Pacific Biosciences

Pacific Biosciences of California, Inc. is an American biotechnology company founded in 2004 that develops and manufactures systems for gene sequencing and some novel real time biological observation.[1][2] PacBio describes its platform as single molecule real time sequencing (SMRT), based on the properties of zero-mode waveguides. The company's 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 subsequent version of the sequencer called the PacBio RS II was released in April 2013.[5] On September 25, 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.[6][7] In 2015, the company launched a new sequencing instrument called the Sequel System with approximately 7-fold greater capacity than the PacBio RS II.[8] Then in April 2019 the company launched the Sequel II system with a further 8-fold increase in throughput.[9]

Pacific Biosciences of California, Inc.
Public
Traded asNASDAQ: PACB
Russell 2000 Component
IndustryBiotechnology
Founded2004 (2004)
Headquarters
Menlo Park, California
,
United States
Key people
Michael Hunkapiller, Chairman, CEO, and President
Websitepacificbiosciences.com

History

The company was founded based on research done at Cornell University that combined semiconductor processing and photonics with biotechnology research.[1] Three graduate students in the lab of Professor Harold Craighead — Steve Turner, Jonas Korlach, and Mathieu Foquet — became the first employees.

It began 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.[10] Key investors included Mohr Davidow Ventures, Kleiner, Perkins, Caufield & Byers, Alloy Ventures, and Wellcome Trust.[1]

Leadership

In 2004, Kleiner Perkin's Entrepreneur-in-Residence Hugh Martin became CEO. On 6 January 2012 board member Michael Hunkapiller, PhD assumed the role of CEO.[11] Hunkapiller is planning his retirement in September 2020. Chairman-of-the-Board Christian Henry will next assume the role of CEO.[12] Henry was a former Executive VP and Chief Commercial Officer of Illumina before joining the board at PacBio in July 2018.[13]

Going public

In an initial public offering on October 27, 2010, Pacific Biosciences sold 12,500,000 shares at a price of $16 per share and raised approximately $200 million. The shares trade on NASDAQ under the symbol PACB.[14]

Illumina

On 1 November 2018, Illumina agreed to purchase PacBio for $1.2 billion US in cash. The deal was expected to close in the fourth quarter of 2019,[15] however the deal was abandoned with an announcement on 2 January 2020. Illumina further agreed to pay Pacific Biosciences a $98 million US termination fee plus previously agreed upon deal extension payments of $22 million US in February and $6 million US in March of 2020.[16]

Recognitions

The company received the Technology Pioneer Award from the World Economic Forum in 2009.[1][17]

In 2010, The Scientist named the company and their first product the top life science innovation of the year,[18] and the company received the 2010 Advanced Sequencing Technology Award from the National Human Genome Research Institute.[19] Technology Review magazine included them in their list of the top 50 most innovative companies for both 2010 and 2011.[20] 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.[21]

Products

Sequencing instruments
A PacBio RSII sequencer
Pacific Biosciences Sequel Sequencer

The company's first scientific instrument, called the “PacBio RS”, was released to a limited set of eleven customers in late 2010.[22] Sequencing provider GATC Biotech was selected by Pacific Biosciences as its first European service provider in late 2010.[23] 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 produced longer sequence reads and offered higher throughput than the original RS instrument.[5] The RS instrument will officially be supported until the end of 2021.[24]

In September 2015, the company released 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.[25]

In April 2019, the company released an upgraded Sequel II system with support for a new SMRT Cell with eight million ZMW's,[26] increasing the expected throughput per SMRT Cell by a factor of eight.[9][27]

Reagents and SMRT Cells

Further information: Single molecule real time sequencing

To use either instrument, customers must also purchase reagent packs for DNA preparation and sequencing and small consumables called “SMRT Cells”. Cells for the RS sequencer are slightly less than one-centimeter square and contains tens of thousands of zero-mode waveguides. Cells for the Sequel sequencer are about 2.5 cm square and contains one million zero-mode waveguides, whereas cells for the Sequel sequencer contain eight million zero-mode waveguides. The cells for the RS sequencer are sold in packs of eight. Cells for the Sequel or Sequel II sequencers are sold in packs of four.

