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At least 1,189 records · Page 66Linked to original sources
PubMed1998

Breast cancer detection: maps of 2 San Francisco Bay area counties.

OBJECTIVES: This study describes the incidence of late-stage and in situ breast cancer among White women, using specialized mapping techniques that reflect incidence adjusted for the population at risk, and applies these maps to characterize areas with high and low risk of breast cancer. METHODS: Data from the Surveillance, Epidemiology, and End Results (SEER) database and the US Census Bureau were used to study the geographic distribution of breast cancer at the census-tract level in 2 San Francisco Bay Area counties for the years 1978 through 1982. Sociodemographic characteristics of areas with high and low incidence of the stage-specific disease were compared by means of a linear discriminant function. RESULTS: For late-stage breast cancer, the most important variables in discriminating high-risk from low-risk areas were college education, percentage of residents over age 65, and median income. The strongest ecologic indicators of high risk for in situ breast cancer were median income and percentage unemployed. CONCLUSIONS: This study demonstrates the usefulness of census tracts and sociodemographic measures of income and education in describing in situ and late-stage breast cancer.

Adolescent↗
PubMed2004

Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex.

Species with fragmented distributions are particularly useful models for investigating processes underlying biological diversification in the Neotropics. The Phaeothlypis wood-warbler complex (Aves: Parulidae) is comprised of six disjunct or parapatric populations. The geographic distribution of these six populations mirrors the classic map of Neotropical areas of endemism that were originally proposed as putative Pleistocene forest refugia, but the magnitude of mitochondrial DNA divergence between these populations suggests that they are each substantially older, with origins in the late Pliocene. Phylogenetic reconstructions based on long mtDNA coding sequences show that the Guiana Shield and Atlantic Forest populations are sister lineages, and group this combined lineage and the remaining four population-specific lineages in a five-way hard polytomy. MtDNA-based phylogenetic reconstructions provide no evidence that the three populations with conspicuous yellow rump and tail feathers currently grouped as the Buff-rumped Warbler (P. fulvicauda) form a monophyletic group. Furthermore, there is a broad discordance between mtDNA and plumage along a transect just east of the Andes, where the contact zone between highly divergent mtDNA clades is more than 1000 km north of the phenotypic hybrid zone between the bright and dark plumage forms. This discordance between mtDNA genotype and plumage phenotype is similar to patterns seen on a finer geographic scale in other avian hybrid zones and may result from asymmetric introgression of the bright plumage trait.

Animal Communication↗
PubMed1998

Estimating African American admixture proportions by use of population-specific alleles.

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations.

Africa↗
PubMed1996

Substance use disorder exacerbates brain electrophysiological abnormalities in a psychiatrically-ill population.

OBJECTIVE: To assess by brain electrical activity mapping whether cocaine and alcohol abuse and dependence would exacerbate electro-physiological abnormalities in a psychiatrically-ill population. DESIGN, SETTING, AND PARTICIPANTS: Utilizing a brain mapping system, we assessed EEG, Spectral Analysis (Quantitative EEG[QEEG]). Evoked Potentials (Auditory and Visual), and P300 (cognitive evoked potential), in a total of 111 probands divided into three groups: controls (N = 16), psychiatrically-ill without comorbid substance use disorder (N = 34), and psychiatrically-ill with comorbid substance use disorder (cocaine and alcohol abuse and dependence) (N = 61), at an outpatient neuropsychiatric clinic. With regard to demographic data, the group participating in this study did not differ significantly. A comparison was made among the groups to assist in differentiating the effects of substance use disorder compared to psychiatric disease on brain electrical activity. MAIN OUTCOME MEASURES: An assessment of electrophysiological abnormalities and their brain location in psychiatric and substance use disorder patients was done with a brain electrical activity mapping test. MAIN RESULTS: Among the non-substance use disorder, psychiatrically-ill (PI) and substance use disorder, psychiatrically-ill (PI/SD) groups, significantly different brain map abnormalities were observed relative to an assessed normal population MANOVA (P = .017). Moreover, with regard to Spectral Analysis, ANOVA was significant at a P = .038, and we found a weighted linear trend of increased abnormal total spectral analysis (P = .0113), whereby substance use was significantly worse than controls. Moreover among the PI and PI/SD groups, significantly greater total evoked potential (EP) brain trap abnormalities were observed when compared with a characterized normal population (P = .0023) with increasing abnormalities as a function of substance use disorder as measured by a weighted linear trend (P = .0022). In order to determine the site of the EPS abnormalities, we evaluated these abnormalities by location. In this regard, we found all temporal abnormalities (AVBITA, see Table 2) among the PI and PI/SD groups to be significantly greater relative to an assessed normal population (P = .0026). Furthermore, we observed a linear trend of increased temporal abnormalities with increasing substance use disorder (P < .0008). In terms of bitemporal abnormalities (AVBIT) among the PI and PI/SD groups, we also found significantly more bitemporal lobe abnormalities in the PI/SD group compared to our control population (P = .009). Additionally, a weighted linear trend of increased abnormal bitemporal lobe abnormalities was observed with increasing substance use disorder (P = .0022). In the frontal lobe similar findings were observed. With AVBIFA the ANOVA was P < .011, with a weighted linear trend of P < .005 and the PI/SD group were significantly more abnormal than PI or CS on a Duncan Range test. It is noteworthy that in a selected group of depressed (Major Depressive Disorder Recurrent, 296.3) patients, we found profound abnormalities in the various brain map parameters tested. MANOVA and Univariate ANOVA's revealed significantly greater abnormalities in the PI and PI/SD groups compared to assessed controls. A MANOVA for total brain abnormalities was significant at P = .043 and univariate ANOVA's for composite measurements of TSA (P = .017), EPS (P = .0002), AVBITA (P = .000015), and AVBIT (P < .00002) are also significant. With regard to EPS and AVBITA a weighted linear trend was observed where there were increasing abnormalities with increasing substance use disorder, P = .0001 and P = .000003, respectively. Most importantly we found that in addition to increased abnormalities with increasing substance use disorder the PI/SD group had significantly more abnormalities compared to the PI group with regard to both the TSA (P < .05) and AVBIT (P < .05) composite parameters as meas

