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Results for “Genetic Variation”

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PubMed2007

Patterns of genetic variation in Swertia przewalskii, an endangered endemic species of the Qinghai-Tibet Plateau.

Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Phi (ST) comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory theta(B)) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.

China↗

PubMed2006

Genetic variation in soluble epoxide hydrolase (EPHX2) and risk of coronary heart disease: The Atherosclerosis Risk in Communities (ARIC) study.

Endothelial dysfunction contributes to the development of coronary heart disease (CHD). Soluble epoxide hydrolase metabolizes epoxyeicosatrienoic acids in the vasculature and regulates endothelial function. We sought to determine whether genetic variation in soluble epoxide hydrolase (EPHX2) was associated with the risk of CHD. We genotyped 2,065 Atherosclerosis Risk in Communities study participants (1,085 incident CHD cases, 980 non-cases) for 10 previously identified polymorphisms in EPHX2. Using a case-cohort design, associations between incident CHD risk and both non-synonymous EPHX2 polymorphisms and phase-reconstructed haplotypes were evaluated using proportional hazards regression. Individuals carrying the K55R polymorphism variant allele demonstrated higher apparent soluble epoxide hydrolase activity in vivo. Presence of the K55R variant allele was significantly more common among Caucasian CHD cases when compared with non-cases (20.8% versus 15.3%, respectively, P=0.012), and was associated with significantly higher risk of incident CHD (adjusted hazard rate ratio 1.45, 95% confidence interval 1.05-2.01, P=0.026). A significant association between the K55R variant allele and risk of CHD was not observed in African-Americans. The distribution of reconstructed haplotypes were significantly different in Caucasian cases when compared with non-cases (P=0.021). Significant differences in haplotype distribution were not observed in African-Americans (P=0.315). Genetic variation in EPHX2 was significantly associated with risk of incident CHD in Caucasians, implicating EPHX2 as a potential cardiovascular disease-susceptibility gene.

Black or African American↗

PubMed1994

Response to environmental change: genetic variation and fitness in Drosophila buzzatii following temperature stress.

Drosophila buzzatii typically may encounter high temperatures in nature, and this species is genetically variable for resistance to stress, both within and among populations. Fitness of survivors to stress, however, was reduced, and observed as a reduction in male fertility and female fecundity. With time following exposure to severe stress, reproductive capacity improved, but lifetime offspring production still was reduced significantly. This effect would greatly reduce a population's recovery from small size, which could occur following exposure to some man-made or environmental extreme. Although the results presented here were obtained for effects of heat stress, such consequences likely apply to a wide range of natural and man-made environmental stresses, including heavy metal toxicity or other pollutants. Low levels of these pollutants may not cause an observable effect on populations, even if some individuals are killed or offspring production is decreased. If genetic variation for resistance is present, higher tolerance may evolve. However, if concentrations are permitted to rise too far, some stress threshold may be reached, as observed for thermal stress, causing mass die-off or sterility and, possibly, local extinction. Understanding the effects of stress is important when preparing programs for the conservation of species. Organisms generally do not become extinct when resources are abundant and the climate benign, but unfortunately, no guarantee can be made that environmental conditions in any locality will remain stable over a long time. Consequently, a high possibility of exposure to an extreme stress in an area would greatly reduce its usefulness as a reserve. Likewise, when choosing organisms for reintroduction, stress resistance of the chosen individuals and high levels of genetic variation within a population would be valuable. The organisms placed there must be able to change. Analysis of stress resistance (at non-lethal levels) among either family groups or for different populations would be very useful when deciding which individuals to reintroduce to an area or place in a reserve. Additionally, analysis may suggest that stress resistance is very low in a population or species. If identified, particular care may be taken to monitor the occurrence of that stress in the environment, and to take action to protect the population from that stress. Preservation of species should be designed for the future, with the goal to preserve, not simply to postpone extinction.

Analysis of Variance↗

PubMedDate not supplied

Genetic variation and exposure related risk estimation: will toxicology enter a new era? DNA repair and cancer as a paradigm.

