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Mountain JL, Knight A, Jobin M, Gignoux C, Miller A, Lin AA et al.. SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Res 12: 1766-1772

Department of Anthropological Sciences, Stanford, California 94305, USA.
Genome Research (Impact Factor: 13.85). 12/2002; 12(11):1766-72. DOI: 10.1101/gr.238602
Source: PubMed

ABSTRACT Each independently evolving segment of the genomes of a sexually reproducing organism has a separate history reflecting part of the evolutionary history of that organism. Uniparentally or clonally inherited DNA segments such as the mitochondrial and chloroplast genomes and the nonrecombining portion of the Y chromosome have provided, to date, most of the known data regarding compound haplotypic variation within and among populations. These comparatively small segments include numerous polymorphic sites and undergo little or no recombination. Recombining autosomes, however, comprise the major repository of genetic variation. Technical challenges and recombination have limited large-scale application of autosomal haplotypes. We have overcome this barrier through development of a general approach to the assessment of short autosomal DNA segments. Each such segment includes one or more single nucleotide polymorphisms (SNPs) and exactly one short tandem repeat (STR) locus. With dramatically different mutation rates, these two types of genetic markers provide complementary evolutionary information. We call the combination of a SNP and a STR polymorphism a SNPSTR, and have developed a simple, rapid method for empirically determining gametic phase for double and triple heterozygotes. Here, we illustrate the approach with two SNPSTR systems. Although even one system provides insight into population history, the power of the approach lies in combining results from multiple SNPSTR systems.

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    • "Several different approaches have been used to solve this problem. For SNPSTRs, Mountain et al. (2002) amplified the STR locus with two differently labelled primers, each designed to match one of the two nucleotides segregating at the flanking SNP, followed by standard fragment sizing on an automated sequencer. This approach is practical only for SNPSTRs (i.e. "
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    • "Microsatellite variation also can be compared and combined with SNP variation to reconstruct human evolutionary history on different timescales (deKnijff 2000; Mountain et al. 2002; Payseur and Cutter 2006). The development of analytical tools for integrating patterns of polymorphism at loci with contrasting mutation rates and mechanisms will be required for building a synthetic view of human genomic variation in its many forms. "
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    • "Thus, LD between multiallelic markers may indeed be greater and extend over longer distances than LD among biallelic SNP markers, which was also found in the LD studies in humans (Pritchard and Przeworski, 2001; Varilo et al., 2003) and cattle (Khatkar et al., 2006a, b). In addition, the relatively high rate of mutation in microsatellite markers makes possible the assessment of recently created LD (Mountain et al., 2002). Thus, microsatellite markers will continue to be useful and informative for studies of LD in the wild. "
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