Effect of NAT2 gene polymorphism on bladder cancer risk in Slovak population

N-acetyltransferase 2 (NAT2) is phase II enzyme with major roles in catalyzing the detoxification of aromatic amines, which are known risk factors for bladder cancer, and are ubiquitously present in the environment. We assessed the association between common polymorphisms in NAT2 gene and the risk of bladder cancer in 90 Slovak patients and 274 ethnicity-matched healthy controls. Effect modifications by smoking, age and gender were also evaluated. Overall, NAT2 slow acetylation was associated with significantly increased risk of bladder cancer (OR = 1.90; 95% CI, 1.15–3.16). In stratified analyses by age and gender, the elevated risk conferred by slow acetylator genotype was evident in older individuals (OR = 3.55; 95% CI, 1.77–7.35) and males (OR = 4.65; 95% CI, 1.68–16.10), with further increasing in NAT2*5B/*6A genotype carriers. Smoking was confirmed to be important risk factor, moreover, the risk was markedly increased in smokers with NAT2 slow acetylator genotype, and NAT2*5B/*6A carriers especially. In summary, these findings are consistent with previous literature suggesting that individual susceptibility to bladder cancer may be modulated by NAT2 polymorphisms, particularly in interaction with relevant environmental exposures such as smoking.     

HLA-DR polymorphism in a Senegalese Mandenka population: DNA oligotyping and population genetics of DRB1 specificities.

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1*1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequent specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52b (DRB3*02) represents as much as 80.7% of all DR52 haplotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the Mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes.     

Extensive polymorphism of the FUT2 gene in an African (Xhosa) population of South Africa

The human secretor type α(1,2)fucosyltrans-ferase gene (FUT2) polymorphism was investigated in Xhosa and Caucasian populations of South Africa by polymerase chain reaction–restriction fragment length polymorphism and DNA sequencing. Six new base substitutions were found in the coding region of FUT2. A single base (C) deletion at nucleotide 778, which led to a frame shift and produced a stop codon at codon 275, was responsible for the enzyme inactivation. Three nonsynonymous base substitutions, A40G (Ile¹⁴Val), C379T (Arg¹²⁷Cys), and G481A (Asp¹⁶¹Asn), and two synonymous base substitutions, A375G (Glu¹²⁵) and C480T (His¹⁶⁰), were also identified in functional alleles. As a result, seven new alleles, Se ⁴⁰ , Se ⁴⁸¹ , Se ^40,481 , Se ^357,480 , Se ^357,379,480 , Se ³⁷⁵ , and se ^357,480,778 were identified. Population studies revealed that an allele containing a nonsense mutation G428A (Trp¹⁴³stop) (se ⁴²⁸ ) was the common null allele in both Xhosa and Caucasian populations, whereas an allele containing a missense A385T (Ile¹²⁹Phe) mutation (se ^357,385 ), which is the common null allele in Orientals, was found to be absent from both populations. The heterozygosity rates of FUT2 genotypes were as high as 0.75 in the Xhosa population and 0.65 in the Caucasian population. Therefore, the extensive polymorphism and race specificity of the FUT2 gene make it suitable for application as a new tool in genetic studies of modern human evolutionary history. Received: 23 March 1998 / Accepted: 9 May 1998     

Estimating population boundaries using regional and local-scale spatial genetic structure: an example in Eucalyptus globulus

Eucalyptus globulus Labill is a foundation tree species over its disjunct distribution in southeastern Australia. The quality of its pulp makes it the most important hardwood species in the world. The importance of E. globulus prompted the establishment of common gardens from seed collected across its geographic range. This enabled us to study the genetic structure of the species, its population boundaries, and gene flow using 444 trees from different open-pollinated families that were genotyped at 16 microsatellite loci. A Bayesian clustering method was used to resolve five genetically distinct groups across the geographical range. These groups were identified as regions, which varied in diameter from 38 to 294?km and contain 4 to 16 putative populations. For two of these regional groups, we used spatial autocorrelation analysis based on assignment of trees to their natural stands to examine gene flow within each region. Consistent significant local-scale spatial structure occurred in both regions. Pairs of individuals within a region showed significant genetic similarity that extended beyond 40?km, suggesting distant movement of pollen. This suggests that breeding populations in E. globulus are much bigger than traditionally accepted in eucalypts. Our results are important for the management of genetic diversity and breeding populations in E. globulus. Similar studies of a variety of eucalypts pollinated by insects and birds will determine whether the local-scale genetic structure of E. globulus is unusual.     

