Skip to main content
SpringerLink
Log in
Book cover

Pyrosequencing® Protocols pp 1–13Cite as

The History of Pyrosequencing®

  • Protocol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 373))

Abstract

One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fullbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. The technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Nyrén, P. (2001) Method for sequencing DNA based on the detection of the relese of pyrophosphate and enzymatic nucleotide degradation. Patents: US 6 258 568BI and WO98/28440.

    Google Scholar 

  2. Ronaghi, M., Uhlén, M., and Nyrén, P. (1998) A sequencing method based on real-time pyrophosphate detection. Science 281, 363–365.

    Article  CAS  PubMed  Google Scholar 

  3. Margulies, M., Egholm, M., Altman, W. E., et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.

    CAS  PubMed  Google Scholar 

  4. Runswick, M. J., Powell, S. J., Nyrén, P., and Walker, J. W. (1987) Sequence of the bovine mitochondrial phosphate carrier protein: structural relationship to ADP/ATP translocase and the brown fat mitochondria uncoupling protein. EMBO J. 6, 1367–1373.

    CAS  PubMed  Google Scholar 

  5. Nyrén, P. and Lundin, A. (1985) Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal. Biochem. 151, 504–509.

    Article  PubMed  Google Scholar 

  6. Nyrén, P., Nore, B. F., and Baltscheffsky, M. (1986) Studies on photosynthetic inorganic pyrophosphate formation in Rhodospirillum rubrum chromatophores. Biochim. Biophys. Acta 851, 276–282.

    Article  Google Scholar 

  7. Nyrén, P., Nore, B. F., and Baltscheffsky, M. (1986) Inorganic pyrophosphate synthesis after a short light flash in chromatophores from Rhodospirillum rubrum. Photobiochem. Photobiophys. 11, 189–196.

    Google Scholar 

  8. Nyrén, P. (1987) Enzymatic method for continuous monitoring of DNA-polymerase activity. Anal. Biochem. 167, 235–238.

    Article  PubMed  Google Scholar 

  9. Melamede, R. J. (1985) Automatable process for sequencing nucleotide. US Patent 4863849.

    Google Scholar 

  10. Ståhl, S., Hultman, T., Moks, T., and Uhlén, M. (1988) Solid phase DNA sequencing using the biotin-avidin system. Nucleic Acids Res. 16, 3025–3038.

    Article  PubMed  Google Scholar 

  11. Nyrén, P. (1994) Apyrase immobilized on paramagnetic beads used to improve detection limits in bioluminometric ATP monitoring. J. Biolumin. Chemilumin. 9, 29–34.

    Article  PubMed  Google Scholar 

  12. Nyrén, P., Pettersson, B., and Uhlén, M. (1993) Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal. Biochem. 208, 171–175.

    Article  PubMed  Google Scholar 

  13. Nyrén, P., Karamouhamed, S., and Ronaghi, M. (1997) Detection of single-base changes using a bioluminometric primer extension assay. Anal. Biochem. 244, 367–373.

    Article  PubMed  Google Scholar 

  14. Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M., and Nyrén, P. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242, 84–89.

    Article  CAS  PubMed  Google Scholar 

  15. Nyrén, P. (1994) A method for the detection of cells, cell lysis or cell-lysing activity, Swedish patent application.

    Google Scholar 

  16. Nyrén, P. and Edwin, V. (1994) Inorganic pyrophosphate-based detections: Detection and enumeration of cells. Anal. Biochem. 220, 39–45.

    Article  PubMed  Google Scholar 

  17. Nyrén, P. and Edwin, V. (1994) Inorganic pyrophosphate-based detections: Detection and quantification of cell lysis and cell-lysing activity. Anal. Biochem. 220, 46–52.

    Article  PubMed  Google Scholar 

  18. Karamohamed, S., Nordström, T., and Nyrén, P. (1999) A real-time bioluminometric method for detection of nucleoside diphosphate kinase activity. Biotechniques 26, 728–734.

    CAS  PubMed  Google Scholar 

  19. Karamouhamed, S., Nilsson, J., Nourizad, K., Ronaghi, M., Pettersson, B., and Nyrén, P. (1999) Production, purification, and real-time functional analysis of recombinant Saccharomyces cervisiae MET3 adenosine triphosphate sulfurylase expressed in Escherichia coli. Protein Expr. Purif. 15, 381–388.