With the vast technological and informational resources increasingly available from investments in "genomics," toxicology and much of biological science, is faced with previously undreamed of opportunities and equally daunting challenges. The ability to generate the large quantities of data becoming routinely available could not be imagined a decade ago. The complexities of data analysis are increasingly the rate-limiting element in scientific advances. The expectations that these large scientific investments will reduce the incidence of human disease and improve health are very high. An emphasis on genetic variation and Toxicogenetics is expected to yield risk estimates for specific rather than average individuals and individuals with varied lifestyles and complex patterns of exposure. Examples from studies of polymorphic variation in DNA repair genes in the healthy population and cancer risk highlight the complexity and challenges of incorporating genetic variation into quantitative estimates of risk associated with environmentally relevant exposures. Similar issues exist in selecting the animal models most appropriate for predicting human risk from environmental exposures to toxic agents.

Animals↗

PubMed1991

Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium.

Several surveys have found evidence for founder effects in Amerindian mitochondrial DNA because of the existence of rare Asian morphs in high frequencies in some Amerindian populations and the occurrence of several new morphs not seen elsewhere in the world. These reports, however, do not address whether or not the present genetic variation in the mtDNA genome in Amerindians has reached the steady-state distribution predicted by the mutation-drift theory of population genetics. The present work suggests that in three Amerindian populations (Pima, Maya, and Ticuna) a steady state has apparently been reached, and hence the initial founder effect has probably dissipated during the evolution of Amerindians in the New World. This result is consistent with the genetic variation in nuclear genes in similar populations, shown through surveys of protein variation in earlier work and, more recently, in studies of restriction fragment length polymorphisms.

DNA, Mitochondrial↗

PubMed2025

Identification of Genetic Variations in HLA Region for Kidney Functions.

HLA allelic polymorphisms are associated with a variety of kidney-related traits in different populations. Although Taiwanese-specific genetic variants associated with kidney function have been reported, the role of HLA alleles is unclear. In this study, the association between eGFR and genetic variations in the HLA region was explored in a cohort of 59,448 Taiwanese subjects. A total of 448 genetic variations in the HLA region are significantly associated with eGFR. HLA-C*03 is associated with decreased eGFR, while HLA-DQA1*03, HLA-DQB1*03:03 and HLA-DQB1*03:03:02 demonstrated protective effects. Moreover, amino acid changes on HLA-C and HLA-DRB1 are significantly associated with eGFR. Finally, the eGFR-associated single nucleotide variations (SNVs) and insertions and deletions (indels) are enriched in the HLA-DQB1 gene. After conditional analysis, we identified two independent signals, including rs2853941, rs3830060. In summary, this study highlights the role of HLA-C, HLA-DQA1, HLA-DQB1 and HLA-DRB1 variations in kidney function in the Taiwan Han Chinese population.

Adult↗

PubMed1992

Genetic variation in liver mass, body mass, and liver:body mass in mice.

Genetic variation for liver mass (LM), body mass (BM), and liver:body mass (LM/BM) was examined for outbred populations of laboratory mice. Liver mass and body mass data were collected on 170 pureline sires at 12 wk of age, representing four outbred stocks of laboratory mice; 523 of their male and female two-way-cross progeny at 9 or 12 wk; and 214 four-way-cross offspring at 12, 14, or 16 wk. Genetic differences for LM, BM, and LM/BM were found among the base sire lines and between two-way crosses. Heritabilities and genetic correlations for LM, BM, LM/BM, and LM/MBM (MBM = BM.75) were estimated using offspring-sire regression within and across characteristics. Estimates of heritabilities and genetic correlations were also derived from full-sib covariances in the two-way-cross generation. Heritability estimates pooled over all analyses were .53, .54, .36, and .40 for LM, BM, LM/BM, and LM/MBM, respectively. Body mass was highly genetically correlated (.87) with LM and lowly correlated with LM/BM. Previous research has indicated possible positive relationships between LM/BM and maintenance energy requirements in mature, nonlactating, nonpregnant animals. A selection index was developed for increasing BM but restricting genetic change in LM to zero. Selection using this index would be 40% as efficient in increasing BM as selection on BM alone but may hold maintenance energy requirements at a stable level.

Animals↗

PubMedDate not supplied

Genetic variation for dorsal-ventral patterning of the Drosophila melanogaster eggshell.