Reduction of sample heterogeneity through use of population substructure: an example from a population of African American families with sarcoidosis

Sarcoidosis is a granulomatous inflammatory disorder of complex etiology with significant linkage to chromosome 5, and marginal linkage was observed to five other chromosomes in African Americans (AAs) in our previously published genome scan. Because genetic factors underlying complex disease are often population specific, genetic analysis of samples with diverse ancestry (i.e., ethnic confounding) can lead to loss of power. Ethnic confounding is often addressed by stratifying on self-reported race, a controversial and less-than-perfect construct. Here, we propose linkage analysis stratified by genetically determined ancestry as an alternative approach for reducing ethnic confounding. Using data from the 380 microsatellite markers genotyped in the aforementioned genome scan, we clustered AA families into subpopulations on the basis of ancestry similarity. Evidence of two genetically distinct groups was found: subpopulation one (S1) comprised 219 of the 229 families, subpopulation two (S2) consisted of six families (the remaining four families were a mixture). Stratified linkage results suggest that only the S1 families contributed to previously identified linkage signals at 1p22, 3p21-14, 11p15, and 17q21 and that only the S2 families contributed to those found at 5p15-13 and 20q13. Signals on 2p25, 5q11, 5q35, and 9q34 remained significant in both subpopulations, and evidence of a new susceptibility locus at 2q37 was found in S2. These results demonstrate the usefulness of stratifying on genetically determined ancestry, to create genetically homogeneous subsets--more reliable and less controversial than race-stratified subsets--in which to identify genetic factors. Our findings support the presence of sarcoidosis-susceptibility genes in regions identified elsewhere but indicate that these genes are likely to be ancestry specific.     

Gastric myoelectrical activity in a population of healthy Croatian subjects

Myoelectrical activity of the stomach was estimated in healthy Croatian subjects using the latest multi-channel percutaneous electrogastrograph. The aim of the study was to determine normal values of gastric myoelectrical activity for the population of Croatia. The study included 120 healthy subjects of both sexes, various age groups, body mass index values, and mode of lead placement. The measurement was performed 60 min before and 60 min after test meal. The following parameters of gastric myoelectrical activity were analyzed: dominant frequency (DF, c/min); dominant frequency within normal range (DFNR, %); coefficient of variation for dominant frequency (CVDF); dominant strength (DS, mV); postprandial increase intensity in dominant strength (PPIIDS; %); bradygastria (c/min, %); tachygastria (c/min, %); and arrhythmia. DF for the study group as a whole was around 3 cpm, at the normal range midpoint, and all other parameters were within the normal limits. On postprandial measurement, the rate of arrhythmias showed a significant decline. Age was found to influence DF, CVDF and arrhythmia in preprandial but not in postprandial period, whereas sex influenced DF, DS and bradygastria in preprandial period, and DF, CVDF, PPIIDS and tachygastria in postprandial period. The mode of lead placement had no impact on the electrogastrographic parameters observed. The values of gastric myoelectrical activity recorded in healthy Croatian subjects were within the normal range of the values defined by previous studies across Europe.     

Problems in determination of skeletal lead burden in archaeological samples: an example from the First African Baptist Church population

Human bone lead content has been demonstrated to be related to socioeconomic status, occupation and other social and environmental correlates. Skeletal tissue samples from 135 individuals from an early nineteenth century Philadelphia cemetery (First African Baptist Church) were studied by electrothermal atomic absorption spectrometry and X-ray fluorescence for lead content. High bone lead levels led to investigation of possible diagenetic effects. These were investigated by several different approaches including distribution of lead within bone by X-ray fluorescence, histological preservation, soil lead concentration and acidity as well as location and depth of burial. Bone lead levels were very high in children, exceeding those of the adult population that were buried in the cemetery, and also those of present day adults. The antemortem age-related increase in bone lead, reported in other studies, was not evidenced in this population. Lead was evenly deposited in areas of taphonomic bone destruction. Synchrotron X-ray fluorescence studies revealed no consistent pattern of lead microdistribution within the bone. Our conclusions are that postmortem diagenesis of lead ion has penetrated these archaeological bones to a degree that makes their original bone lead content irretrievable by any known method. Increased bone porosity is most likely responsible for the very high levels of lead found in bones of newborns and children.     

