Critical factors in the performance and cost of two-dimensional gene scanning: RB1 as a model

Biotechniques. 1998 Oct;25(4):664-8, 670, 672-5. doi: 10.2144/98254dt06.


Two-dimensional (2-D) gene scanning (TDGS) is a method for mutation detection based on the electrophoretic separation of PCR-amplified DNA fragments according to size and base pair sequence. The use of denaturing gradient gel electrophoresis (DGGE) as the second separation step provides virtually 100% sensitivity, while the 2-D format allows the inspection of multiple gene fragments simultaneously. Analysis of many exons in parallel is greatly facilitated by extensive PCR multiplexing based on preamplification by long-distance PCR. Recently, TDGS has been applied to detect mutations in the retinoblastoma tumor suppressor gene RB1. Using RB1 as a model, we have now analyzed each step of the protocol, presenting overall improvements and a detailed cost analysis, where the total cost of the assay is found to be about $40 (US). An overall picture of TDGS cost-performance, as compared to direct sequencing, is provided as a function of the number of target fragments.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Costs and Cost Analysis
  • DNA Mutational Analysis
  • Electrophoresis, Gel, Two-Dimensional / economics
  • Electrophoresis, Gel, Two-Dimensional / methods*
  • Exons / genetics
  • Genes, Retinoblastoma / genetics*
  • Genetic Testing / economics
  • Genetic Testing / methods*
  • Heterozygote
  • Humans
  • Molecular Weight
  • Nucleic Acid Denaturation
  • Nucleic Acid Heteroduplexes
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Retinoblastoma / diagnosis
  • Retinoblastoma / economics
  • Retinoblastoma / genetics
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Temperature
  • Time Factors


  • Nucleic Acid Heteroduplexes