On 19 September 2018, PacBio released the Sequel 6.0 software and 3.0 chemistry. Performance differs between large-insert libraries and high molecular weight DNA versus shorter-insert libraries below ~15,000 bases in length. For larger templates, average read lengths are up to 30,000 bases. For shorter-insert libraries, the average read length is up to 100,000 bases while reading the same molecule in a circle. The latter shorter-insert libraries then yield up to 50 billion bases from a single SMRT® Cell.[28]

On 1 October 2019, PacBio released the 8.0 software and 2.0 chemistry for Sequel II. For larger templates read as "continuous long reads", an example human library yielded N50 read length of 52,456 and yield per cell is 182 GB.[29] For libraries below ~20,000 bases, read in circular consensus sequencing, yield per cell is quoted at 450 GB or about 30 GB of HiFi corrected reads.[30]

Software and Applications

Their secondary analysis bioinformatics product for the RS, called “SMRT Analysis”, was open source.[31] For the Sequel system the secondary analysis software was reorganized as the "SMRT Link" application. In 2013, the company released new bioinformatics tools for automated genome assembly (HGAP) and finishing to 99.999% accuracy (Quiver).[32][33][34]

Key publications

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.[35] 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.[36]

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.[37] 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.[38] 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.[39][40][41] In 2013, scientists estimated that the majority of bacterial and archaeal genomes could be fully sequenced and assembled to closure using PacBio long reads.[42]

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.[43][44][45][46][47] The polymerase that performs the sequencing reaction in the zero-mode waveguides produces kinetic data that can be used to distinguish base modifications.[48] In October 2012, scientists used SMRT sequencing to generate the methylomes of six bacteria, reporting their results in a paper in Nucleic Acids Research.[47]

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.[49] Their findings were published in the journal Nature.[50] 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.[51] 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.[52]

A paper published in December 2012 offered the first demonstration of how to generate sequence data with the PacBio sequencer with no library preparation.[53]

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.[54][55]

gollark: Fine, catwhatever then.
gollark: But then you can't send power.
gollark: If it's in geosynchronous orbit, we can make a space elevator *and* provide good internet access at the same time, actually!
gollark: But you can't run an ethernet cable to space.
gollark: Apparently the most efficient way to store power is something ridiculous like pumping water up hills then extracting energy from it going back down.

