Pacific Biosciences

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Coordinates: 37°28′43″N 122°09′03″W / 37.4787°N 122.1507°W / 37.4787; -122.1507 (headquarters)

Pacific Biosciences of California, Inc.
Public company
Traded as NASDAQPACB
Industry Biotechnology
Founded 2004 (2004)
Headquarters Menlo Park, CA, United States
Key people
Michael Hunkapiller, Chairman, CEO, and President
Website www.pacificbiosciences.com

Pacific Biosciences of California, Inc. is a biotechnology company founded in 2004 that develops and manufactures systems for gene sequencing and some novel real time biological observation.[1][2] They describe their platform as single molecule real time sequencing (SMRT), based on the properties of zero-mode waveguides. Their first commercial product, the PacBio RS, was sold to a limited set of customers in 2010 and was commercially released in early 2011.[3][4] A new version of the sequencer called the PacBio RS II was released in April 2013.[5][6] On 25 September 2013 a partnership between Pacific Biosciences and Roche Diagnostics was announced for the development of in vitro diagnostic products using the technology, with Roche providing US$75,000,000 in the deal.[7][8] In 2015, the company launched a new sequencing instrument called the Sequel System with approximately 7-fold greater capacity than the PacBio RS II.[9][10]

History[edit]

The company was founded based on research done at Cornell University, that combined semiconductor processing and photonics with biotechnology research.[1] It was initially founded under the name Nanofluidics, Inc. The company raised nearly US$400,000,000 in six rounds of primarily venture capital financing, making it one of the most capitalized startups in 2010 leading up to their public offering in October of that year.[11] Key investors included Mohr Davidow Ventures, Kleiner, Perkins, Caufield & Byers, Alloy Ventures, and Wellcome Trust.[1]

Recognitions[edit]

The company received the Technology Pioneer Award from the World Economic Forum in 2009.[1][12]

In 2010, The Scientist named the company and their first product the top life science innovation of the year,[13] and the company received the 2010 Advanced Sequencing Technology Award from the National Human Genome Research Institute.[14] Technology Review magazine included them in their list of the top 50 most innovative companies for both 2010 and 2011.[15] Founder and Chief Technical Officer Dr. Stephen Turner was awarded the 2010 Ewing Marion Kauffman Foundation Outstanding Postdoctoral Entrepreneur award for his work at the company.[16]

Going public[edit]

Pacific Biosciences first offered stock on NASDAQ under the symbol PACB. They sold 12,500,000 shares at an initial price of $16 per share and raised approximately $200 million in an initial public offering of stock on October 27, 2010.[17]

Products[edit]

Sequencing instruments[edit]

The company’s first scientific instrument, called the “PacBio RS”, was released to a limited set of eleven customers in late 2010.[18] Sequencing provider GATC Biotech was selected by Pacific Biosciences as its first European service provider in late 2010.[19] The product was then commercially released in early 2011.[4] A new version of the sequencer called the "PacBio RS II" was released in April 2013; it produces longer sequence reads and offers higher throughput than the original instrument.[5][6] In September 2015, the company announced the launch of a new sequencing instrument, the Sequel System. The sequencer has increased capacity with 1 million zero-mode waveguides compared to 150,000 in the PacBio RS II, and is approximately one-third the size and one-half the price of the PacBio RS II.[20][21] Pacific Biosciences said it would ship about 10 of the new instruments in the final quarter of 2015.[22]

A PacBio RSII sequencer

To use the instrument, customers must also purchase reagent packs for DNA preparation and sequencing and small plastic cells called “SMRT Cells”. Each cell is slightly less than one centimeter square and contains thousands of zero-mode waveguides. The cells are sold in packs of eight. Their secondary analysis bioinformatics product, called “SMRT Analysis”, is open source.[23] In 2013, the company released new bioinformatics tools for automated genome assembly (HGAP) and finishing to 99.999% accuracy (Quiver).[24][25][26]

In May 2010, they published an article in Nature Methods, showing that their instrument can detect methylation of DNA strands without altering the DNA.[27] In 2012 scientists used SMRT sequencing to generate full bacterial methylomes.[28]

Reagents[edit]

P6-C4 chemistry[edit]

On Oct 15, 2014, PacBio announced the release of new chemistry P6-C4, which represents the company's 6th generation of polymerase and 4th generation chemistry, further extends the average read length to 10,000 - 15,000 bases, with the longest reads exceeding 40,000 bases. The throughput with the new chemistry is expected to be between 500 million to 1 billion bases per SMRT® Cell, depending on the sample being sequenced.[29]

P5-C3 chemistry[edit]

On Oct 3, 2013, PacBio released new reagent combination for PacBio RS II, the P5 DNA polymerase with C3 chemistry (P5-C3). Together, they extend sequencing read lengths to an average of approximately 8.5 kb, with the longest reads exceeding 30,000 bases.[30] Throughput per SMRT cell is around 500 million bp based on sequencing results from CHM1 cell line.[31]

