Heritability Analyses Uncover Shared Genetic Effects of Lung Function and Change over Time

Genetic influence on lung functions has been identified in previous studies; however, the relative longitudinal effects of genetic factors and their interactions with smoking on lung function remain unclear. Here, we identified the longitudinal effects of genetic variants on lung function by determining single nucleotide polymorphism (SNP) heritability and genetic correlations, and by analyzing interactions with smoking. Subject-specific means and annual change rates were calculated for eight spirometric measures obtained from 6622 Korean adults aged 40−69 years every two years for 14 years, and their heritabilities were estimated separately. Statistically significant (p < 0.05) heritability for the subject-specific means of all spirometric measures (8~32%) and change rates of forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC; 16%) and post-bronchodilator FEV1/FVC (17%) were detected. Significant genetic correlations of the change rate with the subject-specific mean were observed for FEV1/FVC (ρg = 0.64) and post-bronchodilator FEV1/FVC (ρg = 0.47). Furthermore, post-bronchodilator FEV1/FVC showed significant heritability of SNP-by-smoking interaction (hGXS2 = 0.4) for the annual change rate. The GWAS also detected genome-wide significant SNPs for FEV1 (rs4793538), FEV1/FVC (rs2704589, rs62201158, and rs9391733), and post-bronchodilator FEV1/FVC (rs2445936). We found statistically significant evidence of heritability role on the change in lung function, and this was shared with the effects on cross-sectional measurements. We also found some evidence of interaction with smoking for the change of lung function.

Poisson Regression Modeling of Diarrhea Events in Pasuruan Regency with Maximum Likelihood Estimates and Generalized Method Moment

Context:

Diarrhea characterized by a frequency increased of defecation more than 3 times/ day accompanied by changes in consistency (becoming liquid). The causes of diarrhea can be divided into 2 parts, which are direct causes and indirect causes that can facilitate or accelerate the occurrence of diarrhea, including bacteria, nutritional conditions, hygiene and sanitation, social culture such as population density, economic status, low birth weight, and immunization.

Aims:

The purpose of this study to examine the factors that influence the incidence of diarrhea.

Methods:

This research used secondary data, the prevalence of diarrhea and risk factors in Pasuruan Regency Health Center. Poisson regression approach with maximum likelihood estimator (MLE) estimation and Generalized Method Moment (GMM) used in this study.

Results:

The results showed that GMM estimation method in the Poisson regression model gave better performance in terms of significance parameters compared to the MLE method.

Conclusions:

Factors affecting the increase of diarrhea occurrences in area with an estimated MLE Percentage of non-exclusive breastfeeding and Percentage of normal nutritional status. Whereas the GMM estimation is the percentage of non-exclusive breastfeeding, the percentage of low birth weight, the percentage of population density, the percentage of smokers among family members in the house, the percentage of incomplete immunizations, the percentage of under-five years old children less than 2, the percentage of normal nutritional status, and the percentage of middle class socioeconomic status.

Choosing Interim Sample Sizes in Group Sequential Designs

This manuscript investigates sample sizes for interim analyses in group sequential designs. Traditional group sequential designs (GSD) rely on "information fraction" arguments to define the interim sample sizes. Then, interim maximum likelihood estimators (MLEs) are used to decide whether to stop early or continue the data collection until the next interim analysis. The possibility of early stopping changes the distribution of interim and final MLEs: possible interim decisions on trial stopping excludes some sample space elements. At each interim analysis the distribution of an interim MLE is a mixture of truncated and untruncated distributions. The distributional form of an MLE becomes more and more complicated with each additional interim analysis. Test statistics that are asymptotically normal without a possibly of early stopping, become mixtures of truncated normal distributions under local alternatives. Stage-specific information ratios are equivalent to sample size ratios for independent and identically distributed data. This equivalence is used to justify interim sample sizes in GSDs. Because stage-specific information ratios derived from normally distributed data differ from those derived from non-normally distributed data, the former equivalence is invalid when there is a possibility of early stopping. Tarima and Flournoy [3] have proposed a new GSD where interim sample sizes are determined by a pre-defined sequence of ordered alternative hypotheses, and the calculation of information fractions is not needed. This innovation allows researchers to prescribe interim analyses based on desired power properties. This work compares interim power properties of a classical one-sided three stage Pocock design with a one-sided three stage design driven by three ordered alternatives.

Predictive Accuracy of a Polygenic Risk Score for Postoperative Atrial Fibrillation After Cardiac Surgery

BACKGROUND

Postoperative atrial fibrillation (PoAF) remains a significant risk factor for increased morbidity and mortality after cardiac surgery. The ability to accurately identify patients at risk through clinical risk factors is limited. There is growing evidence that polygenic risk contributes significantly to PoAF and incorporating measures of genetic risk could enhance prediction.

