QSNPlite, a software system for quantitative analysis of SNPs based on capillary array SSCP analysis.
We present a newly developed software called "QSNPlite" that comprehensively interprets the data of SSCP and sequencing analyses obtained from capillary array electrophoresis systems used in the quantitative characterization of SNPs. QSNPlite assists in the genotyping of individuals with SNPs and in estimating the allele frequencies of SNPs using pooled DNA. We show that this estimation is accurate (mean absolute error, 1.4%) by comparing the results of the pooled analysis using QSNPlite with the true frequencies based on the allele counting after performing individual genotypings. The QSNPlite program runs on Windows XP and can be used to determine the allele frequencies of SNPs among a large number of individuals, such as in association studies of disease-responsible genes using the candidate gene approach.
Tahira
Tomoko
T
Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. ttahira@gen.kyushu-u.ac.jp
Okazaki
Yuko
Y
Miura
Kenichi
K
Yoshinaga
Aki
A
Masumoto
Kazumi
K
Higasa
Koichiro
K
Kukita
Yoji
Y
Hayashi
Kenshi
K
D019075:Electrophoresis, Capillary; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D018807:Polymorphism, Single-Stranded Conformational; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software