Patterning of the insect eggshell is an excellent system for exploring the molecular basis of phenotypic variation. In Drosophila melanogaster, two dorsal-anterior respiratory appendages are produced in response to signaling through the Epidermal growth factor receptor (Egfr). Previous work implicates Egfr pathway function in both intraspecific variation for dorsal appendage spacing (DAS) on the eggshell, as well as interspecific differences in dorsal appendage number and location. To test the hypothesis that genetic variation in Egfr contributes to variation in eggshell patterning, we have made use of naturally occurring intraspecific variation for DAS as a model quantitative trait. We found that there is substantial segregating genetic variation for DAS in D. melanogaster, and have tested for associations with 289 common polymorphisms in the Egfr locus. A marginal association was seen with two polymorphic sites in Egfr; however, we failed to replicate these findings in a second population, or in a modified quantitative complementation test designed to specifically test the effects of the putative polymorphisms. Therefore, we conclude that the polymorphisms we have identified in Egfr do not contribute to variation in DAS, and further work is required to understand the genetic architecture of this trait.

Animals↗

PubMed2003

Genetic variations in calpain-10 gene are not a major factor in the occurrence of type 2 diabetes in Japanese.

The 112/121 haplotype combination defined by the UCSNP-43, -19, and -63 alleles in the calpain-10 gene is associated with type 2 diabetes in Mexican Americans. To determine whether this genetic variation constitutes risk of type 2 diabetes in Japanese, we investigated its frequency in 177 patients with type 2 diabetes and 172 controls. Though this variation occurs in Japanese more frequently than in Mexican Americans, there is no significant difference in frequency between diabetic (29.9%) and control (31.9%) subjects. We also screened all exons and the putative promoter of the calpain-10 gene for mutations in 96 of the genotyped patients, resulting in the identification of 7 coding variants, including 3 missense mutations and 5 nucleotide alterations in the promoter. However, their frequencies all are similar in patients and controls, suggesting that these genetic variations are not a major factor in the occurrence of type 2 diabetes in Japanese, although they could yet be associated with various phenotypes of the disease.

Aged↗

PubMed2005

An insight into the genetic variation of Schistosoma japonicum in mainland China using DNA microsatellite markers.

This study presents the first microsatellite investigation into the level of genetic variation among Schistosoma japonicum from different geographical origins. S. japonicum isolates were obtained from seven endemic provinces across mainland China: Zhejiang (Jiashan County), Anhui (Guichi County), Jiangxi (Yongxiu County), Hubei (Wuhan County), Hunan (Yueyang area), Sichuan 1 (Maoshan County), Sichuan 2 (Tianquan County), Yunnan (Dali County), and also one province in the Philippines (Sorsogon). DNA from 20 individuals from each origin were screened against 11 recently isolated and characterized S. japonicum microsatellites, and a set of nine loci were selected based on their polymorphic information content. High levels of polymorphism were obtained between and within population samples, with Chinese and Philippine strains appearing to follow different lineages, and with distinct branching between provinces. Moreover, across mainland China, genotype clustering appeared to be related to habitat type and/or intermediate host morph. These results highlight the suitability of microsatellites for population genetic studies of S. japonicum and suggest that there may be different strains of S. japonicum circulating in mainland China.

Analysis of Variance↗

PubMed2003

Genetic variation of microsatellite loci in the major histocompatibility complex (MHC) region in the southeast Asian house mouse (Mus musculus castaneus).

Major histocompatibility complex (MHC) genes are the most polymorphic loci known for vertebrates. Here we employed five microsatellite loci closely linked to the MHC region in an attempt to study the amount of genetic variation in 19 populations of the southeast Asian house mouse (Mus musculus castaneus) in Taiwan. The overall polymorphism at the five loci was high (He = 0.713), and the level of polymorphism varied from locus to locus. Furthermore, in order to investigate if selection is operating on MHC genes in natural mouse populations, we compared the extent and pattern of genetic variation for the MHC-linked microsatellite loci (the MHC loci) with those for the microsatellite loci located outside the MHC region (the non-MHC loci). The number of alleles and the logarithm of variance in repeat number were significantly higher for the MHC loci than for the non-MHC loci, presumably reflecting linkage to a locus under balancing selection. Although three statistical tests used do not provide support for selection, their lack of support may be due to low statistical power of the tests, to weakness of selection, or to a profound effect of genetic drift reducing the signature of balancing selection. Our results also suggested that the populations in the central and the southwestern regions of Taiwan might be one part of a metapopulation structure.

