property of their respective owners. Publication 106BR13-01 Publication 139BR01-03

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