P4-C2 chemistry[edit]

On Aug 21, 2013, PacBio released new DNA/Polymerase Binding Kit P4. This P4 enzyme has average read lengths of >4,300 bp when paired with the C2 sequencing chemistry and >5,000 bp when paired with the XL chemistry. The enzyme’s accuracy is similar to C2, reaching QV50 between 30X and 40X coverage. The resulting P4 attributes will provide you with higher-quality assemblies using fewer SMRT® Cells, and with improved variant calling. This kit is compatible with both PacBio RS and PacBio RS II instrument.[32]

Key publications[edit]

Before the first commercial release of their sequencer, scientists published in January 2009 the first sequence data generated from a single molecule real time sequencing in the journal Science.[33] Then in April 2010, scientists published a paper in Nature showing that they had used zero-mode waveguides to perform real-time observation of ribosomal translation.[34]

Demonstrating the value for bacterial sequencing, scientists from Pacific Biosciences and other institutions published in January 2011 a paper in the New England Journal of Medicine demonstrating the origin of the 2010 cholera outbreak in Haiti.[35] In August 2011, Pacific Biosciences scientists and collaborators at other organizations published a paper in the New England Journal of Medicine describing the classification of the E. coli strain causing the virulent 2011 outbreak in Germany responsible for hundreds of cases of hemolytic–uremic syndrome.[36] This paper showed that the strain of E. coli responsible for the outbreak had acquired a Shiga-toxin–encoding phage through lateral gene transfer. In July 2012, several papers were published in peer-review journals demonstrating methods to automate genome finishing for bacteria using single molecule real-time sequencing.[37][38][39] In 2013, scientists estimated that the majority of bacterial and archaeal genomes could be fully sequenced and assembled to closure using PacBio long reads.[40]

Several papers published by researchers at Pacific Biosciences demonstrated that the sequencing instrument can be used to collect data on methylation, DNA damage, and other epigenetic information.[41][42][43] The polymerase that performs the sequencing reaction in the zero-mode waveguides produces kinetic data that can be used to distinguish base modifications.[44] In October 2012, scientists used SMRT sequencing to generate the methylomes of six bacteria, reporting their results in a paper in Nucleic Acids Research.[28]

With increasing read length and throughput, mammalian studies increased using the product. In April 2012, scientists from Pacific Biosciences, the University of California, and other institutes used SMRT sequencing to prove the validity of activating internal tandem duplication mutations in FLT3 as a therapeutic target in acute myeloid leukemia.[45] Their findings were published in the journal Nature.[46] In August 2012, scientists at the Broad Institute published a paper reporting the findings of their evaluation of the Pacific Biosciences sequencer for SNP calling and discovery.[47] Scientists reported in Genome Research in October 2012 the use of the PacBio platform to sequence the full repeat expansion in the FMR1 gene responsible for Fragile X Syndrome.[48]

A paper published in December 2012 offered the first demonstration of how to generate sequence data with the PacBio sequencer with no library preparation.[49]

In 2013, scientists published papers demonstrating the use of PacBio sequencing to analyze transcriptomes, showing that long reads were able to fully capture complete isoforms.[50][51]

References[edit]

