Biomics

Improving the technologies of massive parallel DNA sequencing and making them more affordable in clinical studies could lead to the explosive growth of the volume of market sales of sequencers and reagents necessary for their run. The current leader on this market is Illumina that exploits a fluorescence-based technology for reading DNA sequences, although potential for its improvement has been substantially depleted. Semiconductor sequencing technology conceived by Jonathan Rothberg and Ion Torrent lags behind the Illumina platform by a number of parameters but develops rapidly and has a significant unused potential. This review presents a brief description of this technology and the history of its origin. A special attention is focused on unused capabilities of semiconductor sequencing technology and outlooks for its further development.

sequencing, pyrosequencing, DNA, human genome, Rothberg, Ion Torrent, Illumina, PGM, sequencer, CMOS technology, pH-sensing chip, BSI

1. An integrated semiconductor device enabling non-optical genome sequencing / J.M. Rothberg, W. Hinz, T.M. Rearick, et al. / Nature. - 2011. - Vol. 475. - P. 348-352.
2. Progress in Ion Torrent semiconductor chip based sequencing / B. Merriman, Ion Torrent R&D Team, J.M. Rothberg // Electrophoresis. - 2012. - Vol. 33. - P. 3397-3417.
3. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units / C.J. Saunders, N.A. Miller, S.E. Soden, et al. // Sci. Med. - 2012. - Vol. 4. - No 154. - P. 154ra135.
4. http://www.illumina.com/clinical/illumina_clinical_laboratory/igs_for_patients.ilmn
5. Nyrén P., Lundin A. Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis / Anal. Biochem. - 1985. - Vol. 151. - No 2. - P. 504-509.
6. Hyman E.D. A new method of sequencing DNA / Anal. Biochem. - 1988. - Vol.174. - No 2. - P.  423-436.
7. Hyman E.D. Pyrophosphate-based method and apparatus for sequencing nucleic acids / PCT Pat. 1989/009283.
8. The complete genome of an individual by massively parallel DNA sequencing / D.A. Wheeler, M. Srinivasan, M. Egholm, et al. // Nature. - 2008. - Vol. 17. - No 452. - P. 872-876.
9. Sakurai Т., Husimi Y. Real-time monitoring of DNA polymerase reactions by a micro ISFET pH sensor / Anal. Chem. - 1992. - Vol. 64. - No 17. - P. 1996-1997.
10. Toumazou С., Purushothaman S. Sensing apparatus and method / GB Pat. Appl. No 0105831.2 (09.02.2001).
11. Purushothaman S., Toumazou С., Georgiou J. Towards fast solid state DNA sequencing / Circuits and Systems. - 2002. - Vol. 4. - P. 169-172.
12. Purushothaman S., Toumazou С., Ou C.P. Protons and single nucleotide polymorphism detection: A simple use for the ion sensitive field effect transistor / Sensors and Actuators. - 2006. - Vol. 114. - No 2. - P. 964-968.
13. Simultaneous DNA amplification and detection using a pH-sensing semiconductor system / C. Toumazou, L. Shepherd, S.C. Reed, et al. // Nat. Methods. - 2013. - Vol.10. - No 7. - P. 641-646.
14. Toumazou С., Purushothaman S. Sensing apparatus and method / US Pat. Appl. 2004-0134798.
15. Toumazou С., Purushothaman S. Sensing apparatus and method / US Pat. 8114591 B2 (14.02.2012).
16. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing / E. Knierim, B. Lucke, J.M. Schwarz, M. Schuelke, D. Seelow // PLoS ONE. - 2011. - Vol. 6. - No 11. - e28240.
17. Evaluation and optimization of preparative semi-automated electrophoresis systems for Illumina library preparation / M.A. Quail MA, Y. Gu, H. Swerdlow, M. Mayho // Electrophoresis. – 2012. – Vol. 33. - No 23. – P. 3521-3528.
18. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing / M. Meyer, A.W. Briggs, T. Maricic, et al. // Nucleic Acids Research. – 2008. - Vol. 36. - No 1. - e5.
