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Results for “Genetic Variation”

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PubMed2005

Genetic variation of STR loci D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA by GenePrint PowerPlex 16 in a Polish population.

Allele frequencies for the fifteen STRs included in the GenePrint PowerPlex kit were determined in 870 unrelated individuals from Polish population. All loci met Hardy-Weinberg expectations. Exact tests disequilibrium analysis revealed no departures from independence out of 105 pair-wise comparisons. The combined MP and PE for all 15 loci are 6.00x10(-17) and 0.999999, respectively.

Alleles↗

PubMed2004

Population history and natural selection shape patterns of genetic variation in 132 genes.

Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes. Although the signature that natural selection imparts on DNA sequence variation is difficult to disentangle from the effects of neutral processes such as population demographic history, selective and demographic forces can be distinguished by analyzing multiple loci dispersed throughout the genome. We studied the molecular evolution of 132 genes by comprehensively resequencing them in 24 African-Americans and 23 European-Americans. We developed a rigorous computational approach for taking into account multiple hypothesis tests and demographic history and found that while many apparent selective events can instead be explained by demography, there is also strong evidence for positive or balancing selection at eight genes in the European-American population, but none in the African-American population. Our results suggest that the migration of modern humans out of Africa into new environments was accompanied by genetic adaptations to emergent selective forces. In addition, a region containing four contiguous genes on Chromosome 7 showed striking evidence of a recent selective sweep in European-Americans. More generally, our results have important implications for mapping genes underlying complex human diseases.

Black People↗

PubMed2002

Genetic variation of the nine Profiler Plus loci in Russians.

This paper presents allele frequency distributions from a representative population sample of the Russian Federation for the nine loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) which constitute the commercially available Profiler Plus PCR amplification kit. DNA samples of 402 Russian individuals from 57 regions of the Russian Federation were amplified in a multiplex reaction with subsequent genotyping using an ABI Prism 377 DNA sequencer. The population data obtained for genotype and allele frequencies conformed to Hardy-Weinberg expectations (HWE).

Alleles↗

PubMed2006

Modern computational approaches for analysing molecular genetic variation data.

An explosive growth is occurring in the quantity, quality and complexity of molecular variation data that are being collected. Historically, such data have been analysed by using model-based methods. Models are useful for sharpening intuition, for explanation and for prediction: they add to our understanding of how the data were formed, and they can provide quantitative answers to questions of interest. We outline some of these model-based approaches, including the coalescent, and discuss the applicability of the computational methods that are necessary given the highly complex nature of current and future data sets.

Computational Biology↗

PubMed1997

Genetic variation at structural loci in the Glossina morsitans species group.

Gene diversity was investigated in four taxa of tsetse flies (Diptera: Glossinidae) including Glossina morsitans, G.m. centralis, G. Swynnertoni, and G. pallidipes. Histochemical tests were performed for 35-46 isozymes. Polymorphic loci were 20% in G. morsitans, 32% in G.m. centralis, 17.6% in G. swynnertoni, and 26% in G. pallidipes. Mean heterozygosities among all loci were 6.6% in G. morsitans morsitans, 6.0% in G.m. centralis, 7.1% in G. swynnertoni, and 6.8% pallidipes. Allozyme gene diversities were considerably less than those reported for many Diptera. The low gene diversities are probably related to small effective population sizes.

Animals↗

PubMed2006

Genetic variation of the MHC DQB locus in the finless porpoise (Neophocaena phocaenoides).

The Major Histocompatibility Complex (MHC) is a large multigene coding for glycoproteins that play a key role in the initiation of immune responses in vertebrates. The exon 2 region of the MHC DQB locus was analyzed using 160 finless porpoises from 5 populations in Japanese waters. The 5 populations were based on a previous mitochondrial DNA control region analysis, which showed distinct geographical separation. Eight DQB alleles were detected, and the geographical distribution of the alleles indicated that most of them are shared among the populations. Heterozygosity of the DQB alleles in each population ranged from 0.55 to 0.78, and for all 5 populations was 0.78. Low MHC variability is not a common feature in marine mammals, but the finless porpoise populations inhabiting coastal waters had a relatively high MHC heterozygosity. Balancing selection in the MHC DQB alleles of the finless porpoise was indicated by the higher rate of nonsynonymous than synonymous substitutions for PBR; however, an excess of hetrozygotes compared to expectation was not observed. This suggests that the MHC DQB locus in the finless porpoise may have been under balancing selection for a long evolutionary time period, and is influenced by genetic drift beyond the effect of balancing selection for short time periods in small local populations.