Animals↗

PubMed2004

Genetic variation in an endemic salamander, Salamandra atra, using amplified fragment length polymorphism.

The pattern of genetic differentiation of the endemic alpine salamander, Salamandra atra, has been studied using amplified fragment length polymorphism (AFLP) from 11 populations throughout the range of the two currently recognized subspecies, atra and aurorae. Five different primer combinations produced 706 bands and were analyzed by constructing a phylogenetic tree using NJ and principal component analysis. Significant genetic variation was revealed by AFLP between and within populations but, our results show a lack of genetic structure. AFLP markers seems to be unsuitable to investigate complex and recent diversification.

Animals↗

PubMed2006

Challenges of SNP genotyping and genetic variation: its future role in diagnosis and treatment of cancer.

Thorough annotation of common germline genetic variation in the human genome has generated a foundation for the investigation of the contribution of genetics to the etiology and pathogenesis of cancer. For many malignancies, it has become increasingly apparent that numerous alleles, with small-to-moderate effects, additively contribute to cancer susceptibility. The most common genetic variant in the genome, the single nucleotide polymorphism, is of special interest for the study of susceptibility to and protection from cancer. Similarly, intense effort has focused on genetic variants that can predict either response or toxicity to therapeutic interventions. This review discusses the challenges and prospects of genetic association studies in cancer research. On the basis of recent changes in genomics and high-throughput genotyping platforms, future genetic findings of association studies could impact clinical care and public health screening.

Gene Expression Regulation, Neoplastic↗

PubMed1998

Genetic variation and phylogenetic relationships among six populations of corn borers in China.

The genetic variation among and within six populations of the corn borer was determined by using random amplified polymorphic DNA (RAPD) markers. Extensive genetic variability was detected. Of the 802 RAPD markers obtained, 781 (97.4%) were polymorphic among populations. Genetic similarities and distances between each pair of individuals were calculated. UPGMA cluster analysis showed that the YN population (Ostrinia nubilalis Hübner) and the other five populations (Ostrinia furnacalis Guenée) made up branches of the corn borer lineage, instead of deviating; there was no significant genetic differentiation between YN and the other five corn borer populations.

Animals↗

PubMed2005

Plasma level and genetic variation of apolipoprotein E in patients with lipoprotein glomerulopathy.

BACKGROUND: Lipoprotein glomerulopathy (LPG) is a renal disease characterized by thrombus-like lipoproteins in the glomerular capillaries and its abnormal lipoprotein profiles with marked elevation of apolipoprotein E (apoE). In this study, 15 Chinese patients with LPG were involed in exploring the association of the genetic variation and its plasma level in the pathogenesis of LPG. METHODS: A retrospective analysis of the clinical and pathological features was made in 15 patients with LPG. Plasma concentrations of apoE were measured with radial immunodiffusion assay. Genetic variations of apoE gene were detected using polymerase chain reaction and restriction fragment length polymorphism. Glomerular deposition of apoA, apoB and apoE in these patients were detected by immunofluorescence staining using monoclonal antibodies. RESULTS: Biochemical profiles of lipids and lipoproteins revealed markedly elevated levels of triglyceride, apoB and apoE, but approximately normal levels of total cholesterol, apoA1 and lipoprotein(a) [Lp(a)], which resembled familial hypertriglyceridemia. Genetic analysis demonstrated that the genotype distribution of apoE were 7 cases with epsilon3/epsilon4, 4 cases with epsilon3/epsilon3 and 2 cases with epsilon2/epsilon3. The other 2 cases (a mother and her son) showed a same distinct band. The band pattern of later 2 cases was quite similar to the apoE variant of Tokyo type. The calculated allele frequency of epsilon 4 was relatively high in cases with LPG in comparison with that in the normal controls. We further divided the 13 patients into three groups according to their genotypes of apoE. Patients with the genotype of apoE epsilon2/epsilon3 showed a lower level of plasma apoE as compared to those with apoE epsilon3/epsilon4 (P < 0.05). The serum level of high-density lipoprotein (HDL) was the lowest in patients with the genotype of apoE epsilon3/epsilon4. No difference was found among the patients with different apoE genotype in the other clinical and pathological characteristics. CONCLUSIONS: The genotype of apoE epsilon3/epsilon4 is the predominant one in Chinese patients with LPG. Patients with this genotype tend to have a higher plasma level of apoE and more severe lipid dysmetabolism. No correlation was found between the genotype of apoE and the clinical features in patients with LPG.

