PMID- 18215653
OWN - NLM
STAT- MEDLINE
DCOM- 20080212
LR  - 20080124
IS  - 1873-4324 (Electronic)
IS  - 0003-2670 (Linking)
VI  - 608
IP  - 2
DP  - 2008 Feb 11
TI  - Estimation of single-nucleotide polymorphism allele frequency by alternately 
      binding probe competitive polymerase chain reaction.
PG  - 211-6
LID - 10.1016/j.aca.2007.12.015 [doi]
AB  - Estimation of single-nucleotide polymorphism (SNP) allele frequency in pooled DNA 
      samples is a promising approach to clarify the relationships between SNPs and 
      diseases. Here, we present a simple, accurate, and cost-effective method for 
      estimating SNP allele frequency, called alternately binding probe (ABProbe) 
      competitive polymerase chain reaction (ABC-PCR) that entails no expensive devices 
      for real-time fluorescence measurement and complex post-PCR steps. We prepared 
      DNA pools of PCR products derived from homozygous samples of three different SNPs 
      (ALDH2, GNB3, and HTR2A) in different portions, and the allele frequencies of 
      these samples were estimated by ABC-PCR. Two alleles were coamplified by PCR with 
      a fluorescent probe that binds to either alleles, and then fluorescence intensity 
      was measured using a simple fluorometer. The ratio of the two alleles was 
      calculated from the fluorescence intensity of the probe at the end-point. The 
      estimated allele frequencies strongly correlated to the expected ratios for all 
      three SNPs with high accuracy. When the allele frequencies were more than 5%, the 
      relative standard deviations (R.S.D.s) of ABC-PCR were less than 20%. Moreover, 
      we also confirmed that this method was applicable to SNP genotyping.
FAU - Noda, Naohiro
AU  - Noda N
AD  - Institute for Biological Resources and Functions, National Institute of Advanced 
      Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 
      305-8566, Japan.
FAU - Tani, Hidenori
AU  - Tani H
FAU - Morita, Nao
AU  - Morita N
FAU - Kurata, Shinya
AU  - Kurata S
FAU - Nakamura, Kazunori
AU  - Nakamura K
FAU - Kanagawa, Takahiro
AU  - Kanagawa T
FAU - Tsuneda, Satoshi
AU  - Tsuneda S
FAU - Sekiguchi, Yuji
AU  - Sekiguchi Y
LA  - eng
PT  - Comparative Study
PT  - Journal Article
DEP - 20071223
PL  - Netherlands
TA  - Anal Chim Acta
JT  - Analytica chimica acta
JID - 0370534
RN  - 0 (DNA Probes)
SB  - IM
MH  - Binding, Competitive
MH  - DNA Probes/analysis/*genetics/*metabolism
MH  - Gene Frequency/*genetics
MH  - Genotype
MH  - Humans
MH  - Polymerase Chain Reaction/*methods
MH  - Polymorphism, Single Nucleotide/*genetics
EDAT- 2008/01/25 09:00
MHDA- 2008/02/13 09:00
CRDT- 2008/01/25 09:00
PHST- 2007/08/17 00:00 [received]
PHST- 2007/12/07 00:00 [revised]
PHST- 2007/12/10 00:00 [accepted]
PHST- 2008/01/25 09:00 [pubmed]
PHST- 2008/02/13 09:00 [medline]
PHST- 2008/01/25 09:00 [entrez]
AID - S0003-2670(07)02026-0 [pii]
AID - 10.1016/j.aca.2007.12.015 [doi]
PST - ppublish
SO  - Anal Chim Acta. 2008 Feb 11;608(2):211-6. doi: 10.1016/j.aca.2007.12.015. Epub 
      2007 Dec 23.