Estimates of genetic variance in an F2 maize population

Maize (Zea mays L.) breeders have used several genetic-statistical models to study the inheritance of quantitative traits. These models provide information on the importance of additive, dominance, and epistatic genetic variance for a quantitative trait. Estimates of genetic variances are useful in understanding heterosis and determining the response to selection. The objectives of this study were to estimate additive and dominance genetic variances and the average level of dominance for an F2 population derived from the B73 x Mo17 hybrid and use weighted least squares to determine the importance of digenic epistatic variances relative to additive and dominance variances. Genetic variances were estimated using Design III and weighted least squares analyses. Both analyses determined that dominance variance was more important than additive variance for grain yield. For other traits, additive genetic variance was more important than dominance variance. The average level of dominance suggests either overdominant gene effects were present for grain yield or pseudo-overdominance because of linkage disequilibrium in the F2 population. Epistatic variances generally were not significantly different from zero and therefore were relatively less important than additive and dominance variances. For several traits estimates of additive by additive epistatic variance decreased estimates of additive genetic variance, but generally the decrease in additive genetic variance was not significant.     

Trypanosoma brucei gambiense: study of population genetic structure of Central African stocks using amplified fragment length polymorphism (AFLP)

To understand the maintenance and resurgence of historical Human African Trypanosomiasis (HAT) foci, AFLP was used to genotype 100 Central African Trypanosoma brucei s.l. stocks. This technique confirmed the high genetic stability of T. b. gambiense group 1 stocks and the micro genetic variability within Central African T. b. gambiense stocks. It revealed several T. b. gambiense genotypes and allowed the identification of minor and major genotypes in HAT foci. The coexistence of these genotypes in the same focus suggests that clustering of stocks according to HAT focus does not provide the true genetic picture of trypanosome circulating within the disease focus because the minor genotypes are generally underestimated. The presence of minor and major genotypes in HAT foci may explain the persistence and the resurgence of Central African sleeping sickness foci.     

Micronuclei in blood lymphocytes and genetic polymorphism for GSTM1, GSTT1 and NAT2 in pesticide-exposed greenhouse workers.

The frequency of micronuclei (MN) in cultured peripheral lymphocytes was used as a biomarker of genotoxic effects in 34 Italian pesticide-exposed greenhouse workers and 33 unexposed referents matched with the exposed workers for age and smoking habits. The possible influence of the genetic polymorphisms of xenobiotic metabolizing enzymes glutathione S-transferase M1 (GSTM1), T1 (GSTT1), and N-acetyltransferase 2 (NAT2) was also evaluated. To restrict the analysis primarily to cells that have divided once in vitro, MN were scored only in cells showing label after a 42-h incubation with bromodeoxyuridine (BrdU), as detected by immunofluorescence (anti-BrdU technique). Two different concentrations of BrdU (0.5 and 1 microg/ml) were compared. Individual frequencies of micronucleated cells (MNCs) obtained with the two concentrations of BrdU significantly correlated with each other (r=0.55, P<0.001). Higher mean MNCs frequencies (per 1000 cells) were detected among exposed smokers (9.0 at 0.5 microg/ml BrdU and 7.8 at 1 microg/ml BrdU) than in smoking referents (6.3 and 5.9, respectively). In multiple regression analysis controlling for age, sex, smoking and genotypes, a significant elevation of MNC frequency (P=0.004 at 1 microg/ml BrdU; P=0.052 at 0.5 microg/ml BrdU) was observed in greenhouse workers with a work history of extensive pesticide spraying (n=17). Increased MNC frequencies were also associated with ageing at 0.5 microg/ml BrdU, with the GSTM1-positive genotype at both 1 (P=0.028) and 0.5 (P=0.056) microg/ml BrdU in all subjects, and with the NAT2 fast acetylator genotype in smokers at 0.5 microg/ml BrdU (P=0.043). The results indicate that MN rates are increased in greenhouse workers, especially in those involved in pesticide spraying. The GSTM1 positive and NAT2 fast genotypes appear to be associated with elevated MNC frequencies, which contradicts with earlier results on elevated chromosomal aberration rates in GSTM1 null smokers and NAT2 slow subjects.     