19. Quality control of next-generation sequencing library through an integrative digital microfluidic platform / N. Thaitrong, H. Kim, R.F. Renzi, et al. // Electrophoresis. – 2012. – Vol. 33. - No 23. – P. 3506-3513.
20. Real-time DNA sequencing using detection of pyrophosphate release / M. Ronaghi, S. Karamohamed, B. Pettersson, M. Uhlén, P. Nyrén // Anal. Biochem. – 1996. – Vol. 242. - No 1. – P. 84-89.
21. Chemosensors for pyrophosphate / S.K. Kim, D.H. Lee, J.I. Hong, J. Yoon / Acc. Chem. Res. – 2009. – Vol. 42. - No 1. – P. 23-31.
22. A novel NIR fluorescent turn-on sensor for the detection of pyrophosphate anion in complete water system / W. Zhu, et al. // Chem. Commun. – 2012. – Vol. 48. – P. 1784–1786.
23. Novel dinuclear metal complex and pyrophosphate assay using the same / J.I. Hong, et al. // US Pat. Appl. 20050119497.
24. Lee D.H., Hong J.I. A fluorescent confirmation method for DNA amplification in PCR through a fluorescent pyrophosphate sensor // Bull. Korean Chem. Soc. – 2008. - Vol. 29. - No 2. – P. 497-498.
25. Surface immobilizable chelator for label-free electrical detection of pyrophosphate / D.J. Liu, G.M. Credo, X. Su, et al. // Chem. Commun. – 2011. – Vol. 47. – P. 8310–8312.
26. Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices / G.M. Credo, X. Su, K. Wu, et al. // Analyst. – 2012. – Vol. 137. - No 6. – P. 1351–1362.
27. Bergveld Р. Thirty years of ISFETOLOGY: What happened in the past 30 years and what may happen in the next 30 years // Sensors and Actuators B. – 2003. – Vol. 88. – P. 1–20.
28. Ion-sensitive field effect transistors fabricated in a commercial CMOS technology / J. Bausells, J. Carrabina, A. Errachid, A. Merlos // Sensors and Actuators B. – 1999. – Vol. 57. – P.56–62.
29. Milgrew M.J., Hammond P.A.,Cumming D.R.S.The development of scalable sensor arrays using standard CMOS technology / Sensors and Actuators B Chem. – 2004. – Vol. – P. 37–42.
30. Milgrew M.J., Riehle M.O.,Cumming D.R.S.A large transistor-based sensor array chip for direct extracellular imaging / Sensors and Actuators B Chem. - - Vol. 111–112. – P. 347–353.
31. http://www.aptina.com/news/FSI-BSI-WhitePaper.pdf
32. http://www.invisage.com/technology
33. http://image-sensors-world.blogspot.ru/2013/06/fujifilm-and-panasonic-present-organic.html
34. Mikolajick T., Kühnhold R., Ryssel H.The pH-sensing properties of tantalum pentoxide films fabricated by metal organic low pressure chemical vapor deposition / Sensors and Actuators B Chem. – 1997. – Vol. – P. 262–267.
35. Methods and apparatus for measuring analytes / J.M. Rothberg, et al. // US Pat. Appl. 2010/0301398 A1 (02.12.2010).
36. Ruzicka J. Lab-on-valve: Universal microflow analyzer based on sequential and bead injection / Analyst. – 2000. – Vol. 125 – P. 1053-1060.
37. Miró M., Hansen E.H. Recent advances and future prospects of mesofluidic Lab-on-a-Valve platforms in analytical sciences – A critical review / Anal. Chim. Acta. – 2012. – 750. – P. 3-15.
38. Vidigal S., Toth I., Rangel A. Sequential injection lab-on-valve platform as a miniaturisation tool for solid phase extraction / Anal. Methods. – 2013. – Vol. 5. – P. 585–597.
39. Radiation resistance of sequencing chips for in situ life detection / C.E. Carr, H. Rowedder, C.S. Lui, et al. // Astrobiology. – - Vol. 1. - No 6. – P. 560-569.
40. Direct electrical detection of DNA synthesis / N. Pourmand, M. Karhanek, H. Persson, et al. // Proc. Natl. Acad. Sci. USA. – Vol. 103. - No 17. – P. 6466-6470.
41. http://dnae.co.uk/wp-content/uploads/2013/04/2013-04-23-DNAe-Roche-statement.pdf
42. http://www.findaphd.com/search/ProjectDetails.aspx?PJID=44914
43. http://www.insilixa.com/