METHODS

A retrospective cohort study of 1047 patients of White European ancestry who underwent either coronary artery bypass grafting or valve surgery at a tertiary academic center and were free from a history or persistent preoperative atrial fibrillation. The primary outcome was defined as PoAF based on postoperative ECG reports, medical record documentation, and changes in medication. The exposure was a polygenic risk score (PRS) comprising 2746 single-nucleotide polymorphisms previously associated with atrial fibrillation risk. The prediction of PoAF risk was assessed using measures of model discrimination, calibration, and net reclassification improvement.

RESULTS

A total of 259 patients (24.7%) developed PoAF. The PRS was significantly associated with a higher risk for PoAF (odds ratio, 1.63 per SD increase in PRS [95% CI, 1.41-1.90]). Addition of PRS to patient- and procedure-related predictors of PoAF significantly increased the C statistic from 0.742 to 0.782 (change in C statistic, 0.040 [95% CI, 0.021-0.060]) while maintaining good calibration. The addition of the PRS to patient- and procedure-related predictors of PoAF improved model fit (likelihood ratio test, P=2.8×10^-15) and significantly improved measures of reclassification (net reclassification improvement, 0.158 [95% CI, 0.066-0.274]).

CONCLUSIONS

The PRS for PoAF was associated with improved discrimination, calibration, and risk reclassification compared with conventional clinical predictors suggesting that a PoAF PRS may enhance risk prediction of PoAF in patients undergoing coronary artery bypass grafting or valve surgery.

CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths

Evolutionary hypotheses provide important underpinnings of biological and medical sciences, and comprehensive, genome-wide understanding of evolutionary relationships among organisms are needed to test and refine such hypotheses. Theory and empirical evidence clearly indicate that phylogenies (trees) of different genes (loci) should not display precisely matching topologies. The main reason for such phylogenetic incongruence is reticulated evolutionary history of most species due to meiotic sexual recombination in eukaryotes, or horizontal transfers of genetic material in prokaryotes. Nevertheless, many genes should display topologically related phylogenies, and should group into one or more (for genetic hybrids) clusters in poly-dimensional "tree space". Unusual evolutionary histories or effects of selection may result in "outlier" genes with phylogenies that fall outside the main distribution(s) of trees in tree space. We present a new phylogenomic method, CURatio, which uses ratios of total branch lengths in gene trees to help identify phylogenetic outliers in a given set of ortholog groups from multiple genomes. An advantage of CURatio over other methods is that genes absent from and/or duplicated in some genomes can be included in the analysis. We conducted a simulation study under the coalescent model, and showed that, given sufficient species depth and topological difference, these ratios are significantly higher for the "outlier" gene phylogenies. Also, we applied CURatio to a set of annotated genomes of the fungal family, Clavicipitaceae, and identified alkaloid biosynthesis genes as outliers, probably due to a history of duplication and loss. The source code is available at https://github.com/QiwenKang/CURatio, and the empirical data set on Clavicipitaceae and simulated data set are available at Mendeley https://data.mendeley.com/datasets/mrxts7wjrr/1.

Augmenting beta regression for periodontal proportion data via the SAS NLMIXED procedure

Often in clinical dental research, clinical attachment level (CAL) is recorded at several sites throughout the mouth to assess the extent of periodontal disease (PD). One might be interested to quantify PD at the tooth-level via the proportion of diseased sites per tooth type (say, incisors, canines, pre-molars and molars) per subject. However, these studies might consist of relatively disease-free and highly diseased subjects leading to the proportion responses distributed in the interval [0, 1]. While beta regression (BR) is often the model of choice to assess covariate effects for proportion data, the presence (and/or abundance) of zeros and/or ones makes it inapplicable here because the beta support is defined in the interval (0, 1). Avoiding ad hoc data transformation, we explore the potential of the augmented BR framework which augments the beta density with non-zero masses at zero and one while accounting for the clustering induced. Our classical estimation framework using maximum likelihood utilizes the potential of the SAS® Proc NLMIXED procedure. We explore our methodology via simulation studies and application to a real cross-sectional dataset on PD, and we assess the gain in model fit and parameter estimation over other ad hoc alternatives. This reveals newer insights into risk quantification on clustered proportion responses. Our methods can be implemented using standard SAS software routines. The augmented BR model results in a better fit to clustered periodontal proportion data over the standard beta model. We recommend using it as a parametric alternative for fitting proportion data, and avoid ad hoc data transformation.

