Dataset Information

Population-specific FST values for forensic STR markers: A worldwide survey.

ABSTRACT: The interpretation of matching between DNA profiles of a person of interest and an item of evidence is undertaken using population genetic models to predict the probability of matching by chance. Calculation of matching probabilities is straightforward if allelic probabilities are known, or can be estimated, in the relevant population. It is more often the case, however, that the relevant population has not been sampled and allele frequencies are available only from a broader collection of populations as might be represented in a national or regional database. Variation of allele probabilities among the relevant populations is quantified by the population structure quantity FST and this quantity affects matching proportions. Matching within a population can be interpreted only with respect to matching between populations and we show here that FST, can be estimated from sample allelic matching proportions within and between populations. We report such estimates from data we extracted from 250 papers in the forensic literature, representing STR profiles at up to 24 loci from nearly 500,000 people in 446 different populations. The results suggest that theta values in current forensic use do not have the buffer of conservatism often thought.

SUBMITTER: Buckleton J

PROVIDER: S-EPMC4899164 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Population-specific FST values for forensic STR markers: A worldwide survey.

Buckleton John J Curran James J Goudet Jérôme J Taylor Duncan D Thiery Alexandre A Weir B S BS

Forensic science international. Genetics 20160322

The interpretation of matching between DNA profiles of a person of interest and an item of evidence is undertaken using population genetic models to predict the probability of matching by chance. Calculation of matching probabilities is straightforward if allelic probabilities are known, or can be estimated, in the relevant population. It is more often the case, however, that the relevant population has not been sampled and allele frequencies are available only from a broader collection of popul ...[more]

PMID: 27082756

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Project description:Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had the most allelic frequency. Moreover, about the determination of statistical indicators of identification using PowerStats V12 software, CSF1PO locus allocated the most RMP (0.219) and FGA locus the highest heterozygosity (100%) and the highest polymorphic rate (PIC) (0.82). Conclusion: The setup performed in this study showed that with two-step multiplex PCR procedure of four markers, PCR can be carried out for eight loci without additional real-time products that this shows proper conditions that we can use their PCR product in analyzing SRTs with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Besides, the FGA locus was raised as the best loci for identification in the study population concerning the high PD index and high polymorphism.

Project description:Simple Summary The degree of relationship among livestock breeds can be quantified by the Fst statistic, which measures the extent of genetic differentiation between them. An Fst value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, Fst values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that Fst > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of Fst data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds. Abstract (1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.

Dataset Information

Population-specific FST values for forensic STR markers: A worldwide survey.

Publications

Population-specific FST values for forensic STR markers: A worldwide survey.

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