Alleles↗

PubMed1986

Genetic variation of esterase D (EsD) polymorphism in Indian populations.

Data are presented on the phenotypes and gene frequencies of esterase D (EsD) polymorphism in various endogamous caste groups of Patiala and Faridkot districts of Punjab, north-west India. The frequency of the EsD2 allele in these groups varies from a minimum of 0.157 in Khatris to a maximum of 0.253 in Ramdasia Sikhs, a range quite typical of the north Indian populations. Examination of the available data on esterase D system in indigenous populations demonstrates the existence of a north-south cline in the distribution of the EsD2 allele in India.

Carboxylesterase↗

PubMed1995

Genetic variation of serum proteins (GC, TF and PI subtypes) in the Baigas of Madhya Pradesh, India.

The distribution of group specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) subtypes was determined by isoelectric focusing of plasma samples from 140 unrelated individuals belonging to the Baiga tribe of Madhya Pradesh, India. The allele frequencies observed for GC (GC*1S = 0.6742, GC*1F = 0.1326 and GC*2 = 0.1932), TF (TF*C1 = 0.7920, TF*C2 = 0.1606, TF*C3 = 0.0146 and TF*D = 0.0328) and PI (PI*M1 = 0.7179, PI*M2 = 0.1750, PI*M3 = 0.0893, PI*S = 0.0107 and PI*F = 0.0071) demonstrate appreciable heterogeneity of the Baigas compared to other populations of the region.

Alleles↗

PubMed1999

The role of community review in evaluating the risks of human genetic variation research.

The practicality and moral value of community review of human genetic research has become a focus of debate. Examples from two Native American communities are used to address four aspects of that debate: (1) the value of community review in larger, geographically dispersed populations; (2) the identification of culturally specific risks; (3) the potential conflict between individual and group assessments of research-related risks; and (4) the confusion of social categories with biological categories. Our experiences working with these two communities suggest that: (1) successful community review may require the involvement of private social units (e.g., families); (2) culturally specific implications of genetic research may be identifiable only by community members and are of valid concern in their moral universes; (3) community concerns can be incorporated into existing review mechanisms without necessarily giving communities the power to veto research proposals; and (4) the conflation of social and biological categories presents recruitment problems for genetic studies. These conclusions argue for the use of community review to identify and minimize research-related risks posed by genetic studies. Community review also can assist in facilitating participant recruitment and retention, as well as in developing partnerships between researchers and communities.

Evaluation Studies as Topic↗

PubMed1997

Limited range of genetic variation in Echinococcus multilocularis.

DNA sequencing of 1.3 kb of rDNA containing both internal transcribed spacers (ITS1, ITS2) and adjoining rRNA coding regions in each of 11 Echinococcus multilocularis isolates from Germany, Japan, and Alaska resulted in identical nucleotide sequences except for a single polymorphic locus 54 bp upstream of the 3' end of the 18S coding region, separating Eurasian isolates from an Alaskan isolate. The same base substitution was found in each of 2 additional isolates from Alaska. The distribution of the resulting genotypes with regard to their origin is highly significant (>99.9%) and corresponds to the traditional subspecies Echinococcus multilocularis multilocularis and Echinococcus multilocularis sibiricensis.

Animals↗

PubMed2006

Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts.

