Abstract
Single nucleotide alternations such as single nucleotide polymorphisms (SNPs) or single nucleotide mutations are useful genetic markers for molecular diagnosis, prognosis, drug response, and predisposition to diseases. Rapid identification of SNPs or mutations is clinically important, especially for determining drug responses and selection of molecular-targeted therapy. Here, we describe a rapid genotyping assay based on the allele-specific polymerase chain reaction (AS-PCR) by using our droplet-PCR machine (droplet-AS-PCR).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aomori T, Yamamoto K, Oguchi-Katayama A, Kawai Y, Ishidao T, Mitani Y, Kogo Y, Lezhava A, Fujita Y, Obayashi K, Nakamura K, Kohnke H, Wadelius M, Ekström L, Skogastierna C, Rane A, Kurabayashi M, Murakami M, Cizdziel PE, Hayashizaki Y, Horiuchi R (2009) Rapid single-nucleotide polymorphism detection of cytochrome P450 (CYP2C9) and vitamin K epoxide reductase (VKORC1) genes for the warfarin dose adjustment by the SMart-amplification process version 2. Clin Chem 55:804–812
Yin T, Miyata T (2007) Warfarin dose and the pharmacogenomics of CYP2C9 and VKORC1: rationale and perspectives. Thromb Res 120:1–10
Oguro R, Kamide K, Katsuya T, Akasaka H, Sugimoto K, Congrains A, Arai Y, Hirose N, Saitoh S, Ohishi M, Miura T, Rakugi H (2012) A single nucleotide polymorphism of the adenosine deaminase, RNA-specific gene is associated with the serum triglyceride level, abdominal circumference, and serum adiponectin concentration. Exp Gerontol 47:183–187
Wagner KW, Ye Y, Lin J, Vaporciyan AA, Roth JA, Wu X (2012) Genetic variations in epigenetic genes are predictors of recurrence in stage I or II non-small cell lung cancer patients. Clin Cancer Res 18:585–592
Park C, Han S, Lee KM, Choi JY, Song N, Jeon S, Park SK, Ahn HS, Shin HY, Kang HJ, Koo HH, Seo JJ, Choi JE, Kang D (2012) Association between CASP7 and CASP14 genetic polymorphisms and the risk of childhood leukemia. Hum Immunol 73:736–739
Matsuda K, Yamaguchi A, Taira C, Sueki A, Koeda H, Takagi F, Sugano M, Honda T (2012) A novel high-speed droplet-polymerase chain reaction can detect human influenza virus in less than 30 min. Clin Chim Acta 413:1742–1745
Sueki A, Matsuda K, Taira C, Yamaguchi A, Koeda H, Takagi F, Kobayashi Y, Sugano M, Honda T (2013) Rapid detection of PML-RARA fusion gene by novel high-speed droplet-reverse transcriptase-polymerase chain reaction: possibility for molecular diagnosis without lagging behind the morphological analyses. Clin Chim Acta 415:276–278
Taira C, Matsuda K, Yamaguchi A, Sueki A, Koeda H, Takagi F, Kobayashi Y, Sugano M, Honda T (2013) Novel high-speed droplet-allele specific-polymerase chain reaction: application in the rapid genotyping of single nucleotide polymorphisms. Clin Chim Acta 424:39–46
Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17:2503–2516
Matsuda K, Sakashita K, Taira C, Tanaka-Yanagisawa M, Yanagisawa R, Shiohara M, Kanegane H, Hasegawa D, Kawasaki K, Endo M, Yajima S, Sasaki S, Kato K, Koike K, Kikuchi A, Ogawa A, Watanabe A, Sotomatsu M, Nonoyama S, Koike K (2010) Quantitative assessment of PTPN11 or RAS mutations at the neonatal period and during the clinical course in patients with juvenile myelomonocytic leukaemia. Br J Haematol 148:593–599
Taira C, Matsuda K, Kamijyo Y, Sakashita K, Ishida F, Kumagai T, Yamauchi K, Okumura N, Honda T (2011) Quantitative monitoring of single nucleotide mutations by allele-specific quantitative PCR can be used for the assessment of minimal residual disease in patients with hematological malignancies throughout their clinical course. Clin Chim Acta 412:53–58
Taira C, Matsuda K, Saito S, Sakashita K, Sugano M, Okumura N, Honda T (2012) Application of allele-specific quantitative PCR using genomic DNA to monitor minimal residual disease based on mutant gene levels following allogeneic hematopoietic stem cell transplantation in patients with hematological malignancies: comparison of mutant levels with autologous DNA percentage by short tandem repeat-PCR. Clin Chim Acta 413:516–519
Matsuda K, Sugano M, Honda T (2012) PCR for monitoring of minimal residual disease in hematologic malignancy. Clin Chim Acta 413:74–80
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Matsuda, K., Honda, T. (2015). High-Speed Droplet-Allele-Specific Polymerase Chain Reaction for Genotyping of Single Nucleotide Polymorphisms. In: Bugert, P. (eds) Molecular Typing of Blood Cell Antigens. Methods in Molecular Biology, vol 1310. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2690-9_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2690-9_3
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2689-3
Online ISBN: 978-1-4939-2690-9
eBook Packages: Springer Protocols