Alcoholism↗
PubMed2005

Survival analysis of life span quantitative trait loci in Drosophila melanogaster.

We used quantitative trait loci (QTL) mapping to evaluate the age specificity of naturally segregating alleles affecting life span. Estimates of age-specific mortality rates were obtained from observing 51,778 mated males and females from a panel of 144 recombinant inbred lines (RILs). Twenty-five QTL were found, having 80 significant effects on life span and weekly mortality rates. Generation of RILs from heterozygous parents enabled us to contrast effects of QTL alleles with the means of RIL populations. Most of the low-frequency alleles increased mortality, especially at younger ages. Two QTL had negatively correlated effects on mortality at different ages, while the remainder were positively correlated. Chromosomal positions of QTL were roughly concordant with estimates from other mapping populations. Our findings are broadly consistent with a mix of transient deleterious mutations and a few polymorphisms maintained by balancing selection, which together contribute to standing genetic variation in life span.

Alleles↗
PubMed2002

Genetic mechanisms of floral trait correlations in a natural population.

Genetic correlations among traits are important in evolution, as they can constrain evolutionary change or reflect past selection for combinations of traits. Constraints and integration depend on whether the correlations are caused by pleiotropy or linkage disequilibrium, but these genetic mechanisms underlying correlations remain largely unknown in natural populations. Quantitative trait locus (QTL) mapping studies do not adequately address the mechanisms of within-population genetic correlations because they rely on crosses between distinct species, inbred lines or selected lines (see ref. 5), and they cannot distinguish moderate linkage disequilibrium from pleiotropy because they commonly rely on only one or two episodes of recombination. Here I report that after nine generations of enforced random mating (nine episodes of recombination), correlations between six floral traits in wild radish plants are unchanged, showing that pleiotropy generates the correlations. There is no evidence for linkage disequilibrium despite previous correlational selection acting on one functionally integrated pair of traits. This study provides direct evidence of the genetic mechanisms underlying correlations between quantitative traits in a natural population and suggests that there may be constraints on the independent evolution of pairs of highly correlated traits.

Biological Evolution↗
PubMed2000

Genetic architecture of a morphological shape difference between two Drosophila species.

The size and shape of the posterior lobe of the male genital arch differs dramatically between Drosophila simulans and D. mauritiana. This difference can be quantified with a morphometric descriptor (PC1) based on elliptical Fourier and principal components analyses. The genetic basis of the interspecific difference in PC1 was investigated by the application of quantitative trait locus (QTL) mapping procedures to segregating backcross populations. The parental difference (35 environmental standard deviations) and the heritability of PC1 in backcross populations (>90%) are both very large. The use of multiple interval mapping gives evidence for 19 different QTL. The greatest additive effect estimate accounts for 11. 4% of the parental difference but could represent multiple closely linked QTL. Dominance parameter estimates vary among loci from essentially no dominance to complete dominance, and mauritiana alleles tend to be dominant over simulans alleles. Epistasis appears to be relatively unimportant as a source of variation. All but one of the additive effect estimates have the same sign, which means that one species has nearly all plus alleles and the other nearly all minus alleles. This result is unexpected under many evolutionary scenarios and suggests a history of strong directional selection acting on the posterior lobe.