References
  1. "Bloomberg - Are you a robot?". bloomberg.com.
  2. Brakmann, Susanne (April 5, 2010). "A ribosome in action". Nature. 464 (7291): 987–988. doi:10.1038/464987a. PMID 20393548.
  3. "PacBio Reveals Beta System Specs for RS; Says Commercial Release is on Track for First Half of 2011". GenomeWeb.
  4. "PacBio Ships First Two Commercial Systems; Order Backlog Grows to 44". GenomeWeb.
  5. "New Products: PacBio's RS II; Cufflinks". GenomeWeb.
  6. "Pacific Biosciences to Partner With Roche on In Vitro Diagnostics Products". Archived from the original on Sep 25, 2013.
  7. Speights, Keith (September 25, 2013). "Pacific Biosciences Rockets on Roche Diagnostics Deal". The Motley Fool.
  8. "PacBio Launches Higher-Throughput, Lower-Cost Single-Molecule Sequencing System". GenomeWeb.
  9. "Pacific Biosciences Launches New Sequel II System, Featuring ~8 Times the DNA Sequencing Data Output" (Press release). Pacific Biosciences. April 24, 2019. Archived from the original on Jan 4, 2020. Retrieved Jan 4, 2020 – via GlobeNewswire.
  10. Austin, Colleen DeBaise And Scott (March 9, 2010). "Sizing Up Promising Young Firms" – via www.wsj.com.
  11. "Michael Hunkapiller In, Hugh Martin Out as CEO of Pacific Biosciences". January 6, 2012. Retrieved Aug 10, 2020.
  12. "Pacific Biosciences names Christian Henry as president and CEO". August 7, 2020. Retrieved Aug 10, 2020.
  13. "People in the News: Christian Henry, Mike Hunkapiller, Karen Tay Koh, Michael Vounatsos, More". March 6, 2020. Retrieved Aug 10, 2020.
  14. "Pacific Biosciences of California (PACB) IPO Profile". October 30, 2010. Archived from the original on Oct 30, 2010.
  15. Farr, Christina (November 1, 2018). "DNA sequencing giant Illumina just bought rival Pac Bio for $1.2 billion — here's why". CNBC. Archived from the original on Jul 14, 2019.
  16. "Illumina abandons $1.2 billion deal to buy rival Pacific Biosciences". CNBC. January 2, 2020. Archived from the original on Jan 3, 2020. Retrieved Jan 3, 2020.
  17. Kim, Ryan; Writer, Chronicle Staff (December 4, 2009). "World Economic Forum honors Bay Area techies". SFGate.
  18. "Top Ten Innovations 2010". The Scientist Magazine®.
  19. "Factbox: Companies riding the genome wave". April 5, 2010 – via www.reuters.com.
  20. Review, MIT Technology. "Pacific Biosciences". MIT Technology Review.
  21. "Two Postdoctural Entrepreneurs are Recognized for Excellence" (Press release). Philadelphia: Ewing Marion Kauffman Foundation. March 12, 2010. Archived from the original on Jun 21, 2010.
  22. "PacBio Names First 10 Customers for $695,000 Single-Molecule Sequencer; First Shipments Slated for Q2". GenomeWeb.
  23. "GATC Biotech to be First European Service Provider for PacBio RS". GenomeWeb.
  24. "PacBio Plans Sequel Upgrades, Will Sunset RSII in 2021". GenomeWeb.
  25. http://www.pacb.com/blog/introducing-the-sequel-system-the-scalable-platform-for-smrt-sequencing/
  26. "Bio-IT World". bio-itworld.com.
  27. http://investor.pacificbiosciences.com/static-files/e53d5ef9-02cd-42ab-9d86-3037ad9deaec
  28. "JK announces launch of new chemistry (Sequel System 6.0 Release) in the next month - 2x thruput increase = up to 20 Gb/SMRT Cell & avg. read length up to 30 kb #PBUGMpic.twitter.com/eF8wy2mlVa". September 19, 2018.
  29. "pic.twitter.com/PVelpLc24c". September 25, 2019.
  30. Larrea, Andy (September 25, 2019). "JK: Yowza! This new 2.0 chemistry on the Sequel II is generating a LOT of 15kb #HiFireads. #PBUGMpic.twitter.com/Dzjoxbna8y".
  31. Pacific Biosciences (Feb 23, 2015) "Analysis"
  32. "New Products: PacBio's SMRT Analysis 1.4". GenomeWeb.
  33. "Finishing Genomes with HGAP". May 6, 2013.
