Use of susceptibility scoring in conjunction with the genotypic transmission disequilibrium test

We explored the utility of selecting a genetically predisposed subgroup to increase the finding of a genetic signal in the Genetic Analysis Workshop 14 Collaborative Study on the Genetics of Alcoholism dataset. A subgroup of affected probands with low environmental risk exposures was defined using a susceptibility score calculated from an environmental risk model. Thirty-nine probands with highly positive scores were selected, along with their parents, for use in a genotypic transmission disequilibrium test (TDT) test. We compared the results of the genotypic TDT in this subgroup to the TDT results using all probands and their parents. For some markers, the susceptibility scoring approach resulted in smaller p-values, while for other markers, evidence for a genetic signal weakened. Further explorations into genetic and environmental population characteristics that benefit from this approach are warranted

Susceptibility scoring in family-based association testing

BACKGROUND: Family-based association testing is an important part of genetic epidemiology. Tests are available to include multiple siblings, unaffected offspring, and to adjust for environmental covariates. We explore a susceptibility residual method of adjustment for covariates. RESULTS: Through simulation, we show that environmental adjustments that down-weight persons who are "destined" to be affected decrease the power to detect genetic association. We used the residual adjusted method on the Framingham Heart Study offspring data, provided for Genetic Analysis Workshop 13, and got mixed results. CONCLUSION: When the genetic effect and environmental effects are independent, a susceptibility residual method of adjustment for environmental covariates reduces the power of the association test. Further study is necessary to determine if residual adjustment is appropriate in more complex disease models

Analysis of gene × environment interactions in sibships using mixed models

BACKGROUND: Gene × environment models are widely used to assess genetic and environmental risks and their association with a phenotype of interest for many complex diseases. Mixed generalized linear models were used to assess gene × environment interactions with respect to systolic blood pressure on sibships adjusting for repeated measures and hierarchical nesting structures. A data set containing 410 sibships from the Framingham Heart Study offspring cohort (part of the Genetic Analysis Workshop 13 data) was used for all analyses. Three mixed gene × environment models, all adjusting for repeated measurement and varying levels of nesting, were compared for precision of estimates: 1) all sibships with adjustment for two levels of nesting (sibs within sibships and sibs within pedigrees), 2) all sibships with adjustment for one level of nesting (sibs within sibships), and 3) 100 data sets containing random draws of one sibship per extended pedigree adjusting for one level of nesting. RESULTS: The main effects were: gender, baseline age, body mass index (BMI), hypertensive treatment, cigarettes per day, grams of alcohol per day, and marker GATA48G07A. The interaction fixed effects were: baseline age by gender, baseline age by cigarettes per day, baseline age by hypertensive treatment, baseline age by BMI, hypertensive treatment by BMI, and baseline age by marker GATA48G07A. The estimates for all three nesting techniques were not widely discrepant, but precision of estimates and determination of significant effects did change with the change in adjustment for nesting. CONCLUSION: Our results show the importance of the adjustment for all levels of hierarchical nesting of sibs in the presence of repeated measures

Comparison of type I error for multiple test corrections in large single-nucleotide polymorphism studies using principal components versus haplotype blocking algorithms

Although permutation testing has been the gold standard for assessing significance levels in studies using multiple markers, it is time-consuming. A Bonferroni correction to the nominal p-value that uses the underlying pair-wise linkage disequilibrium (LD) structure among the markers to determine the number of effectively independent tests has recently been proposed. We propose using the number of independent LD blocks plus the number of independent single-nucleotide polymorphisms for correction. Using the Collaborative Study on the Genetics of Alcoholism LD data for chromosome 21, we simulated 1,000 replicates of parent-child trio data under the null hypothesis with two levels of LD: moderate and high. Assuming haplotype blocks were independent, we calculated the number of independent statistical tests using 3 haplotype blocking algorithms. We then compared the type I error rates using a principal components-based method, the three blocking methods, a traditional Bonferroni correction, and the unadjusted p-values obtained from FBAT. Under high LD conditions, the PC method and one of the blocking methods were slightly conservative, whereas the 2 other blocking methods exceeded the target type I error rate. Under conditions of moderate LD, we show that the blocking algorithm corrections are closest to the desired type I error, although still slightly conservative, with the principal components-based method being almost as conservative as the traditional Bonferroni correction

Hydrochlorothiazide Is Superior to Isradipine for Reduction of Left Ventricular Mass: Results of a Multicenter Trial fn1fn1This study was supported by an unrestricted grant from Sandoz Pharmaceuticals, East Hanover, New Jersey.fn2fn2To discuss this article on-line, visit the ACC Home Page at http://www.acc.org/membersand click on the JACC Forum