Animals↗
PubMed2006

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits.

BACKGROUND: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. RESULTS: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. CONCLUSION: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Chromosome Mapping↗
PubMed2000

Mixed model analysis of quantitative trait loci.

We develop a mixed model approach of quantitative trait locus (QTL) mapping for a hybrid population derived from the crosses of two or more distinguished outbred populations. Under the mixed model, we treat the mean allelic value of each source population as the fixed effect and the allelic deviations from the mean as random effects so that we can partition the total genetic variance into between- and within-population variances. Statistical inference of the QTL parameters is obtained by using the Bayesian method implemented by Markov chain Monte Carlo (MCMC). This unified QTL mapping algorithm treats the fixed and random model approaches as special cases of the general mixed model methodology. Utility and flexibility of the method are demonstrated by using a set of simulated data.

Algorithms↗
PubMed2004

Genetic control of dormancy in a Triumph/Morex cross in barley.

Seed dormancy in barley ( Hordeum vulgare L.) is one of the most important parameters affecting malting. Seed dormancy is quantitatively inherited and variously influenced by the environment. The objectives of the present study were to determine the genome location and effects of quantitative trait loci (QTLs) involved in the expression of seed dormancy in a barley cross between two varieties derived from different germplasm pools. Using a doubled-haploid population of 107 lines of the cross between the malting types Triumph (two-row, dormant) and Morex (six-row, non-dormant), seed dormancy phenotypic data sets from five environments and a 147-marker linkage map were developed in order to perform QTL analyses with simple interval mapping and simplified composite interval mapping procedures. Two different types of variables were considered for seed dormancy characterization: (1) level of dormancy induced during seed development, which was indirectly measured as germination percentage at 3 days and 7 days, GP3 and GP7 respectively; (2) rate of dormancy release in the course of a period after seed harvest (after-ripening). Different mechanisms of genetic control were detected for these two types of dormancy-related traits. A major and consistent dormancy QTL near the centromere on chromosome 7(5H) was associated with the establishment of dormancy during seed development and accounted for 52% and 33% of the variability for GP3 and GP7, respectively. Two other QTLs located in the vicinity of the vrs1 locus on chromosome 2(2H) and near the long arm telomere on chromosome 7(5H) explained 9% and 19% of variation, respectively, for the rate of dormancy release during after-ripening. Likewise, seed dormancy was assessed in an F(2) population derived from the cross between two dormant types of distinct germplasm groups, Triumph (European, two-row, malt) and Steptoe (North American, six-row, feed), which showed similar but not identical genetic control for dormancy. Interestingly, there is remarkable dormancy QTL conservation in both regions on chromosome 7(5H) identified in this study and among other barley mapping populations. These widely conserved QTLs show potential as targets for selection of a moderate level of seed dormancy in breeding programs.

Chromosome Mapping↗
PubMed1987

Aldehyde dehydrogenase polymorphism: molecular basis and phenotypic relationship to alcohol sensitivity.

Individual differences in response to alcohol have been observed in various ethnic and racial groups. A positive correlation between alcohol sensitivity and elevated blood acetaldehyde level in conjunction with deficiency of an isozyme of aldehyde dehydrogenase (ALDH I) was noted in Japanese subjects given an acute dose of alcohol. Invariably, significantly higher blood acetaldehyde levels were measured in ALDH I-deficient subjects after ethanol loading. The initial flushing in Orientals after alcohol ingestion might be due to their inability to metabolize acetaldehyde quickly and effectively in the absence of the low Km ALDH I isozyme. While Oriental populations of Mongoloid origin showed varying degree of isozyme deficiency, none of the Caucasian or Negroid populations have this isozyme abnormality.

Alcohol Drinking↗
PubMed2004

Effect of population stratification on case-control association studies. II. False-positive rates and their limiting behavior as number of subpopulations increases.

There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test's type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.

Bias↗
PubMed2002

Metapopulation dynamics and spatial heterogeneity in cancer.

