Daniel Rabinowitz

A Unified Approach to Adjusting Association Tests for Population Admixture with Arbitrary Pedigree Structure and Arbitrary Missing Marker Information

A general approach to family-based examinations of association between marker alleles and traits is proposed. The approach is based on computing p values by comparing test statistics for association to their conditional distributions given the minimal sufficient statistic under the null hypothesis for the genetic model, sampling plan and population admixture. The approach can be applied with any test statistic, so any kind of phenotype and multi-allelic markers may be examined, and covariates may be included in analyses. By virtue of the conditioning, the approach results in correct type I error probabilities regardless of population admixture, the true genetic model and the sampling strategy. An algorithm for computing the conditional distributions is described, and the results of the algorithm for configurations of nuclear families are presented. The algorithm is applicable with all pedigree structures and all patterns of missing marker allele information.

A Transmission Disequilibrium Test for Quantitative Trait Loci

The transmission disequilibrium test uses association between marker alleles and dichotomous traits for precise genetic mapping while avoiding confounding due to population admixture. Here, the methodology is generalized from dichotomous traits to quantitative traits. The generalization is computationally straightforward and may be used with multiple alleles and with siblings. Parametric assumptions on the distribution of the quantitative traits are not needed. Environmental and demographic covariates may be incorporated into the analysis. The results of simulation studies that provide information about the power of the approach are reported.

NETWORKS OF COACTIVE NEURONS IN DEVELOPING LAYER 1

Spontaneous neuronal activity plays an important role in the development of cortical circuitry, yet its spatio-temporal dynamics are poorly understood. Cajal-Retzius (CR) neurons in developing layer 1 are necessary for correct cortical lamination and are strategically located to coordinate early circuit activity. To characterize the spontaneous activity of CR and other layer 1 neurons during cortical development, we imaged calcium transients in populations of layer 1 neurons in hemispheres and slices from postnatal rat somato-sensory neocortex. The spontaneous activity in layer 1 had complex spatio-temporal patterns. Groups of non-CR cells showed synchronous activations and formed networks of correlated neurons superimposed in the same territory. Correlated activity among non-CR cells was mediated by a depolarizing effect of GABA and was modulated by glutamate, probably released by CR cells. Our findings demonstrate that developing layer 1 can sustain complex patterns of correlated activity and reveal a circuit mechanism that can mediate this patterned activity.

Genetic Risk Factors for Portopulmonary Hypertension in Patients with Advanced Liver Disease

RATIONALE Portopulmonary hypertension (PPHTN) occurs in 6% of liver transplant candidates. The pathogenesis of this complication of portal hypertension is poorly understood. OBJECTIVES To identify genetic risk factors for PPHTN in patients with advanced liver disease. METHODS We performed a multicenter case-control study of patients with portal hypertension. Cases had a mean pulmonary artery pressure >25 mm Hg, pulmonary vascular resistance >240 dynes.s(-1).cm(-5), and pulmonary capillary wedge pressure < or =15 mm Hg. Controls had a right ventricular systolic pressure < 40 mm Hg (if estimated) and normal right-sided cardiac morphology by transthoracic echocardiography. We genotyped 1,079 common single nucleotide polymorphisms (SNPs) in 93 candidate genes in each patient. MEASUREMENTS AND MAIN RESULTS The study sample included 31 cases and 104 controls. Twenty-nine SNPs in 15 candidate genes were associated with the risk of PPHTN (P < 0.05). Multiple SNPs in the genes coding for estrogen receptor 1, aromatase, phosphodiesterase 5, angiopoietin 1, and calcium binding protein A4 were associated with the risk of PPHTN. The biological relevance of one of the aromatase SNPs was supported by an association with plasma estradiol levels. CONCLUSIONS Genetic variation in estrogen signaling and cell growth regulators is associated with the risk of PPHTN. These biologic pathways may elucidate the mechanism for the development of PPHTN in certain patients with severe liver disease.

Association between the HOXA1 A218G polymorphism and increased head circumference in patients with autism

BACKGROUND The HOXA1 gene plays a major role in brainstem and cranial morphogenesis. The G allele of the HOXA1 A218G polymorphism has been previously found associated with autism. METHODS We performed case-control and family-based association analyses, contrasting 127 autistic patients with 174 ethnically matched controls, and assessing for allelic transmission disequilibrium in 189 complete trios. RESULTS A, and not G, alleles were associated with autism using both case-control (chi(2) = 8.96 and 5.71, 1 df, p <.005 and <.025 for genotypes and alleles, respectively), and family-based (transmission/disequilibrium test chi(2) = 8.80, 1 df, p <.005) association analyses. The head circumference of 31 patients carrying one or two copies of the G allele displayed significantly larger median values (95.0th vs. 82.5th percentile, p <.05) and dramatically reduced interindividual variability (p <.0001), compared with 166 patients carrying the A/A genotype. CONCLUSIONS The HOXA1 A218G polymorphism explains approximately 5% of the variance in the head circumference of autistic patients and represents to our knowledge the first known gene variant providing sizable contributions to cranial morphology. The disease specificity of this finding is currently being investigated. Nonreplications in genetic linkage/association studies could partly stem from the dyshomogeneous distribution of an endophenotype morphologically defined by cranial circumference.

