Comparative sequence analysis (CSA): a new sequence-based method for the identification and characterization of mutations in DNA

Hum Mutat. 2000 Nov;16(5):437-43. doi: 10.1002/1098-1004(200011)16:5<437::AID-HUMU9>3.0.CO;2-Q.


Direct sequencing analysis is largely used to confirm and characterize mutations previously detected by more rapid tests. We have developed a method-Comparative Sequence Analysis (CSA)-that simplifies the analysis of sequencing data facilitating its use as a first screen for mutation detection. Sequence data were split into their component electrophoretograms and the use of a size standard enabled equivalent traces from different individuals to be overlaid. This allowed simple and rapid visual analysis of the results. Using this technique in a blind study, we tested 576 samples for mutations in the Von Hippel-Lindau tumor suppressor gene, VHL. We were able to identify and characterize all 78 known mutations present within the sample set (100% sensitivity and specificity).

Publication types

  • Comparative Study

MeSH terms

  • DNA Mutational Analysis / methods*
  • DNA, Complementary / genetics
  • DNA, Complementary / metabolism
  • Dideoxynucleosides / metabolism
  • Electrophoresis / methods
  • Fluorescent Dyes / metabolism
  • Frameshift Mutation
  • Genes, Tumor Suppressor / genetics
  • Humans
  • Point Mutation
  • Polymerase Chain Reaction / methods
  • Sequence Analysis, DNA / methods*
  • Single-Blind Method
  • Software
  • von Hippel-Lindau Disease / diagnosis
  • von Hippel-Lindau Disease / genetics


  • DNA, Complementary
  • Dideoxynucleosides
  • Fluorescent Dyes