  34. Chin, Chen-Shan; Alexander, David H.; Marks, Patrick; Klammer, Aaron A.; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E.; Turner, Stephen W.; Korlach, Jonas (June 5, 2013). "Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data". Nature Methods. 10 (6): 563–569. doi:10.1038/nmeth.2474. PMID 23644548.
  35. Eid, John; Fehr, Adrian; Gray, Jeremy; Luong, Khai; Lyle, John; Otto, Geoff; Peluso, Paul; Rank, David; Baybayan, Primo; Bettman, Brad; Bibillo, Arkadiusz; Bjornson, Keith; Chaudhuri, Bidhan; Christians, Frederick; Cicero, Ronald; Clark, Sonya; Dalal, Ravindra; deWinter, Alex; Dixon, John; Foquet, Mathieu; Gaertner, Alfred; Hardenbol, Paul; Heiner, Cheryl; Hester, Kevin; Holden, David; Kearns, Gregory; Kong, Xiangxu; Kuse, Ronald; Lacroix, Yves; Lin, Steven; Lundquist, Paul; Ma, Congcong; Marks, Patrick; Maxham, Mark; Murphy, Devon; Park, Insil; Pham, Thang; Phillips, Michael; Roy, Joy; Sebra, Robert; Shen, Gene; Sorenson, Jon; Tomaney, Austin; Travers, Kevin; Trulson, Mark; Vieceli, John; Wegener, Jeffrey; Wu, Dawn; Yang, Alicia; Zaccarin, Denis; Zhao, Peter; Zhong, Frank; Korlach, Jonas; Turner, Stephen (January 2, 2009). "Real-Time DNA Sequencing from Single Polymerase Molecules". Science. 323 (5910): 133–138. Bibcode:2009Sci...323..133E. doi:10.1126/science.1162986. PMID 19023044.
  36. Uemura, Sotaro; Aitken, Colin Echeverría; Korlach, Jonas; Flusberg, Benjamin A.; Turner, Stephen W.; Puglisi, Joseph D. (April 5, 2010). "Real-time tRNA transit on single translating ribosomes at codon resolution". Nature. 464 (7291): 1012–1017. Bibcode:2010Natur.464.1012U. doi:10.1038/nature08925. PMC 4466108. PMID 20393556.
  37. Chin, Chen-Shan; Sorenson, Jon; Harris, Jason B.; Robins, William P.; Charles, Richelle C.; Jean-Charles, Roger R.; Bullard, James; Webster, Dale R.; Kasarskis, Andrew; Peluso, Paul; Paxinos, Ellen E.; Yamaichi, Yoshiharu; Calderwood, Stephen B.; Mekalanos, John J.; Schadt, Eric E.; Waldor, Matthew K. (January 6, 2011). "The Origin of the Haitian Cholera Outbreak Strain". New England Journal of Medicine. 364 (1): 33–42. doi:10.1056/NEJMoa1012928. PMC 3030187. PMID 21142692.
  38. Rasko, David A.; Webster, Dale R.; Sahl, Jason W.; Bashir, Ali; Boisen, Nadia; Scheutz, Flemming; Paxinos, Ellen E.; Sebra, Robert; Chin, Chen-Shan; Iliopoulos, Dimitris; Klammer, Aaron; Peluso, Paul; Lee, Lawrence; Kislyuk, Andrey O.; Bullard, James; Kasarskis, Andrew; Wang, Susanna; Eid, John; Rank, David; Redman, Julia C.; Steyert, Susan R.; Frimodt-Møller, Jakob; Struve, Carsten; Petersen, Andreas M.; Krogfelt, Karen A.; Nataro, James P.; Schadt, Eric E.; Waldor, Matthew K. (August 25, 2011). "Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany". New England Journal of Medicine. 365 (8): 709–717. doi:10.1056/NEJMoa1106920. PMC 3168948. PMID 21793740.
  39. Ribeiro, Filipe J.; Przybylski, Dariusz; Yin, Shuangye; Sharpe, Ted; Gnerre, Sante; Abouelleil, Amr; Berlin, Aaron M.; Montmayeur, Anna; Shea, Terrance P.; Walker, Bruce J.; Young, Sarah K.; Russ, Carsten; Nusbaum, Chad; MacCallum, Iain; Jaffe, David B. (November 1, 2012). "Finished bacterial genomes from shotgun sequence data". Genome Research. 22 (11): 2270–2277. doi:10.1101/gr.141515.112. PMC 3483556. PMID 22829535.
  40. Bashir, Ali; Klammer, Aaron A.; Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M.; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E. (July 5, 2012). "A hybrid approach for the automated finishing of bacterial genomes". Nature Biotechnology. 30 (7): 701–707. doi:10.1038/nbt.2288. PMC 3731737. PMID 22750883.
  41. Koren, Sergey; Schatz, Michael C.; Walenz, Brian P.; Martin, Jeffrey; Howard, Jason T.; Ganapathy, Ganeshkumar; Wang, Zhong; Rasko, David A.; McCombie, W. Richard; Jarvis, Erich D.; Phillippy, Adam M. (July 5, 2012). "Hybrid error correction and de novo assembly of single-molecule sequencing reads". Nature Biotechnology. 30 (7): 693–700. doi:10.1038/nbt.2280. PMC 3707490. PMID 22750884.