Preclinical molecular imaging: development of instrumentation for translational research with small laboratory animals

OBJECTIVE:

To present the result of upgrading a clinical gamma-camera to be used to obtain in vivo tomographic images of small animal organs, and its application to register cardiac, renal and neurological images.

METHODS:

An updated version of the miniSPECT upgrading device was built, which is composed of mechanical, electronic and software subsystems. The device was attached to a Discovery VH (General Electric Healthcare) gamma-camera, which was retired from the clinical service and installed at the Centro de Imagem Pré-Clínica of the Hospital Israelita Albert Einstein. The combined system was characterized, determining operational parameters, such as spatial resolution, magnification, maximum acceptable target size, number of projections, and acquisition and reconstruction times.

RESULTS:

Images were obtained with 0.5mm spatial resolution, with acquisition and reconstruction times between 30 and 45 minutes, using iterative reconstruction with 10 to 20 iterations and 4 projection subsets. The system was validated acquiring in vivo tomographic images of the heart, kidneys and brain of normal animals (mice and adult rats), using the radiopharmaceuticals technetium-labeled hexakis-2-methoxy-isobutyl isonitrile (99mTc-Sestamibi), technetium-labeled dimercaptosuccinic acid (99mTc-DMSA) and technetium-labeled hexamethyl propyleneamine oxime (99mTc-HMPAO).

CONCLUSION:

This kind of application, which consists in the adaptation for an alternative objective of already existing instrumentation, resulted in a low-cost infrastructure option, allowing to carry out large scale in vivo studies with enhanced quality in several areas, such as neurology, nephrology, cardiology, among others.

OBJETIVO:

Apresentar o resultado da adaptação de uma gama câmara clínica para uso dedicado na obtenção de imagens tomográficas in vivo de órgãos de pequenos animais de experimentação, e de sua aplicação na obtenção de imagens cardíacas, renais e neurológicas.

MÉTODOS:

Foi construída uma versão atualizada do dispositivo de adaptação miniSPECT, composto por três subsistemas: mecânico, eletrônico e de software. O dispositivo foi montado em uma câmara Discovery VH da General Electric Healthcare, retirada do serviço clínico e instalada no Centro de Imagem Pré-Clínica do Hospital Israelita Albert Einstein. O sistema combinado foi caracterizado, determinando parâmetros de funcionamento como resolução espacial, magnificação, limites de tamanho dos alvos de estudo, número de projeções, tempo de registro e tempo de reconstrução das imagens tomográficas.

RESULTADOS:

Foram obtidas imagens com resolução espacial de até 0,5mm, com tempos de registro e reconstrução de 30 a 45 minutos, utilizando reconstrução iterativa com 10 a 20 iterações e 4 subconjuntos de projeções. O sistema foi validado obtendo imagens tomográficas in vivo do coração, dos rins e do cérebro de animais normais (camundongos e ratos adultos), utilizando os radiofármacos hexaquis-2-metoxi-isobutil-isonitrila marcado com 99mTc (Sestamibi-99mTc), ácido dimercaptosuccínico marcado com 99mTc (DMSA-99mTc) e hexametil-propileno-amina-oxima marcada com 99mTc (HMPAO-99mTc).

CONCLUSÃO:

Este tipo de aplicação, que consiste na adaptação para um objetivo alternativo de instrumentação já existente, constituiu-se em uma opção de infraestrutura de baixo custo, que permite realizar estudos in vivo em larga escala, com qualidade aprimorada, em áreas diversas, como neurologia, nefrologia, cardiologia, entre outras.

Incorporation of detailed family history from the Swedish Family Cancer Database into the PCPT risk calculator

PURPOSE

A detailed family history provides an inexpensive alternative to genetic profiling for individual risk assessment. We updated the PCPT Risk Calculator to include detailed family histories.

MATERIALS AND METHODS

The study included 55,168 prostate cancer cases and 638,218 controls from the Swedish Family Cancer Database who were 55 years old or older in 1999 and had at least 1 male first-degree relative 40 years old or older and 1 female first-degree relative 30 years old or older. Likelihood ratios, calculated as the ratio of risk of observing a specific family history pattern in a prostate cancer case compared to a control, were used to update the PCPT Risk Calculator.

RESULTS

Having at least 1 relative with prostate cancer increased the risk of prostate cancer. The likelihood ratio was 1.63 for 1 first-degree relative 60 years old or older at diagnosis (10.1% of cancer cases vs 6.2% of controls), 2.47 if the relative was younger than 60 years (1.5% vs 0.6%), 3.46 for 2 or more relatives 60 years old or older (1.2% vs 0.3%) and 5.68 for 2 or more relatives younger than 60 years (0.05% vs 0.009%). Among men with no diagnosed first-degree relatives the likelihood ratio was 1.09 for 1 or more second-degree relatives diagnosed with prostate cancer (12.7% vs 11.7%). Additional first-degree relatives with breast cancer, or first-degree or second-degree relatives with prostate cancer compounded these risks.