With the advent of drugs targeting specific molecular defects in cancerous cells [Gorre, M. E., et al. (2001) Science 293, 876-880], it is important to understand the degree of genetic heterogeneity present in tumor cell populations and the rules that govern microdiversity in human cancer. Here, we first show that populations with different genotypes in genes influencing cell growth and programmed cell death coexist in advanced malignant tumors of the colon, exhibiting microsatellite instability. Detailed, physical mapping of the diverse populations shows them to be arranged in small, intermingling areas, resulting in a variegated pattern of diversity. Using computational modeling of the experimental data, we find that the coexistence between similar competitors is enhanced, instead of deterred, by spatial dynamics [Hanski, I. (1999) Metapopulation Dynamics (Oxford Univ. Press, New York)]. The model suggests a simple and plausible scenario for the generation of spatial heterogeneity during tumor progression. The emergence and persistence of the patterns of diversity encountered in the tumors can be generated without a need to invoke differences in mutation rates, neutrality of interactions, or separated time scales. We posit that the rules that apply to spatial ecology and explain the maintenance of diversity are also at work in tumors and may underlie tumor microheterogeneity.

Adenocarcinoma↗
PubMed2000

Confirmation of the DRB1-DQB1 loci as the major component of IDDM1 in the isolated founder population of Sardinia.

There is considerable uncertainty and debate concerning the application of linkage disequilibrium (LD) mapping in common multifactorial diseases, including the choice of population and the density of the marker map. Previously, it has been shown that, in the large cosmopolitan population of the UK, the established type 1 diabetes IDDM1 locus in the HLA region could be mapped with high resolution by LD. The LD curve peaked at marker D6S2444, 85 kb from the HLA class II gene DQB1, which is known to be a major determinant of IDDM1. However, given the many unknown parameters underlying LD, a validation of the approach in a genetically distinct population is necessary. In the present report we have achieved this by the LD mapping of IDDM1 in the isolated founder population of Sardinia. Using a dense map of microsatellite markers, we determined the peak of LD to be located at marker D6S2447, which is only 6.5 kb from DQB1. Next, we typed a large number of SNPs defining allelic variation at functional candidate genes within the critical region. The association curve, with both classes of marker, peaked at the loci DRB1-DQB1. These results, while representing conclusive evidence that the class II loci DRB1-DQB1 dominate the association of the HLA region to type 1 diabetes, provide empirical support for LD mapping.

Diabetes Mellitus, Type 1↗
PubMed2005

Prospects for whole genome linkage disequilibrium mapping in thoroughbreds.

Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D' coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D' coefficient for LD mapping of a trait in a thoroughbred population. Microsatellite genotype data and grey coat colour as a trait model in a thoroughbred population were used to assess the extent of LD. We demonstrated that LD mapping was a reasonable approach for initial genome-wide scans in a thoroughbred population. Significant LD was demonstrated at approximately 7 cM, implying that roughly 430 appropriately spaced microsatellites were needed for systematic whole-genome LD mapping in this model. LD mapping methods using D' in a thoroughbred population were useful for identifying the chromosomal regions for diseases and economic trait loci (ETL). It was suggested that a thoroughbred population represented a population particularly suitable for LD mapping.

Animals↗
PubMed2005

Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach.

Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detecting linkage. In this study, we develop a reverse regression method to analyze linkage of Kofendrerd Personality Disorder affection status in the New York population of the Genetic Analysis Workshop 14 (GAW14) simulated dataset. When we used the multivariate phenotype, we obtained significant evidence of linkage near four of the six putative loci in at least 25% of the replicates. On the other hand, the linkage analysis based on Kofendrerd Personality Disorder status as a phenotype produced significant findings only near two of the loci and in a smaller proportion of replicates.

Chromosome Mapping↗
PubMed2003

[Location of the fertility restorer gene for T-type CMS wheat by microsatellite marker].

Through the genetic analysis of a F2 population, derived from CMS line 75-3369A (T-type CMS wheat) and the restorer line 7269-10, the result indicated that the restorer line was conditioned by two dominant genes. A F2 population was used to map the fertility restorer (Rf) gene by microsatellite and BSA (bulked segregant analysis). Restorer and sterile DNA pools were established using the extreme fertile and sterile plants of F2 population, respectively. Among the 230 pairs of microsatellite primers, two markers were found polymorphic between the two pools. Linkage analysis showed that microsatellite marker Xgwm136 and Xgwm550 were linked with the two fertility restorer genes, respectively. One of the Rf gene was located on 1AS and the genetic distance between the SSR marker Xgwm136 and this Rf gene was 6.7 cM, the other Rf gene was located on 1BS and with a genetic distance of 5.1 cM to marker Xgwm550.

Chromosome Mapping↗