AbstractObjectives. We sought to determine the efficacy of isradipine in reducing left ventricular (LV) mass and wall thickness in hypertensive patients.Background. LV hypertrophy on the echocardiogram is a strong predictor of cardiovascular events. Reduction of LV mass may be a desirable goal of drug therapy for hypertension. However, although thiazide diuretic drugs have been advocated as first-line therapy for hypertension, their efficacy in reducing LV mass has been questioned.Methods. Patients with mild to moderate diastolic hypertension and LV mass in excess of 1 SD of normal values were randomized to isradipine (n = 89) or hydrochlorothiazide therapy (n = 45). Evaluations were obtained at baseline, after 3 and 6 months of treatment and 2 weeks after treatment was stopped.Results. At 6 months, LV mass decreased by 43 ± 45 g (mean ± SD) with hydrochlorothiazide (p < 0.001) but only by 11 ± 48 g with isradipine (p = NS; between-group comparison, p < 0.001). Two weeks after drug therapy was stopped, LV mass remained 24 ± 41 g lower than that at baseline in the hydrochlorothiazide group (p = 0.003) but only 7 ± 50 g lower in the isradipine group (p = NS). Septal and posterior wall thicknesses were significantly and equally reduced with both isradipine and hydrochlorothiazide. Greater LV mass reduction with hydrochlorothiazide was related to a 2.8 ± 3.3-mm reduction of LV cavity size with hydrochlorothiazide but no reduction with isradipine. At 6 months of treatment, diastolic blood pressure (BP) by design was equally reduced in both treatment groups. At 3 months, systolic BP was reduced by 17 ± 15 mm Hg with isradipine and by 26 ± 15 and 25 ± 17 mm Hg at 3 and 6 months, respectively, with hydrochlorothiazide (p = 0.003, between-group comparison). However, on stepwise multivariable regression analysis, treatment selection (partial r2= 0.082, p = 0.001), change in average 24-h systolic BP (partial r2= 0.032, p = 0.029) and change in average sitting systolic BP (partial r2= 0.017, p = 0.096) were predictive of LV mass reduction.Conclusions. Despite an equivalent reduction of diastolic BP, 6 months of therapy with hydrochlorothiazide is associated with a substantial reduction of LV mass, greater than that with isradipine. The superior efficacy of hydrochlorothiazide for LV mass reduction is associated with a greater reduction of systolic BP as well as drug selection itself. These data may have important therapeutic implications

Optimal Signal Processing of Frequency-Stepped CW Radar Data

An optimal signal processing algorithm is derived for estimating the time delay and amplitude of each scatterer reflection using a frequency-stepped CW system. The channel is assumed to be composed of abrupt changes in the reflection coefficient profile. The optimization technique is intended to maximize the target range resolution achievable from any set of frequency-stepped CW radar measurements made in such an environment. The algorithm is composed of an iterative two-step procedure. First, the amplitudes of the echoes are optimized by solving an overdetermined least squares set of equations. Then, a nonlinear objective function is scanned in an organized fashion to find its global minimum. The result is a set of echo strengths and time delay estimates. Although this paper addresses the specific problem of resolving the time delay between the first two echoes, the derivation is general in the number of echoes. Performance of the optimization approach is illustrated using measured data obtained from an HP-X510 network analyzer. It is demonstrated that the optimization approach offers a significant resolution enhancement over the standard processing approach that employs an IFFT. Degradation in the performance of the algorithm due to suboptimal model order selection and the effects of additive white Gaussion noise are addressed

The impact of population heterogeneity on risk estimation in genetic counseling

BACKGROUND: Genetic counseling has been an important tool for evaluating and communicating disease susceptibility for decades, and it has been applied to predict risks for a wide class of hereditary disorders. Most diseases are complex in nature and are affected by multiple genes and environmental conditions; it is highly likely that DNA tests alone do not define all the genetic factors responsible for a disease, so that persons classified into the same risk group by DNA testing actually could have different disease susceptibilities. Ignorance of population heterogeneity may lead to biased risk estimates, whereas additional information on population heterogeneity may improve the precision of such estimates. METHODS: Although DNA tests are widely used, few studies have investigated the accuracy of the predicted risks. We examined the impact of population heterogeneity on predicted disease risks by simulation of three different heterogeneity scenarios and studied the precision and accuracy of the risks estimated from a logistic regression model that ignored population heterogeneity. Moreover, we also incorporated information about population heterogeneity into our original model and investigated the resulting improvement in the accuracy of risk estimation. RESULTS: We found that heterogeneity in one or more categories could lead to biased estimates not only in the "contaminated" categories but also in other homogeneous categories. Incorporating information about population heterogeneity into the original model greatly improved the accuracy of risk estimation. CONCLUSIONS: Our findings imply that without thorough knowledge about genetic basis of the disease, risks estimated from DNA tests may be misleading. Caution should be taken when evaluating the predicted risks obtained from genetic counseling. On the other hand, the improved accuracy of risk estimates after incorporating population heterogeneity information into the model did point out a promising direction for genetic counseling, since more and more new techniques are being invented and disease etiology is being better understood