Inter-ethnic differences in genetic polymorphisms of xenobiotic-metabolizing enzymes (CYP1A1, CYP2D6, NAT1 and NAT2) in healthy populations: correlation with the functional in silico prediction

Several studies have shown that many polymorphisms of the xenobiotic-metabolizing enzymes (XME) affect either enzymatic functions or are associated with various aspects of human health. Owing to the presence of these single nucleotide variants (SNVs), differences in detoxification capacity have been observed between many ethnicities. The aim of this investigation was to study the prevalence of four polymorphisms in XME among various ethnic groups. Attention was focused on polymorphisms of CYP2D6 (rs1058172, G>A, p.Arg365His), CYP1A1 (rs4646421, c.-26-728C>T), NAT1 (rs4921880, c.-85-1014T>A) and NAT2 (rs1208, A>G, p.Arg268Lys). These polymorphisms were analyzed in 261 healthy Tunisians individuals in comparison with different ethnic backgrounds from hapmap database. In addition, in silico functional prediction was also performed to determine the loss of function variants. Our results demonstrated that population’s origins widely affect the genetic variability of XME enzymes and Tunisians show a characteristic pattern. In silico predictions showed a deleterious effect for p.Arg268Lys substitution on CYP2D6 function, findings confirmed its key role played in cancer susceptibility. These data show that detoxification genes structures depend on the studied population. This suggests that ethnic differences impact on disease risk or response to drugs and therefore should be taken into consideration in genetic association studies focusing on XME enzymes. Our results provide the first report on these SNV in Tunisian population and could be useful for further epidemiological investigations including targeted therapy.     

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae)

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.     

Hereditary polymorphism in the haptoglobin system of schizophrenic patients and healthy subjects]

Hereditary polymorphism of haptoglobin is studied by means of starch gel electrophoresis in schizophrenic patients (200 persons) and in healthy people (154 persons), in habitants of Minsk. It is concluded that Minsk inhabitants do not differ considerably from the rest European population in their frequencies of haptoglobin alleles. No reliable differences in the distribution of haptoglobin genotypes were found between patients and healthy persons. However, hereditary types of haptoglobins turned to be markers of the course and the prognosis of schizophrenia.     

Polyomavirus JC genotypes in an urban United States population reflect the history of African origin and genetic admixture in modern African Americans

The human polyomavirus JC (JC virus), a small, circular, double-stranded DNA virus, has a worldwide distribution and is excreted harmlessly in urine by 20% to 70% of adults. DNA sequence analysis has identified seven distinct genotypes that likely coevolved with modern humans, although the mode of virus transmission is unknown. Type 1 is European in its distribution. Types 2 and 7 are Asian, while Types 3 and 6 are African. Type 4, closely related to Type 1, is of uncertain origin, having been found in population groups in parts of Europe and in the United States, but not in Africa. Here we have studied the JCV partial genomic DNA sequences amplified by polymerase chain reaction techniques from urines of an urban, mainly African American population cohort from Washington, D.C. The predominant genotype identified was Type 4 (32/78 JCV strains, 41%). Type 1 strain was found in 32% of African Americans, while JCV Type 3 strain was found in 18% of African Americans. These African strains have persisted in modern African Americans after 200 to 400 years of minority existence and genetic admixture in the New World. An ancient West African genotype, Type 6, was absent in this African American cohort. However, one Type 6 strain was found in a patient from Sierra Leone (West Africa), domiciled in the United States for 20 years. Type 2A, the most common subtype in Native Americans, was seen in only two African-Americans (3%). A Type 7 strain, previously reported only in Taiwan and South China, was identified in a Vietnamese immigrant. These data support the history of African origin, migration, and genetic admixture of modern African Americans. Analysis of JCV strains in the present American populations provides a novel tool for reconstructing human migrations and genetic admixture in the New World.     

