Molecular Biology and Evolution, Vol 7, 111-122, Copyright © 1990 by Society for Molecular Biology and Evolution
AG Clark
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.
REVIEW ARTICLE
Inference of haplotypes from PCR-amplified samples of diploid populations
Department of Biology, Pennsylvania State University, University Park 16802.
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