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STR Loci (str + locus)

Distribution by Scientific Domains

Life Sciences	66%

Selected Abstracts

Allele Frequencies of 15 STR Loci in the Population of the City of Quito, Ecuador

JOURNAL OF FORENSIC SCIENCES, Issue 2 2008
María Atilia Gómez Ph.D.
Population: Quito City Population (Ecuador, South America, n = 116,207). [source]

DNA Sequence Characterization of the FGA STR Locus in the Free State Population of South Africa

JOURNAL OF FORENSIC SCIENCES, Issue 1 2006
André de Kock Ph.D.
POPULATION: African (n=52), Mixed Ancestry (n=5), Caucasian (n=4) SAN (n=1). [source]

Direct STR Amplification from Whole Blood and Blood- or Saliva-Spotted FTA® without DNA Purification,

JOURNAL OF FORENSIC SCIENCES, Issue 2 2008
Su Jeong Park Ph.D.
Abstract:, The DNA purification step has been thought to be essential for typing of STR DNA. However, this process is time-consuming, and there is a risk of unexpected cross-contamination during purification. We report a new method for direct short tandem repeat (STR) amplification using a newly developed direct PCR buffer, AnyDirectÔ, which can amplify STR loci from whole blood and blood- or saliva-spotted FTA® cards without DNA purification. The autosomal and Y chromosomal STR loci were analyzed for whole blood and blood or saliva spots of random individuals, followed by comparison of the results with those of corresponding purified DNA. The results from whole blood and blood spots showed perfect concordance with those from purified DNA without allele or locus drop-out. However, in the case of saliva spots, no amplification or locus drop-out was observed in some of the samples, which offers a topic for further study. Additionally, some commercial hot-start DNA polymerases other than AmpliTaq Gold® DNA polymerase were also found to be compatible with this buffer system. Therefore, this direct PCR buffer was demonstrated to be useful for fast forensic DNA analysis or criminal DNA databases for which there is no need to store DNA samples. [source]

The Application of Miniplex Primer Sets in the Analysis of Degraded DNA from Human Skeletal Remains§

JOURNAL OF FORENSIC SCIENCES, Issue 2 2006
Kerry L. Opel M.A.
ABSTRACT: A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50,280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex® 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex® 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains. [source]

Genetic profiling of the Azores Islands (Portugal): Data from 10 X-chromosome STRs

AMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 2 2010
Francisca Silva
The populations from the Azores islands have been the target of several genetic studies, using data derived from monoparental and recombining genetic systems. These studies have provided a complex picture of the genetic landscape of the three groups of Azorean islands, and further data are required to assess its genetic profile. We present a study of the polymorphism in 10 X-chromosome STR loci (DSXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902, DXS6789) conducted on a total of 304 chromosomes (97 females and 110 males) of unrelated individuals with Azorean ancestry. Average gene diversity was 74.47%, ranging from 66.21% (DXS7133) to 81.19% (GATA172D05). No shared haplotypes were found. Genotype frequencies among females displayed conformity with Hardy-Weinberg expectations for all loci. Pairwise linkage disequilibrium tests did not reveal evidences of association between the studied markers. Significant differences in allelic frequencies between the Western and the Eastern group of islands are in agreement with previous results from mitochondrial DNA and Y chromosome studies, providing further evidence that the Azores cannot be considered an homogeneous population. Moreover, differences between the Western group and the North of Portugal are also reported, supporting the pertinence of a specific database for the Azores populations, on what concerns the genetic markers analyzed. Am. J. Hum. Biol., 2010. © 2009 Wiley-Liss, Inc. [source]

Maximum likelihood estimates of admixture in northeastern Mexico using 13 short tandem repeat loci

AMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2002
Ricardo M. Cerda-Flores
Tetrameric short tandem repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% ± 3.44, 39.99% ± 2.57, and 5.02% ± 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% ± 5.94, 36.99% ± 5.04, and 3.02% ± 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico. Am. J. Hum. Biol. 14:429,439, 2002. © 2002 Wiley-Liss, Inc. [source]

The genetic structure of populations from Haiti and Jamaica reflect divergent demographic histories

