title: Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology.
abstract: 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.
authors.affiliation: 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.
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Mitani
authors.forename: Alexander
authors.initials: A
authors.lastname: Lezhava
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kawai
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kikuchi
authors.forename: Atsuko
authors.initials: A
authors.lastname: Oguchi-Katayama
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Kogo
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Itoh
authors.forename: Toru
authors.initials: T
authors.lastname: Miyagi
authors.forename: Hideki
authors.initials: H
authors.lastname: Takakura
authors.forename: Kanako
authors.initials: K
authors.lastname: Hoshi
authors.forename: Chiaki
authors.initials: C
authors.lastname: Kato
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Shibata
authors.forename: Kenji
authors.initials: K
authors.lastname: Fukui
authors.forename: Ryoji
authors.initials: R
authors.lastname: Masui
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
authors.forename: Kazuma
authors.initials: K
authors.lastname: Kiyotani
authors.forename: Alistair
authors.initials: A
authors.lastname: Chalk
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Tsunekawa
authors.forename: Masami
authors.initials: M
authors.lastname: Murakami
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Kamataki
authors.forename: Takanori
authors.initials: T
authors.lastname: Oka
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shimada
authors.forename: Paul E
authors.initials: PE
authors.lastname: Cizdziel
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch / Q000235:genetics*; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D013489:Suppression, Genetic / Q000235:genetics*; D013696:Temperature
chemical_list: D017931:DNA Primers