Inference of haplotypes from PCR-amplified samples of diploid populations

Mol Biol Evol. 1990 Mar;7(2):111-22. doi: 10.1093/oxfordjournals.molbev.a040591.


Direct sequencing of genomic DNA from diploid individuals leads to ambiguities on sequencing gels whenever there is more than one mismatching site in the sequences of the two orthologous copies of a gene. While these ambiguities cannot be resolved from a single sample without resorting to other experimental methods (such as cloning in the traditional way), population samples may be useful for inferring haplotypes. For each individual in the sample that is homozygous for the amplified sequence, there are no ambiguities in the identification of the allele's sequence. The sequences of other alleles can be inferred by taking the remaining sequence after "subtracting off" the sequencing ladder of each known site. Details of the algorithm for extracting allelic sequences from such data are presented here, along with some population-genetic considerations that influence the likelihood for success of the method. The algorithm also applies to the problem of inferring haplotype frequencies of closely linked restriction-site polymorphisms.

Publication types

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

MeSH terms

  • Algorithms
  • Alleles
  • Animals
  • Base Sequence
  • DNA / genetics
  • Diploidy*
  • Drosophila melanogaster / genetics
  • Haplotypes / genetics*
  • Models, Genetic
  • Polymerase Chain Reaction
  • Polymorphism, Genetic
  • Probability


  • DNA