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010
Tanya M. Simms
Abstract The West Indies represent an amalgamation of African, European and in some cases, East Asian sources, but the contributions from each ethnic group remain relatively unexplored from a genetic perspective. In the present study, we report, for the first time, allelic frequency data across the complete set of 15 autosomal STR loci for general collections from Haiti and Jamaica, which were subsequently used to examine the genetic diversity present in each island population. Our results indicate that although both Haiti and Jamaica display genetic affinities with the continental African collections, a stronger African signal is detected in Haiti than in Jamaica. Although only minimal contributions from non-African sources were observed in Haiti, Jamaica displays genetic input from both European and East Asian sources, an admixture profile similar to other New World collections of African descent analyzed in this report. The divergent genetic signatures present in these populations allude to the different migratory events of Africans, Europeans, and East Asians into the New World. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source]

Population-specific deviations of global human craniometric variation from a neutral model

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010
John H. Relethford
Abstract Past studies have revealed that much of human craniometric variation follows a neutral model of population relationships. At the same time, there is evidence for the influence of natural selection in having shaped some global diversity in craniometrics. In order to partition these effects, and to explore other potential population-specific influences, this article analyzes residuals of craniometric distances from a geographically based neutral model of population structure. W.W. Howells' global craniometric data set was used for these analyses, consisting of 57 measurements for 22 populations around the world, excluding Polynesia and Micronesia because of the relatively recent settlement of these regions. Phenotypic and geographic distances were derived between all pairs of populations. Three-dimensional multidimensional scaling configurations were obtained for both distance matrices, and compared using a Procrustes rotation method to show which populations do not fit the geographic model. This analysis revealed three major deviations: the Buriat, Greenland Inuit, and Peru. The deviations of the Buriat and Greenland Inuit appear to be related to long-term adaptation to cold environments. The Peruvian sample is more similar to other New World populations than expected based on geographic distance alone. This deviation likely reflects the evolutionarily recent movement of human populations into South America, such that these populations are further from genetic equilibrium. This same pattern is seen in South American populations in a comparative analysis of classical genetic markers, but not in a comparative analysis of STR loci, perhaps reflecting the higher mutation rate for the latter. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source]

A microsatellite study to disentangle the ambiguity of linguistic, geographic, ethnic and genetic influences on tribes of India to get a better clarity of the antiquity and peopling of South Asia

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2009
S. Krithika
Abstract An understanding of the genetic affinity and the past history of the tribal populations of India requires the untangling of the confounding influences of language, ethnicity, and geography on the extant diverse tribes. The present study examines the genetic relationship of linguistically (Dravidian, Austro-Asiatic, and Tibeto-Burman) and ethnically (Australian and East Asian) diverse tribal populations (46) inhabiting different regions of the Indian subcontinent. For the purpose, we have utilized the published data on allele frequency of 15 autosomal STR loci of our study on six Adi sub-tribes of Arunachal Pradesh and compared the same with the reported allele frequency data, for nine common autosomal STR loci, of 40 other tribes. Phylogenetic and principal component analyses exhibit geography based clustering of Tibeto-Burman speakers and separation of the Mundari and Mon-Khmer speaking Austro-Asiatic populations. The combined analyses of all 46 populations show clustering of the groups belonging to same ethnicity and inhabiting contiguous geographic regions, irrespective of their different languages. These results help us to reconstruct and understand three plausible scenarios of the antiquity of Indian tribal populations: the Dravidian and Austro-Asiatic (Mundari) tribes were possibly derived from common early settlers; the Tibeto-Burman tribes possibly belonged to a different ancestry and the Mon-Khmer speaking Austro-Asiatic populations share a common ancestry with some of the Tibeto-Burman speakers. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source]

A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci

ANIMAL GENETICS, Issue 2 2010
L. H. P. Van De Goor
Summary In this study, a proposal is presented for the allele nomenclature of 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) for equine genotyping (Equus caballus). The nomenclature is based on sequence data of the polymorphic region of the STR loci as recommended by the DNA commission of the International Society for Forensic Genetics for human DNA typing. For each STR locus, several alleles were selected and animals homozygous for those alleles were subjected to sequence analysis. The alleles of the 17 STR loci consisted either of simple (10), compound (6) or complex repeat patterns (1). Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats, including all variable regions within the amplified fragment. [source]

A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci

ANIMAL GENETICS, Issue 5 2009
L. H. P. Van De Goor
Summary In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci (BM1824, BM2113, ETH10, ETH225, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH3, TGLA53, BM1818, CSRM60, CSSM66, HAUT27 and ILSTS006) for bovine genotyping (Bos taurus). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis. [source]