The Yakuts (also known as Sakha), Turkic-speaking cattle- and horse-breeders, inhabit a vast territory in Central and northeastern Siberia. On the basis of the archaeological, ethnographic and linguistic evidence, they are assumed to have migrated north from their original area of settlement in the vicinity of Lake Baykal in South Siberia under the pressure of the Mongol expansion during the thirteenth to fifteenth century AD: . During their initial migration and subsequent expansion, the ancestors of the Yakuts settled in the territory originally occupied by Tungusic- and Uralic-speaking reindeer-herders and hunters. In this paper we use mtDNA and Y-chromosomal analyses to elucidate whether the Yakut immigration and expansion was accompanied by admixture with the indigenous populations of their new area of settlement or whether the Yakuts displaced the original inhabitants without intermarriage. The mtDNA results show a very close affinity of the Yakuts with Central Asian and South Siberian groups, which confirms their southern origin. There is no conclusive evidence for admixture with indigenous populations, though a small amount cannot be excluded on the basis of the mtDNA data alone. The Y-chromosomal results confirm previous findings of a very strong bottleneck in the Yakuts, the age of which is in good accordance with the hypothesis that the Yakuts migrated north under Mongol pressure. Furthermore, the genetic results show that the Yakuts are a very homogenous population, notwithstanding their current spread over a very large territory. This confirms the historical accounts that they spread over their current area of settlement fairly recently.

Chromosomes, Human, Y↗

PubMed2003

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits.

Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is expected to be hindered by the putatively high gene flow. We determined the geographical distribution of molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.) in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at 23%. The proportion of total genetic variation that is between sites is much larger for the morphological additive genetic variation (QST = 0.416) than for allozyme (FST = 0.000-0.022) and mitochondrial DNA cytochrome-c-oxidase-1 sequence variation (phiST = 0.017). Divergent selection must be involved and intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low levels of isolation.

Analysis of Variance↗

PubMedDate not supplied

Genetic variation of the amplified VNTR polymorphism COL2A1 in Chinese and German populations.

The amplifiable VNTR polymorphic system COL2A1 has been investigated in Chinese and German population samples. In order to accurately identify COL2A1 alleles, a number of human allele ladders were prepared. A total of 14 different alleles in 23 genotypes was observed in the Chinese population, while in the German population there were 11 alleles in 24 genotypes. Four new alleles were observed. All of them were found in the Chinese and one was also observed in the German population. There was no statistical difference in the allele distribution between two German populations from Münster and Köln, while the allele frequency distribution in the Chinese population differed significantly from the German.

Alleles↗

PubMed1999

[Genetic variation of the mitochondrial DNA gene encoding cytochrome b in the Magadan population of sable Martes zibellina L].

The population of sable Martez zibellina consisting of two subspecies (M. z. kamtschadalica and M. z. jacutensis) on the territory of the Magadan oblast was analyzed for the variation of the 1300-bp mtDNA gene region encoding cytochrome b. Three haplotypes were revealed among the animals studied (n = 52). Six out of nine restriction endonucleases that had recognizable sites within the studied region of mtDNA genome had polymorphic sites. An index of gene diversity h was 0.27. The high level of polymorphism is a result of the fact that the population studied comprised two clearly differentiated subspecies. The ratio of dominating haplotypes corresponds to the percentage of females introduced from Kamchatka and Khabarovsk Krai, which suggests that in the period which has elapsed both maternal lineages remained fairly unchanged.

Animals↗

PubMed1975

Genetic variation in the development of mouse brain and behavior: evidence from the middle postnatal period.

Six inbred strains and 3 F2 hybrid crosses of mice were assessed for developmental status at 32 days after conception (about 13 days after birth). Phenotypes measured included body weight, brain weight, maturity of 14 reflexive behaviors, myelination of 80 fiber tracts, and thickness of the external granular layer of the cerebellum. All measures of brain and behavior showed a similar pattern of results: hybrids were generally more advanced than either of their inbred parent strains; differences among inbred strains were large, but differences among hybrid crosses were quite small. Acceleration of F2 mice compared to their homozygous relatives ranged from .5 to 2.4 days mean difference. Developmental ages of inbred litters ranged from 28.7 to 32.2 days, whereas hybrid litters ranged from 31.5 to 32.7 days.

Animals↗

PubMed1992

Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups.