  42. Koren, Sergey; Harhay, Gregory P.; Smith, Timothy PL; Bono, James L.; Harhay, Dayna M.; Mcvey, Scott D.; Radune, Diana; Bergman, Nicholas H.; Phillippy, Adam M. (September 13, 2013). "Reducing assembly complexity of microbial genomes with single-molecule sequencing". Genome Biology. 14 (9): R101. arXiv:1304.3752. Bibcode:2013arXiv1304.3752K. doi:10.1186/gb-2013-14-9-r101. PMC 4053942. PMID 24034426.
  43. Clark, Tyson A.; Spittle, Kristi E.; Turner, Stephen W.; Korlach, Jonas (December 20, 2011). "Direct Detection and Sequencing of Damaged DNA Bases". Genome Integrity. 2 (1): 10. doi:10.1186/2041-9414-2-10. PMC 3264494. PMID 22185597.
  44. Clark, Tyson A.; Murray, Iain A.; Morgan, Richard D.; Kislyuk, Andrey O.; Spittle, Kristi E.; Boitano, Matthew; Fomenkov, Alexey; Roberts, Richard J.; Korlach, Jonas (February 1, 2012). "Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing". Nucleic Acids Research. 40 (4): e29. doi:10.1093/nar/gkr1146. PMC 3287169. PMID 22156058.
  45. Song, Chun-Xiao; Clark, Tyson A.; Lu, Xing-Yu; Kislyuk, Andrey; Dai, Qing; Turner, Stephen W.; He, Chuan; Korlach, Jonas (January 5, 2012). "Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine". Nature Methods. 9 (1): 75–77. doi:10.1038/nmeth.1779. PMC 3646335. PMID 22101853.
  46. "Pacific Biosciences Team Demonstrates Method for Directly Detecting Methylation During SMRT Sequencing". GenomeWeb.
  47. Murray, Iain A.; Clark, Tyson A.; Morgan, Richard D.; Boitano, Matthew; Anton, Brian P.; Luong, Khai; Fomenkov, Alexey; Turner, Stephen W.; Korlach, Jonas; Roberts, Richard J. (December 1, 2012). "The methylomes of six bacteria". Nucleic Acids Research. 40 (22): 11450–11462. doi:10.1093/nar/gks891. PMC 3526280. PMID 23034806 – via academic.oup.com.
  48. "PacBio, U Chicago Develop Single-Molecule Hydroxymethylation Sequencing Technique". GenomeWeb.
  49. "Investigators Validate FLT3 Kinase Domain as Acute Myeloid Leukemia Target". April 16, 2012.
  50. Smith, Catherine C.; Wang, Qi; Chin, Chen-Shan; Salerno, Sara; Damon, Lauren E.; Levis, Mark J.; Perl, Alexander E.; Travers, Kevin J.; Wang, Susana; Hunt, Jeremy P.; Zarrinkar, Patrick P.; Schadt, Eric E.; Kasarskis, Andrew; Kuriyan, John; Shah, Neil P. (May 5, 2012). "Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia". Nature. 485 (7397): 260–263. Bibcode:2012Natur.485..260S. doi:10.1038/nature11016. PMC 3390926. PMID 22504184.
  51. Carneiro, Mauricio O.; Russ, Carsten; Ross, Michael G.; Gabriel, Stacey B.; Nusbaum, Chad; DePristo, Mark A. (August 5, 2012). "Pacific biosciences sequencing technology for genotyping and variation discovery in human data". BMC Genomics. 13 (1): 375. doi:10.1186/1471-2164-13-375. PMC 3443046. PMID 22863213.
  52. Loomis, Erick W.; Eid, John S.; Peluso, Paul; Yin, Jun; Hickey, Luke; Rank, David; McCalmon, Sarah; Hagerman, Randi J.; Tassone, Flora; Hagerman, Paul J. (October 11, 2012). "Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene". Genome Research. 23 (1): 121–128. doi:10.1101/gr.141705.112. PMC 3530672. PMID 23064752 – via genome.cshlp.org.
  53. "Biotechniques (Dec 2012) "Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation"". Archived from the original on Sep 3, 2017.
  54. Sharon, Donald; Tilgner, Hagen; Grubert, Fabian; Snyder, Michael (November 5, 2013). "A single-molecule long-read survey of the human transcriptome". Nature Biotechnology. 31 (11): 1009–1014. doi:10.1038/nbt.2705. PMC 4075632. PMID 24108091.
  55. Proceedings of the National Academy of Scientists USA (Nov 26, 2013) "Characterization of the human ESC transcriptome by hybrid sequencing"
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