title: Genotyping HapSTR loci: phase determination from direct sequencing of PCR products.
abstract: HapSTRs combine information from a microsatellite (or simple tandem repeat, STR) with one or more single nucleotide polymorphisms in the DNA sequence immediately flanking the STR. These loci may offer increased power for the estimation of demographic parameters, but also present some challenges for data collection and analysis. We describe a process for inferring HapSTR alleles, including the flanking haplotypes, STR alleles and their phase relative to each other, directly from DNA sequence electropherograms of PCR products from heterozygous individuals. Our approach eliminates the need for more costly and time-consuming processes, such as cloning or acrylamide gel electrophoresis to separate alleles prior to sequencing.
authors.affiliation: Department of Biology, Boston University, 5 Cummington St., Boston, MA 02215, USA. msoren@bu.edu
authors.forename: Michael D
authors.initials: MD
authors.lastname: Sorenson
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: DaCosta
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017931:DNA Primers / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D046109:Passeriformes / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers