Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA)

Koichiro Higasa, Yoji Kukita, Shingo Baba, Kenshi Hayashi

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)

Abstract

PCR single-stranded conformational polymorphism (SSCP) analysis is a simple and rapid electrophoretic technique for the sensitive detection of sequence variants of PCR products. Here we describe a cross-platform program package, quantitative interpretation of SSCP in capillary array (QUISCA), which allows semi-automated quantitative detection of sequence variants separated by multicolor fluorescence-based SSCP electrophoresis using various capillary array apparatus. The program, together with the QUISCAview as a graphical user interface, takes trace data in ASCII format and processes them with three modules: signal denoising/baseline subtraction, color-matrix construction/application, and calibration of peak positions between multiple capillary runs using internal standard peaks. QUISCA is compatible with data from various widely used capillary array sequencers and is suitable not only for finding or typing SNPs in individual DNAs but also for the accurate estimation of the allele frequencies of many SNPs using a pooled DNA strategy. QUISCA can also serve as a versatile core program for various fragment analyses.

Original languageEnglish
Pages (from-to)1342-1348
Number of pages7
JournalBioTechniques
Volume33
Issue number6
DOIs
Publication statusPublished - Dec 1 2002

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

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