    Article  Google Scholar 

  20. Ronaghi, M. (2000) Improved performance of Pyrosequencing using single-stranded DNA-binding protein. Anal. Biochem. 286, 282–288.

    Article  CAS  PubMed  Google Scholar 

  21. Nordström, T., Gharizadeh, B., Pourmand, N., Nyrén, P., and Ronaghi. M. (2001) Method enabling fast partial sequencing of cDNA clones. Anal. Biochem. 292, 266–271.

    Article  PubMed  Google Scholar 

  22. Nordström, T., Ronaghi, M., and Nyrén, P. (1999) Automation of a novel DNA sequencing method. In: Bioluminescence and Chemiluminescence: Perspective for the 21st Century, (Roda, A., Pazzagli, M., Kricka, L. J., and Stanley, P. E., eds.), John Wiley and Sons, Hoboken, NJ, pp. 528–531.

    Google Scholar 

  23. Gharizadeh, B., Nordström, T., Ahmadian, A., Ronaghi, M., and Nyrén, P. (2002) Long read Pyrosequencing using pure 2′-deoxyadenosine-5′-O′-(1-thiotriphosphate) Sp-isomer. Anal. Biochem. 301, 82–90.

    Article  CAS  PubMed  Google Scholar 

  24. Eriksson, J., Gharizadeh, B., Nourizad, N., and Nyrén, P. (2004) 7-deaza-2′-deoxyadenosine-5′-triphosphate as an alternative nucleotide for the Pyrosequencing technology. Nucleosides Nucleotides Nucleic Acids 23, 1583–1594.

    Article  CAS  PubMed  Google Scholar 

  25. Gharizadeh, B., Eriksson, J., Nourizad, N., Nordström, T., and Nyrén, P. (2004) Improvements in Pyrosequencing technology by employing Sequenase polymerase. Anal. Biochem. 330, 272–280.

    Article  CAS  PubMed  Google Scholar 

  26. Eriksson, J., Nordström, T., and Nyrén, P. (2003) Method enabling firefly luciferase based bioluminometric assays at elevated temperature. Anal. Biochem. 314, 158–161.

    Article  CAS  PubMed  Google Scholar 

  27. Eriksson, J., Gharizadeh, B., Nordström, T., and Nyrén, P. (2004) Pyrosequencing technology at elevated temperature. Electrophoresis 25, 20–27.

    Article  CAS  PubMed  Google Scholar 

  28. Nordström, T., Ronaghi, M., Morgenstern, R., Ekström, L., de Faire, U., and Nyrén, P. (2000) Direct analysis of single nucleotide polymorphism on double-stranded DNA. Biotechnol. Appl. Biochem. 31, 107–112.

    Article  PubMed  Google Scholar 

  29. Nordström, T., Nourizad, K., Ronaghi, M., and Nyrén, P. (2000) Method enabling Pyrosequencing on double-stranded DNA. Anal. Biochem. 282, 186–193.

    Article  PubMed  Google Scholar 

  30. Nordström, T., Alderborn, A., and Nyrén, P. (2002) Method for one-step preparation of double-stranded DNA template applicable for use with Pyrosequencing technology. J. Biochem. Biophys. Methods 52, 71–82.

    Article  PubMed  Google Scholar 

  31. Garcia, C. A., Ahmadian, A., Garizadeh, B., Lundeberg, J., Ronaghi, M., and Nyrén, P. (2000) Mutation detection by Pyrosequencing: sequencing of exons 5 to 8 of the p53 tumor suppressor gene. Gene 253, 249–257.

    Article  CAS  PubMed  Google Scholar 

  32. Nourizad, N., Gharizadeh, B., and Nyrén, P. (2003) Method for clone checking. Electrophoresis 24, 1712–1715.

    Article  CAS  PubMed  Google Scholar 

  33. Gharizadeh, B., Ghaderi, M., Donnelly, D., Wallin, K-L., and Nyrén, P. (2003) Multiple-primer DNA sequencing method. Electrophoresis 24, 1145–1151.

    Article  CAS  PubMed  Google Scholar 

  34. Gharizadeh, B., Ohlin, A., Mölling, P., et al. (2003) Multiple group-specific sequencing primers for reliable and rapid DNA sequencing. Mol. Cell. Probe 17, 203–210.