Adolescent↗

PubMed1994

Genetic variation of the St. Lawrence beluga whale population assessed by DNA fingerprinting.

Recent surveys suggest that the endangered St. Lawrence beluga (Delphinapterus leucas) population is not recovering significantly despite 20 years of protection. Dead individuals that have been autopsied show high levels of tumours and infections. This situation could be a result of pollution, loss of genetic variation, inbreeding depression or a combination of these factors. Analyses of DNA fingerprints from St. Lawrence belugas with three minisatellite probes (Jeffreys 33.6, 33.15 and M13) indicate a reduced level of genetic variation compared to Beaufort Sea animals. The average band-sharing between individuals of the St. Lawrence beluga population for the three probes (0.534, 0.573 and 0.478, respectively) was significantly higher than that of the Beaufort Sea beluga population (0.343, 0.424, 0.314, respectively). Higher levels of mean allele frequency in the St. Lawrence belugas (0.33 vs. 0.21) suggest that this population is composed of individuals which are related. Inbreeding depression could therefore be a factor in the lack of recovery of the St. Lawrence beluga population.

Alleles↗

PubMed2003

Genetic variation in hypoxia-inducible factor 1alpha and its possible association with high altitude adaptation in Sherpas.

Hypoxic stress at high altitude requires adaptations in several physiological functions to ensure the optimal oxygenation of all cells. Several lines of evidence suggested that high-altitude native populations such as Sherpas have been genetically adapted to their stressful environment. We investigated the genetic variation in the hypoxia-inducible factor (HIF)-1alpha gene in Sherpas as compared with Japanese, native lowlanders, and found a novel dinucleotide repeat polymorphism in intron 13 of the HIF-1alpha gene. GT15 allele was more frequent in Japanese than in Sherpas with statistical significance, while GT14 allele was significantly more frequent in Sherpas as compared with Japanese. A possible genetic variation in the HIF-1alpha gene might function in adaptation to living at high altitude. Because the activity of HIF-1 is regulated by multiple steps including the transcriptional level, the effect of the polymorphism in intron 13 on the cellular hypoxic responses remains to be elucidated.

Adaptation, Physiological↗

PubMed2005

Genetic variations in the glucocorticoid receptor gene are not related to glucocorticoid resistance in childhood acute lymphoblastic leukemia.

UNLABELLED: Glucocorticoid sensitivity is an important prognostic factor in pediatric acute lymphoblastic leukemia (ALL). For its antileukemic effect, glucocorticoid binds the intracellular glucocorticoid receptor (GR) subsequently regulating transcription of downstream genes. We analyzed whether genetic variations within the GR gene are related to differences in the cellular response to glucocorticoids. METHODS: In leukemic samples of 57 children, the GR gene was screened for nucleotide variations using a PCR/single-strand conformational polymorphism sequencing strategy. Data were linked to in vivo and in vitro glucocorticoid resistance. RESULTS: No somatic mutations were detected in the GR gene coding region, but six polymorphisms (i.e., ER22/23EK, N363S, BclI, intron mutation 16 bp upstream of exon 5, H588H, and N766N) were identified. In 67% of ALL cases, at least one minor allele of these polymorphisms was detected. Although only borderline significant, the incidence for the N363S polymorphism minor allele was higher (12% versus 6%, P = 0.06) and for the ER22/23EK minor allele lower (4% versus 7.6%, P = 0.1) than in a healthy, comparable population. The different genotypes of the polymorphisms were not related to prednisone resistance. In conclusion, polymorphisms but not somatic mutations in the GR gene coding region occur in leukemic blasts of children with ALL. Our data suggest that these genetic variations are not a major contributor for differences in cellular response to glucocorticoids in childhood ALL. The higher incidence of the N363S minor allele and the lower incidence of the ER22/23EK minor allele in our ALL population as compared with a normal population warrants further research.

Base Sequence↗