CONCLUSIONS

A detailed family history is an independent predictor of prostate cancer compared to commonly used risk factors. It should be incorporated into decision making for biopsy. Compared with other costly biomarkers it is inexpensive and universally available.

Transmission potential of Rift Valley fever virus over the course of the 2010 epidemic in South Africa

A Rift Valley fever (RVF) epidemic affecting animals on domestic livestock farms was reported in South Africa during January-August 2010. The first cases occurred after heavy rainfall, and the virus subsequently spread countrywide. To determine the possible effect of environmental conditions and vaccination on RVF virus transmissibility, we estimated the effective reproduction number (Re) for the virus over the course of the epidemic by extending the Wallinga and Teunis algorithm with spatial information. Re reached its highest value in mid-February and fell below unity around mid-March, when vaccination coverage was 7.5%-45.7% and vector-suitable environmental conditions were maintained. The epidemic fade-out likely resulted first from the immunization of animals following natural infection or vaccination. The decline in vector-suitable environmental conditions from April onwards and further vaccination helped maintain Re below unity. Increased availability of vaccine use data would enable evaluation of the effect of RVF vaccination campaigns.

Maximum penalized likelihood estimation in a gamma-frailty model

The shared frailty models allow for unobserved heterogeneity or for statistical dependence between observed survival data. The most commonly used estimation procedure in frailty models is the EM algorithm, but this approach yields a discrete estimator of the distribution and consequently does not allow direct estimation of the hazard function. We show how maximum penalized likelihood estimation can be applied to nonparametric estimation of a continuous hazard function in a shared gamma-frailty model withright-censored and left-truncated data. We examine the problem of obtaining variance estimators for regression coefficients, the frailty parameter and baseline hazard functions. Some simulations for the proposed estimation procedure are presented. A prospective cohort (Paquid) with grouped survival data serves to illustrate the method which was used to analyze the relationship between environmental factors and the risk of dementia.

Prostate-specific antigen testing accuracy in community practice

BACKGROUND

Most data on prostate-specific antigen (PSA) testing come from urologic cohorts comprised of volunteers for screening programs. We evaluated the diagnostic accuracy of PSA testing for detecting prostate cancer in community practice.

METHODS

PSA testing results were compared with a reference standard of prostate biopsy. Subjects were 2,620 men 40 years and older undergoing (PSA) testing and biopsy from 1/1/95 through 12/31/98 in the Albuquerque, New Mexico metropolitan area. Diagnostic measures included the area under the receiver-operating characteristic curve, sensitivity, specificity, and likelihood ratios.

RESULTS

Cancer was detected in 930 subjects (35%). The area under the ROC curve was 0.67 and the PSA cutpoint of 4 ng/ml had a sensitivity of 86% and a specificity of 33%. The likelihood ratio for a positive test (LR+) was 1.28 and 0.42 for a negative test (LR-). PSA testing was most sensitive (90%) but least specific (27%) in older men. Age-specific reference ranges improved specificity in older men (49%) but decreased sensitivity (70%), with an LR+ of 1.38. Lowering the PSA cutpoint to 2 ng/ml resulted in a sensitivity of 95%, a specificity of 20%, and an LR+ of 1.19.

CONCLUSIONS

PSA testing had fair discriminating power for detecting prostate cancer in community practice. The PSA cutpoint of 4 ng/ml was sensitive but relatively non-specific and associated likelihood ratios only moderately revised probabilities for cancer. Using age-specific reference ranges and a PSA cutpoint below 4 ng/ml improved test specificity and sensitivity, respectively, but did not improve the overall accuracy of PSA testing.

Maximum-likelihood density modification

A likelihood-based approach to density modification is developed that can be applied to a wide variety of cases where some information about the electron density at various points in the unit cell is available. The key to the approach consists of developing likelihood functions that represent the probability that a particular value of electron density is consistent with prior expectations for the electron density at that point in the unit cell. These likelihood functions are then combined with likelihood functions based on experimental observations and with others containing any prior knowledge about structure factors to form a combined likelihood function for each structure factor. A simple and general approach to maximizing the combined likelihood function is developed. It is found that this likelihood-based approach yields greater phase improvement in model and real test cases than either conventional solvent flattening and histogram matching or a recent reciprocal-space solvent-flattening procedure [Terwilliger (1999), Acta Cryst. D55, 1863-1871].