    Article  CAS  Google Scholar 

  35. Gharizadeh, B., Oggionni, M., Zheng, B., et al. (2005) Type-specific multiple sequencing primers: a novel strategy for reliable and rapid genotyping of human papillomaviruses by Pyrosequencing technology. J. Mol. Diagn. 7, 198–205.

    Article  CAS  PubMed  Google Scholar 

  36. Leamon, J. H., Lee, W. L., Tartaro, K. R., et al. (2003) A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reaction. Electrophoresis 24, 3769–3777.

    Article  CAS  PubMed  Google Scholar 

  37. Ahmadian, A., Gharizadeh, B., Gustafsson, A., et al. (2000) Single nucleotide polymorphism analysis by Pyrosequencing. Anal. Biochem. 280, 103–110.

    Article  CAS  PubMed  Google Scholar 

  38. Gruber, J. D., Colligan, P. B., and Wolford, J. K. (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using Pyrosequencing. Hum. Genet. 110, 395–401.

    Article  CAS  PubMed  Google Scholar 

  39. Uhlmann, K., Brinckmann, A., Toliat, M. R., Ritter, H., and Nurnberg, P. (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 23, 4072–4079.

    Article  CAS  PubMed  Google Scholar 

  40. Ahmadian, A., Lundeberg J., Nyrén, P., Uhlén, M., and Ronaghi, M. (2000) Analysis of the p53 tumor supressor gene by Pyrosequencing. Biotechniques 28, 140–147.

    CAS  PubMed  Google Scholar 

  41. Goriely, A, McVean, G. A., Rojmyr, M., Ingemarsson, B., and Wilkie, A.O. (2003) Evidence for selective advantage of pathogenic FGFR2 mutations in the male germ line. Science 301, 643–646.

    Article  CAS  PubMed  Google Scholar 

  42. Andreasson, H., Asp, A., Alderborn, A., Gyllensten, U., and Allen, M. (2002) Mitochondrial sequence analysis for forensic identification using Pyrosequencing technology. Biotechniques 32, 124–133.

    CAS  PubMed  Google Scholar 

  43. Allen, M. and Andreasson, H. (2005) Mitochondrial D-loop and coding sequence analysis using Pyrosequencing. Methods Mol. Biol. 297, 179–196.

    CAS  PubMed  Google Scholar 

  44. Cebula, T. A., Brown, E. W., Jackson, S. A., Mammel, M. K., Mukherjee, A., and LeClerc, J. E. (2005) Molecular applications for identifying microbial pathogens in the post-9/11 era. Expert Rev. Mol. Diagn. 5, 431–445.

    Article  CAS  PubMed  Google Scholar 

  45. Gharizadeh, B., Norberg, E., Löffler, J., et al. (2004) Identification of medically important fungi by Pyrosequencing technology. Mycoses 47, 29–33.

    Article  CAS  PubMed  Google Scholar 

  46. Gharizadeh, B., Kalantari, M., Garcia, C., Johansson, B., and Nyrén, P. (2001) Typing of human papillomavirus (HPV) by Pyrosequencing. Laboratory Investigation 81, 673–679.

    Article  CAS  PubMed  Google Scholar 

  47. Milan, D., Jeon, J. T., Looft, C., et al. (2000) A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science 19, 1248–1251.

    Article  Google Scholar 

  48. Mochida, K., Yamazaki, Y., and Ogihara, Y. (2003) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Genet. Genomics 270, 371–377.

    Article  CAS  PubMed  Google Scholar 

  49. Svantesson, S., Westermark, P. O., Hellgren Kotaleski, J., Gharizadeh, B., Lansner, A., and Nyrén, P. (2004) A mathematical model of the Pyrosequencing reaction system. Biophys. Chemist. 110, 129–145.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology, AlbaNova University Center, Stockholm, Sweden

    Pål Nyrén

Authors
  1. Pål Nyrén
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Division of Oncology, Washington University School of Medicine, St. Louis, MO

    Sharon Marsh

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Humana Press Inc.

About this protocol

Cite this protocol

Nyrén, P. (2007). The History of Pyrosequencing®. In: Walker, J.M., Marsh, S. (eds) Pyrosequencing® Protocols. Methods in Molecular Biology™, vol 373. Humana Press. https://doi.org/10.1385/1-59745-377-3:1

Download citation

  • DOI: https://doi.org/10.1385/1-59745-377-3:1

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-645-0

  • Online ISBN: 978-1-59745-377-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation