We developed a rapid single nucleotide polymorphism (SNP) detection system named smart amplification process version 2 (SMAP 2). Because DNA amplification only occurred with a perfect primer match, amplification alone was sufficient to identify the target allele. To achieve the requisite fidelity to support this claim, we used two new and complementary approaches to suppress exponential background DNA amplification that resulted from mispriming events. SMAP 2 is isothermal and achieved SNP detection from whole human blood in 30 min when performed with a new DNA polymerase that was cloned and isolated from Alicyclobacillus acidocaldarius (Aac pol). Furthermore, to assist the scientific community in configuring SMAP 2 assays, we developed software specific for SMAP 2 primer design. With these new tools, a high-precision and rapid DNA amplification technology becomes available to aid in pharmacogenomic research and molecular-diagnostics applications.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

  2. 2.

    et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

  3. 3.

    et al. High-density single-nucleotide polymorphism maps of the human genome. Genomics 86, 117–126 (2005).

  4. 4.

    Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004).

  5. 5.

    et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).

  6. 6.

    et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673–678 (2003).

  7. 7.

    et al. Large-scale genotyping of complex DNA. Nat. Biotechnol. 21, 1233–1237 (2003).

  8. 8.

    et al. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17, 292–296 (1999).

  9. 9.

    et al. High-throughput SNP genotyping on universal bead arrays. Mutat. Res. 573, 70–82 (2005).

  10. 10.

    & Identification and characterization of a thermostable MutS homolog from Thermus aquaticus. J. Biol. Chem. 271, 5040–5048 (1996).

  11. 11.

    & Validation of the loop-mediated isothermal amplification method for single nucleotide polymorphism genotyping with whole blood. Genome Lett. 2, 119–126 (2003).

  12. 12.

    et al. Association between a novel variant of the human type 2 deiodinase gene Thr92Ala and insulin resistance. Diabetes 51, 880–883 (2002).

  13. 13.

    , , , & Investigation of genetic risk factors associated with alcoholism. Alcohol. Clin. Exp. Res. 20, 293A–296A (1996).

  14. 14.

    & New strategy for detection of ALDH2 mutant. Alcohol Alcohol. (Suppl.) 1A, 11–13 (1993).

  15. 15.

    et al. The major genetic defect responsible for the polymorphism of S-mephenytoin metabolism in humans. J. Biol. Chem. 269, 15419–15422 (1994).

  16. 16.

    & Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365–386 (2000).

  17. 17.

    et al. Time of onset of non-insulin-dependent diabetes mellitus and genetic variation in the beta 3-adrenergic-receptor gene. N. Engl. J. Med. 333, 343–347 (1995).

  18. 18.

    , , & DNA nucleic acid sequence-based amplification-based genotyping for polymorphism analysis. Biotechniques 37, 680–686 (2004).

  19. 19.

    et al. Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms. Nucleic Acids Res. 30, e60 (2002).

  20. 20.

    , , , & Homogeneous real-time detection of single-nucleotide polymorphisms by strand displacement amplification on the BD ProbeTec ET system. Clin. Chem. 49, 1599–1607 (2003).

Download references


We thank A. Wada for support and encouragement, T. Ishikawa (Tokyo Institute of Technology) for his constructive discussion about the application of this technology and future prospects, M. Matsunaga, J. Nakashima, M. Matsushita and S. Uno for technical assistance. We acknowledge K. Nakano (NTT Software Corporation) for assistance in web support and software design. We also thank H. Daub and M. Nishikawa (RIKEN) for their editorial and coordination efforts. This study was mainly supported by the research grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japan (MEXT) to Y. Hayashizaki, and RIKEN “Research Collaborations with Industry” Program to K. Shibata. S. Kuramitsu is supported by the Research Grant for National Project on Protein Structure and Functional Analysis from MEXT.

