Polymorphism ratio sequencing: a new approach for single nucleotide polymorphism discovery and genotyping

Genome Res. 2003 Feb;13(2):287-93. doi: 10.1101/gr.396203.


Polymorphism ratio sequencing (PRS) combines the advantages of high-throughput DNA sequencing with new labeling and pooling schemes to produce a powerful assay for sensitive single nucleotide polymorphism (SNP) discovery, rapid genotyping, and accurate, multiplexed allele frequency determination. In the PRS method, dideoxy-terminator extension ladders generated from a sample and reference template are labeled with different energy-transfer fluorescent dyes and coinjected into a separation capillary for comparison of relative signal intensities. We demonstrate the PRS method by screening two human mitochondrial genomes for sequence variations using a microfabricated capillary array electrophoresis device. A titration of multiplexed DNA samples places the limit of minor allele frequency detection at 5%. PRS is a sensitive and robust polymorphism detection method for the analysis of individual or multiplexed samples that is compatible with any four-color fluorescence DNA sequencer.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Codon / genetics
  • DNA, Mitochondrial / genetics
  • Genes, rRNA / genetics
  • Genetic Variation / genetics
  • Genome
  • Genotype
  • Humans
  • Mitochondria / genetics
  • Mitochondrial Proteins / genetics
  • Polymorphism, Genetic / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • RNA / genetics
  • RNA, Mitochondrial
  • RNA, Transfer / genetics
  • Sequence Analysis, DNA / methods*


  • Codon
  • DNA, Mitochondrial
  • Mitochondrial Proteins
  • RNA, Mitochondrial
  • RNA
  • RNA, Transfer