Mesoamerican urbanism revisited: Environmental change, adaptation, resilience, persistence, and collapse

Urban adaptation to climate change is a global challenge requiring a broad response that can be informed by how urban societies in the past responded to environmental shocks. Yet, interdisciplinary efforts to leverage insights from the urban past have been stymied by disciplinary silos and entrenched misconceptions regarding the nature and diversity of premodern human settlements and institutions, especially in the case of prehispanic Mesoamerica. Long recognized as a distinct cultural region, prehispanic Mesoamerica was the setting for one of the world’s original urbanization episodes despite the impediments to communication and resource extraction due to the lack of beasts of burden and wheeled transport, and the limited and relatively late use of metal implements. Our knowledge of prehispanic urbanism in Mesoamerica has been significantly enhanced over the past two decades due to significant advances in excavating, analyzing, and contextualizing archaeological materials. We now understand that Mesoamerican urbanism was as much a story about resilience and adaptation to environmental change as it was about collapse. Here we call for a dialogue among Mesoamerican urban archaeologists, sustainability scientists, and researchers interested in urban adaptation to climate change through a synthetic perspective on the organizational diversity of urbanism. Such a dialogue, seeking insights into what facilitates and hinders urban adaptation to environmental change, can be animated by shifting the long-held emphasis on failure and collapse to a more empirically grounded account of resilience and the factors that fostered adaptation and sustainability

Using mixture models to characterize disease-related traits

We consider 12 event-related potentials and one electroencephalogram measure as disease-related traits to compare alcohol-dependent individuals (cases) to unaffected individuals (controls). We use two approaches: 1) two-way analysis of variance (with sex and alcohol dependency as the factors), and 2) likelihood ratio tests comparing sex adjusted values of cases to controls assuming that within each group the trait has a 2 (or 3) component normal mixture distribution. In the second approach, we test the null hypothesis that the parameters of the mixtures are equal for the cases and controls. Based on the two-way analysis of variance, we find 1) males have significantly (p < 0.05) lower mean response values than females for 7 of these traits. 2) Alcohol-dependent cases have significantly lower mean response than controls for 3 traits. The mixture analysis of sex-adjusted values of 1 of these traits, the event-related potential obtained at the parietal midline channel (ttth4), found the appearance of a 3-component normal mixture in cases and controls. The mixtures differed in that the cases had significantly lower mean values than controls and significantly different mixing proportions in 2 of the 3 components. Implications of this study are: 1) Sex needs to be taken into account when studying risk factors for alcohol dependency to prevent finding a spurious association between alcohol dependency and the risk factor. 2) Mixture analysis indicates that for the event-related potential "ttth4", the difference observed reflects strong evidence of heterogeneity of response in both the cases and controls

Spitzer spectral line mapping of protostellar outflows: I. Basic data and outflow energetics

We report the results of spectroscopic mapping observations carried out toward protostellar outflows in the BHR71, L1157, L1448, NGC 2071, and VLA 1623 molecular regions using the Infrared Spectrograph (IRS) of the Spitzer Space Telescope. These observations, covering the 5.2 - 37 micron spectral region, provide detailed maps of the 8 lowest pure rotational lines of molecular hydrogen and of the [SI] 25.25 micron and [FeII] 26.0 micron fine structure lines. The molecular hydrogen lines, believed to account for a large fraction of the radiative cooling from warm molecular gas that has been heated by a non-dissociative shock, allow the energetics of the outflows to be elucidated. Within the regions mapped towards these 5 outflow sources, total H2 luminosities ranging from 0.02 to 0.75 L(solar) were inferred for the sum of the 8 lowest pure rotational transitions. By contrast, the much weaker [FeII] 26.0 micron fine structure transition traces faster, dissociative shocks; here, only a small fraction of the fast shock luminosity emerges as line radiation that can be detected with Spitzer/IRS.Comment: 38 pages including 17 figures. Accepted for publication in Ap