Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology.
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.
Mitani
Yasumasa
Y
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.
Lezhava
Alexander
A
Kawai
Yuki
Y
Kikuchi
Takeshi
T
Oguchi-Katayama
Atsuko
A
Kogo
Yasushi
Y
Itoh
Masayoshi
M
Miyagi
Toru
T
Takakura
Hideki
H
Hoshi
Kanako
K
Kato
Chiaki
C
Arakawa
Takahiro
T
Shibata
Kazuhiro
K
Fukui
Kenji
K
Masui
Ryoji
R
Kuramitsu
Seiki
S
Kiyotani
Kazuma
K
Chalk
Alistair
A
Tsunekawa
Katsuhiko
K
Murakami
Masami
M
Kamataki
Tetsuya
T
Oka
Takanori
T
Shimada
Hiroshi
H
Cizdziel
Paul E
PE
Hayashizaki
Yoshihide
Y
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
D017931:DNA Primers