Snpstr

Abstract: There has been widespread and growing interest in genetic markers suitable for drawing population genetic inferences about past demographic events and to detect the effects of selection. In addition to single nucleotide polymorphisms (SNPs), microsatellites (or short tandem repeats, STRs) have received great attention in the analysis of human population history. In the SNPSTR database (http://www.imperial.ac.uk/theoreticalgenomics/data-software) we catalogue a relatively new type of compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 bp apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers. Thus, SNPSTRs have the potential to become a very useful tool in the field of population genetics. The SNPSTR database contains all inferable human SNPSTRs as well as those in mouse, rat, dog and chicken, i.e. all model organisms for which extensive SNP datasets are available.

Abstract: Single nucleotide polymorphisms (SNPs) in the flanking regions of microsatellite loci (SNPSTRs) help to increase the power of discrimination of short tandem repeat (STR) loci. SNPs are positions in the genome that have been well-conserved over the course of evolution, so analysing them can help distinguish between STR alleles in which the number of repetitions matches due to descent from those which match by chance. This provides support for the determination of biological paternity and other kinship analyses in which mutation needs to be ruled out as grounds for exclusion. Locus D7S820 shows a variable position, SNP rs59186128, in the 5′ flanking region. This study is set out (1) to determine the frequencies of SNP rs59186128 in populations with various geographical origins and (2) to estimate the possible contribution of rs59186128 to the allele discrimination of locus D7S820. To that end, individuals from European Caucasoid, Hispanic, and Afro-American populations are studied using denaturing high-performance liquid chromatography, which enables locus rs59186128 to be quickly and highly cost-effectively screened. Moreover, a method is established for determining the haplotypes of SNPSTR rs59186128_D7820. The results show that SNP rs59186128 has a T allele frequency of more than 0.15 in one of the Afro-American populations studied, and the haplotype analysis shows that there is no preferential association between the alleles of SNPSTR rs59186128_D7S820, which supports the idea that they could be useful in forensic applications.

Abstract: Instead of testing the additional STR loci, SNPSTR was included in the paternity testing for an alleged father–son duo case, with one inconsistency at the CSF1PO locus. We have chosen CSF1PO STR and five closely linked SNPs rs10077461, rs2569076, rs2228422, rs3733673 and rs3829987 to establish the SNPSTR and examined its potential use in paternity testing. A total of 152 haplotypes from 76 unrelated individuals were obtained by the nested-AS-PCR and 60 SNPSTR haplotypes were observed. The discrimination power of the SNPSTR haplotype was greater than either the STR or SNP haplotype alone. Its SNP part could be used to distinguish fathers from uncles. When SNPSTR was introduced into the calculation of parentage statistics, the paternity probability increased to 99.998%. Based on our findings, we concluded that SNPSTR could be considered a useful tool in forensic science.