Trimeric and tetrameric short tandem repeats (STRs) represent a rich source of highly polymorphic markers in the human genome that may be studied with the polymerase chain reaction (PCR). We report the analysis of a multilocus genotype survey of 97-380 chromosomes in U.S. Black, White, Mexican-American, and Asian populations at five STR loci located on chromosomes 1, 4, 11, and X. The heterozygote frequencies of the loci ranged from 0.36 to 0.91 and the number of alleles from 6 to 20 for the 20 population and locus combinations. Relative allele frequencies exhibited differences between populations and unimodal, bimodal, and complex distributions. Although deviations were noted at some locus-population test combinations, genotype data from the loci were consistent overall with Hardy-Weinberg equilibrium by three tests. Population subheterogeneity within each ethnic group was not detected by two additional tests. No mutations were detected in a total of 860 meioses for two loci studied in the CEPH kindreds and five loci studied in other families. An indirect estimate of the mutation rates gave values from 2.3 x 10(-5) to 15.9 x 10(-5) for the five loci. Higher mutation rates appear to be associated with greater numbers of tandem repeats in the core motif. The most frequent genotype for all five loci combined appears to have a frequency of 7.59 x 10(-4). Together, these results suggest that trimeric and tetrameric STR loci are useful markers for the study of new mutations and genetic linkage analysis and for application to personal identification in the medical and forensic sciences.

Alleles↗

PubMed2002

[Genetic variations in plasminogen activator inhibitor-1 gene and beta fibrinogen gene associated with glomerular microthrombosis in lupus nephritis and the gene dosage effect].

OBJECTIVE: To explore the relationship of plasminogen activator inhibitor-1 (PAI-1) gene -675 4G/5G and beta fibrinogen gene -455 G/A variations to glomerular microthrombosis(T) in lupus nephritis(LN). METHODS: One hundred and one patients with biopsy proven LN were divided into two groups according to the presence or absence of glomerular microthrombus, i.e. group LN+T(n=46) and group LN-T(n=55). The genotypes of PAI-1 gene and beta fibrinogen gene were profiled by polymerase chain reaction-sequence length polymorphism (PCR-SLP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) respectively. Clinical baseline data at the time of renal biopsy were collected. Normal controls consisted of 128 unrelated healthy adults. The etiologic fractions (EF) were calculated for estimating the contribution of risk genotypes of the two candidate genes to an increase in susceptibility to glomerular microthrombosis in LN patients. RESULTS: Both the 4G/4G genotype and the 4G allele of PAI-1 gene occurred more frequently in group LN+T (47.83% and 0.685) than in group LN-T (23.64% and 0.507)(P<0.05) and normal controls (28.13% and 0.570) (P<0.05). The PAI-1 4G/4G genotype was significantly associated with microthrombosis (OR=2.96, 95%CI:1.26-6.92). Besides, the prevalence of the genotypes carrying the A allele of beta fibrinogen gene, i.e. G/A and A/A, as well as the prevalence of the A allele per se, was increased in group LN+T (47.83% and 0.261) versus group LN-T (27.27% and 0.145)(P<0.05). LN patients carrying the A allele had a high risk of glomerular thrombosis(OR=2.44, 95%CI:0.98-5.59). In addition, the presence of the PAI-1 4G/4G genotype together with the A allele of the beta fibrinogen gene was found to be a greater risk factor (OR=4.5, 95%CI: 1.34-15.12) for glomerular thrombosis in LN than the 4G/4G genotype or the A allele alone. The pooled EF (45.98%) for the risk genotypes of both PAI-1 gene and beta fibrinogen gene was also higher than that for the risk genotypes of either gene (31.67% and 28.23%). CONCLUSION: The above findings indicated that genetic variations in PAI-1 and beta fibrinogen loci might represent risk factors for glomerular microthrombosis in LN. They may have synergetic impact and present gene dosage effect on the susceptibility to this pathological subphenotype.

Adolescent↗

PubMed2000

Genetic variation of European beech (Fagus sylvatica L.) along an altitudinal transect at Mount Vogelsberg in Hesse, Germany.

Allelic and genotypic variation at 13 different enzyme loci of autochthonous European beech (Fagus sylvatica L.) was investigated in six 110-160-year-old stands growing at elevations between 150 and 660 m above sea level on the western slope of mount Vogelsberg in central Germany. The highest elevated population showed the highest number of effective alleles (Ne), the highest total heterozygosity (He) and the highest population differentiation deltaT. Also, the genotype SKD-A2A3 of shikimate dehydrogenase was significantly more frequent at the two highest elevated stands (P = 11%) than at the three lowest elevated stands (P = 1%). Further differences in genotype frequencies between 11 of 15 stand pairs were elevation independent.

Alcohol Oxidoreductases↗