Author information


  1. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

    • Yasumasa Mitani
    • , Alexander Lezhava
    • , Yuki Kawai
    • , Takeshi Kikuchi
    • , Atsuko Oguchi-Katayama
    • , Yasushi Kogo
    • , Hideki Takakura
    • , Kanako Hoshi
    • , Takahiro Arakawa
    • , Paul E Cizdziel
    •  & Yoshihide Hayashizaki
  2. K.K. Dnaform, 75-1, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan.

    • Yasumasa Mitani
    • , Yuki Kawai
    • , Takeshi Kikuchi
    •  & Chiaki Kato
  3. Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.

    • Masayoshi Itoh
    • , Kazuhiro Shibata
    •  & Yoshihide Hayashizaki
  4. Wakunaga Pharmaceutical Co. Ltd., 1624 Shimokotachi, Koda-cho, Akitakata-shi, Hiroshima, 739-1195, Japan.

    • Toru Miyagi
    •  & Takanori Oka
  5. Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, 3-9, Fukuura Kanazawa-ku, Yokohama, 236-0004, Japan.

    • Hideki Takakura
    • , Kanako Hoshi
    •  & Hiroshi Shimada
  6. Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

    • Kenji Fukui
    • , Ryoji Masui
    •  & Seiki Kuramitsu
  7. RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kohto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

    • Kenji Fukui
    • , Ryoji Masui
    •  & Seiki Kuramitsu
  8. Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma 370-0033, Japan.

    • Kazuma Kiyotani
    •  & Tetsuya Kamataki
  9. Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.

    • Alistair Chalk
  10. Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan.

    • Katsuhiko Tsunekawa
    •  & Masami Murakami


  1. Search for Yasumasa Mitani in:

  2. Search for Alexander Lezhava in:

  3. Search for Yuki Kawai in:

  4. Search for Takeshi Kikuchi in:

  5. Search for Atsuko Oguchi-Katayama in:

  6. Search for Yasushi Kogo in:

  7. Search for Masayoshi Itoh in:

  8. Search for Toru Miyagi in:

  9. Search for Hideki Takakura in:

  10. Search for Kanako Hoshi in:

  11. Search for Chiaki Kato in:

  12. Search for Takahiro Arakawa in:

  13. Search for Kazuhiro Shibata in:

  14. Search for Kenji Fukui in:

  15. Search for Ryoji Masui in:

  16. Search for Seiki Kuramitsu in:

  17. Search for Kazuma Kiyotani in:

  18. Search for Alistair Chalk in:

  19. Search for Katsuhiko Tsunekawa in:

  20. Search for Masami Murakami in:

  21. Search for Tetsuya Kamataki in:

  22. Search for Takanori Oka in:

  23. Search for Hiroshi Shimada in:

  24. Search for Paul E Cizdziel in:

  25. Search for Yoshihide Hayashizaki in:

Competing interests

Some of the authors of this manuscript are employed by or affiliated with the corporations K.K. DNAFORM and Wakunaga Pharmaceutical Co. Ltd. Y.M., Y.K., T.K. and C.K. are employed by K.K. DNAFORM. T.M. and T.O. are employed by Wakunaga Pharmaceutical Co., Ltd.

It is the intention of K.K. DNAFORM to commercialize the technology described in this manuscript for research and diagnostic purposes.

Corresponding author

Correspondence to Yoshihide Hayashizaki.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Comparison of background amplification pathways of SMAP ver.2 and LAMP.

  2. 2.

    Supplementary Fig. 2

    SMAP ver.2 amplification of the type 2 iodothyronine deiodinase (DIO2) gene.

  3. 3.

    Supplementary Fig. 3

    Amplification time course of DIO2 allele by SMAP and LAMP methods.

  4. 4.

    Supplementary Fig. 4

    Electrophoresis photograph of SMAP and LAMP amplification products.

  5. 5.

    Supplementary Fig. 5

    SMAP ver.2 amplification of the human b3 adrenergic receptor (ADRB3) gene.

  6. 6.

    Supplementary Fig. 6

    Sensitivity determination of SMAP ver.2.

  7. 7.

    Supplementary Methods

About this article

Publication history






Further reading