  1. ^ a b c d Businessweek (Dec 3, 2009) "WEF Announces 2010 Tech Pioneers"open access publication – free to read
  2. ^ Nature Methods (Apr 15, 2010) "Single-molecule analysis: A ribosome in action"closed access publication – behind paywall
  3. ^ GenomeWeb (Dec 7, 2010) "PacBio Reveals Beta System Specs for RS; Says Commercial Release is on Track for First Half of 2011"closed access publication – behind paywall
  4. ^ a b GenomeWeb (May 3, 2011) "PacBio Ships First Two Commercial Systems; Order Backlog Grows to 44"closed access publication – behind paywall
  5. ^ a b Next Gen Seq (Apr 11, 2013) "PacBio Launches PacBio RS II Sequencer"
  6. ^ a b GenomeWeb (Apr 16, 2013) "New Products: PacBio's RS II; Cufflinks"closed access publication – behind paywall
  7. ^ Pacific Biosciences to Partner With Roche on In Vitro Diagnostics Products Archived September 25, 2013, at the Wayback Machine.
  8. ^ The Motley Fool (Sep 25, 2013) "Pacific Biosciences Rockets on Roche Diagnostics Deal"
  9. ^ https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule-sequencing-system
  10. ^ http://www.bio-itworld.com/2015/9/30/pacbio-announces-sequel-sequencing-system.aspx
  11. ^ Wall Street Journal (Mar 9, 2010) "Sizing Up Promising Young Firms"open access publication – free to read
  12. ^ San Francisco Chronicle (Dec 4, 2009) "World Economic Forum honors Bay Area techies"open access publication – free to read
  13. ^ The Scientist (1 Dec, 2010) "Top Ten Innovations 2010"open access publication – free to read
  14. ^ Reuters (Apr 5, 2010) "Factbox: Companies riding the genome wave"
  15. ^ Technology Review (2010, 2011) "Company Profile: Pacific Biosciences"
  16. ^ Ewing Marion Kauffman Foundation (Mar 12, 2010) "Two Postdoctural Entrepreneurs are Recognized for Excellence" Archived June 21, 2010, at the Wayback Machine.
  17. ^ Renaissance Capital (Oct 30, 2010) "Pacific Biosciences of California (PACB)"
  18. ^ Genome Web (Feb 23, 2010) "PacBio Names First 10 Customers for $695,000 Single-Molecule Sequencer; First Shipments Slated for Q2"closed access publication – behind paywall
  19. ^ GenomeWeb (Sep 21, 2010) "GATC Biotech to be First European Service Provider for PacBio RS"closed access publication – behind paywall
  20. ^ http://www.bio-itworld.com/2015/9/30/pacbio-announces-sequel-sequencing-system.aspx
  21. ^ http://www.pacb.com/blog/introducing-the-sequel-system-the-scalable-platform-for-smrt-sequencing/
  22. ^ https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule-sequencing-system
  23. ^ Pacific Biosciences (Feb 23, 2015) "Analysis"[self-published source]
  24. ^ GenomeWeb (Jan 29, 2013) "New Products: PacBio's SMRT Analysis 1.4"closed access publication – behind paywall
  25. ^ Genetic Engineering & Biotechnology News (May 6, 2013) "Finishing Genomes with HGAP"open access publication – free to read
  26. ^ Nature Methods (May 5, 2013) "Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data"closed access publication – behind paywall
  27. ^ GenomeWeb (May 10, 2010) "Pacific Biosciences Team Demonstrates Method for Directly Detecting Methylation During SMRT Sequencing"closed access publication – behind paywall
  28. ^ a b Nucleic Acids Research (Oct 2, 2012) "The methylomes of six bacteria"open access publication – free to read
  29. ^ http://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=876252
  30. ^ http://blog.pacificbiosciences.com/2013/10/new-chemistry-for-pacbio-rs-ii-provides.html
  31. ^ http://www.nature.com/nature/journal/v517/n7536/abs/nature13907.html
  32. ^ http://blog.pacificbiosciences.com/2013/08/new-dna-polymerase-p4-delivers-higher.html
  33. ^ Science (Nov 20, 2008) "Real-Time DNA Sequencing from Single Polymerase Molecules"closed access publication – behind paywall
  34. ^ Nature (Apr 15, 2010) "Real-time tRNA transit on single translating ribosomes at codon resolution"closed access publication – behind paywall
  35. ^ New England Journal of Medicine (Jan 6, 2011) "The Origin of the Haitian Cholera Outbreak Strain"open access publication – free to read
  36. ^ New England Journal of Medicine (Aug 25, 2011) "Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany"open access publication – free to read
  37. ^ Genome Research (Jul 24, 2012) "Finished bacterial genomes from shotgun sequence data"open access publication – free to read
  38. ^ Nature Biotechnology (Jul 1, 2012) "A hybrid approach for the automated finishing of bacterial genomes"closed access publication – behind paywall
  39. ^ Nature Biotechnology (Jul 1, 2012) "Hybrid error correction and de novo assembly of single-molecule sequencing reads"closed access publication – behind paywall
  40. ^ Genome Biology (Sep 13, 2013) "Reducing assembly complexity of microbial genomes with single-molecule sequencing"open access publication – free to read
  41. ^ Genome Integrity (Dec 20, 2011) "Direct Detection and Sequencing of Damaged DNA Bases"open access publication – free to read
  42. ^ Nucleic Acids Research (Dec 7, 2011) "Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing"open access publication – free to read
  43. ^ Nature Methods (Nov 20, 2011) "Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine"closed access publication – behind paywall
  44. ^ GenomeWeb (Dec 6, 2011) "PacBio, U Chicago Develop Single-Molecule Hydroxymethylation Sequencing Technique"closed access publication – behind paywall
  45. ^ Genetic Engineering & Biotechnology News (Apr 16, 2012) "Investigators Validate FLT3 Kinase Domain as Acute Myeloid Leukemia Target"open access publication – free to read
  46. ^ Nature (Apr 15, 2012) "Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia"closed access publication – behind paywall
  47. ^ BMC Genomics (Aug 5, 2012) "Pacific biosciences sequencing technology for genotyping and variation discovery in human data"open access publication – free to read
  48. ^ Genome Research (Oct 11, 2012) "Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene"open access publication – free to read
  49. ^ Biotechniques (Dec 2012) "Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation"open access publication – free to read
  50. ^ Nature Biotechnology (Oct 13, 2013) "A single-molecule long-read survey of the human transcriptome"closed access publication – behind paywall
  51. ^ Proceedings of the National Academy of Scientists USA (Nov 26, 2013) "Characterization of the human ESC transcriptome by hybrid sequencing"open access publication – free to read

External links[edit]