Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6146-51. doi: 10.1073/pnas.0700921104. Epub 2007 Mar 27.


The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or column-based approaches to analyze DNA repeats. Individual STR alleles are separated and distinguished according to fragment length; thus the assay is generally hampered by its low multiplex capacity. However, use of DNA microarray would employ a simple hybridization and detection for field forensics and biology. Here we demonstrate a rapid, highly sensitive method for STR analysis that utilizes DNA microarray technology. We describe two adaptations to accomplish this: the use of competitive hybridization to remove unpaired ssDNA from an array and the use of neural network classification to automate the analysis. The competitive displacement technique mimics the branch migration process that occurs during DNA recombination. Our technique will facilitate the rapid deduction of identity, length, and number of repeats for the multiple STRs in an unknown DNA sample.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA / chemistry*
  • Forensic Genetics / methods*
  • Microsatellite Repeats / genetics*
  • Neural Networks, Computer
  • Nucleic Acid Hybridization / methods
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotides


  • Oligonucleotides
  • DNA