The importance of reproductive strategies in population genetic approaches to conservation: an example from the marine angiosperm genus Zostera

Knowledge of the levels of genetic diversity maintained in natural populations can play a central role in conservation programmes, particularly in threatened habitats or species. Fluctuations in population size can lead to loss of variation and, consequently, increase the risk of extinction. We have examined whether such a genetic bottleneck has occurred in populations of two species in the seagrass genus Zostera, which are believed to have been affected by an outbreak of wasting disease at the start of the last century. A test for heterozygote excess at five nuclear microsatellite loci did not suggest the occurrence of a genetic bottleneck, but analysis of seven chloroplast microsatellite loci and sequence data from two regions did suggest a bottleneck in the chloroplast genome. Extremely low levels of between-population diversity suggest that all subpopulations can be treated as a single management unit for each species. Comparable levels of nuclear genetic diversity were found in the three populations of the primarily sexual Zostera marina var. angustifolia studied but a wider range of within-population diversity was found in Zostera noltii, which displays both sexual and vegetative reproductive strategies. This may be due to an increase in sexual recruitment due to localised fresh water inflow into the study site near to the most diverse population. Such populations should be prioritised as source material for any replanting or remediation due to natural or anthropogenic loss of Zostera beds in the area.     

JP-3 gene polymorphism in a healthy population of Serbia and Montenegro

Expansions of CTG repeats inJP-3 gene are associated with a phenotype similar to Huntington disease. These expansions are the cause of Huntington disease like-2 (HDL-2) phenotype. CTG repeats inJP-3 gene are polymorphic in healthy population. Analyses of CTG repeat polymorphism ofJP-3 gene in various healthy populations could help in estimating the population at risk for developing HDL-2. CTG repeat polymorphism ofJP-3 gene was analysed in healthy population of Serbia and Montenegro. Study included 198 unrelated subjects. Analyses ofJP-3 locus were performed using PCR and sequencing. Six differentJP-3 alleles were obtained and they were in the range of 11 to 18 CTG repeats showing a bimodal distribution, with peaks at 14 and 16. Results show that the distribution ofJP-3 alleles in population of Serbia and Montenegro is consistent with distributions in other analysed populations. The absence of alleles with more then 18 CTG repeats suggests that HDL-2 is very rare in the populations of Serbia and Montenegro.     

Fine scale population genetic structure of pumas in the Intermountain West

In this study, I examined the population genetic structure of subpopulations of pumas (Puma concolor) in Idaho and surrounding states. Patterns of genetic diversity, population structure, levels of inbreeding, and the relationship between genetic differentiation and dispersal distance within and between 15 subpopulations of pumas were compared. Spatial analyses revealed that the Snake River plain was an important barrier to movement between northern and southern regions of Idaho. In addition, subpopulations south of the Snake River plain exhibited lower levels of genetic diversity, higher levels of inbreeding, and a stronger pattern of isolation by distance relative to subpopulations north of the Snake River plain. Lower levels of diversity and restricted gene flow are likely the result of historically lower population sizes in conjunction with more recent changes in habitat use and available dispersal corridors for movement. The subdivision of puma populations north and south of the Snake River plain, along with the patterns of genetic diversity within regions, indicate that landscape features are affecting the population genetic structure of pumas in Idaho. These results indicate that information about the effects of landscape features on the distribution of genetic diversity should be considered when designing plans for the management and conservation of pumas.     

Molecular investigation of African isolates of Trichinella reveals genetic polymorphism in Trichinella nelsoni

Molecular genetic studies were carried out on three isolates of Trichinella nelsoni (from Kenya, Tanzania and South Africa) and three isolates of Trichinella T8 (from South Africa and Namibia) from sylvatic carnivores and from a sylvatic swine. A probe (pT7.3) specific for T. nelsoni was obtained by screening a pUC18 genomic library. The pT7.3 sequence was 346 bp in length with an AT content of 70%. The sequence is present approximately 200 times per haploid genome. Southern blot analysis of Hind III digested DNAs of the three isolates of T. nelsoni revealed that the hybridisation patterns of the isolates from Kenya and Tanzania were identical and that they differed from that of the isolate from South Africa, indicating the presence of polymorphism in this species. A pUC18 genomic library of Trichinella T8 was also screened, and one clone (pT8.3) was found to be specific for homologous DNA by dot blot, but Southern blot analysis of DNA samples from eight genotypes showed different hybridisation signals for both Trichinella T8 and Trichinella britovi DNAs. No differences in the nucleotide sequences of the expansion segment V were observed for the T. nelsoni isolates. However, they differed from those of Trichinella T8. The presence of Trichinella T8 in Africa south of the Sahara and its genetic relationship with T. britovi remain unclear and warrant detailed investigations.