A Principal-Components Approach Based on Heritability for Combining Phenotype Information

For many traits, genetically relevant disease definition is unclear. For this reason, researchers applying linkage analysis often obtain information on a variety of items. With a large number of items, however, the test statistic from a multivariate analysis may require a prohibitively expensive correction for the multiple comparisons. The researcher is faced, therefore, with the issue of choosing which variables or combinations of variables to use in the linkage analysis. One approach to combining items is to first subject the data to a principal components analysis, and then perform the linkage analysis of the first few principal components. However, principal-components analyses do not take family structure into account. Here, an approach is developed in which family structure is taken into account when combining the data. The essence of the approach is to define principal components of heritability as the scores with maximum heritability in the data set, subject to being uncorrelated with each other. The principal components of heritability may be calculated as the solutions to a generalized eigensystem problem. Four simulation experiments are used to compare the power of linkage analyses based on the principal components of heritability and the usual principal components. The first of the experiments corresponds to the null hypothesis of no linkage. The second corresponds to a setting where the two kinds of principal components coincide. The third corresponds to a setting in which they are quite different and where the first of the usual principal components is not expected to have any power beyond the type I error rate. The fourth set of experiments corresponds to a setting where the usual principal components and the principal components of heritability differ, but where the first of the usual principal components is not without power. The results of the simulation experiments indicate that the principal components of heritability can be substantially different from the standard principal components and that when they are different, substantial gains in power can result by using the principal components of heritability in place of the standard principal components in linkage analyses.

Familial clustering of seizure types within the idiopathic generalized epilepsies

Objective: To examine the genetic relationships among epilepsies with different seizure types—myoclonic, absence, and generalized tonic-clonic—within the idiopathic generalized epilepsies (IGEs). Background: Careful phenotype definition in the epilepsies may allow division into groups that share susceptibility genes. Examination of seizure type, a phenotypic characteristic less complex than IGE syndrome, may help to define more homogeneous subgroups. Methods: Using the approach that found evidence of distinct genetic effects on myoclonic vs absence seizures in families from the Epilepsy Family Study of Columbia University, the authors examined an independent sample of families from Australia and Israel. They also examined the familial clustering of generalized tonic-clonic seizures (GTCs) within the IGEs in two combined data sets. Families were defined as concordant if all affected members had the same type of seizure or IGE syndrome, as appropriate for the analysis performed. Results: The proportion of families concordant for myoclonic vs absence seizures was greater than expected by chance in the Australian families. In addition, GTCs clustered in families with IGEs to a degree greater than expected by chance. Conclusions: These results provide additional evidence for distinct genetic effects on myoclonic vs absence seizures in an independent set of families and suggest that there is a genetic influence on the occurrence of generalized tonic-clonic seizures within the idiopathic generalized epilepsies.

Body Mass Index and Hospitalization in the Elderly

Objectives: To explore the association between body mass index (BMI) and hospital usage in the elderly.

Genetic influences on myoclonic and absence seizures

Objective: To examine the relationship between genotype and phenotype in idiopathic generalized epilepsies (IGEs) using a novel approach that focuses on seizure type rather than syndrome. Methods: The authors evaluated whether the genetic effects on myoclonic seizures differ from the genetic effects on absence seizures. For this purpose, they studied 34 families containing 2 or more members with IGEs and assessed whether the number of families concordant for seizure type exceeded that expected by chance. The authors performed a similar analysis to examine the genetic contributions to juvenile myoclonic epilepsy (JME), juvenile absence epilepsy (JAE), and childhood absence epilepsy (CAE). Results: The observed number of families concordant for seizure type (myoclonic, absence, or both) was greater than expected (20 vs 7.51; p < 0.0001). The observed number of families concordant for syndrome was greater than expected when JME was compared with absence epilepsies (JAE+CAE) (17 vs 11.9; p < 0.012) but not when JAE was compared with CAE (8 vs 6.82; p = 0.516). Conclusions: These results provide evidence for distinct genetic effects on absence and myoclonic seizures, suggesting that examining the two seizure types separately would be useful in linkage studies of idiopathic generalized epilepsies. The approach presented here can also be used to discover other clinical features that could direct division of epilepsies into groups likely to share susceptibility genes.

Pulmonary Hyperinflation and Left Ventricular Mass The Multi-Ethnic Study of Atherosclerosis COPD Study

Background— Left ventricular (LV) mass is an important predictor of heart failure and cardiovascular mortality, yet determinants of LV mass are incompletely understood. Pulmonary hyperinflation in chronic obstructive pulmonary disease (COPD) may contribute to changes in intrathoracic pressure that increase LV wall stress. We therefore hypothesized that residual lung volume in COPD would be associated with greater LV mass. Methods and Results— The Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited smokers 50 to 79 years of age who were free of clinical cardiovascular disease. LV mass was measured by cardiac magnetic resonance. Pulmonary function testing was performed according to guidelines. Regression models were used to adjust for age, sex, body size, blood pressure, and other cardiac risk factors. Among 119 MESA COPD Study participants, the mean age was 69±6 years, 55% were male, and 65% had COPD, mostly of mild or moderate severity. Mean LV mass was 128±34 g. Residual lung volume was independently associated with greater LV mass (7.2 g per 1-SD increase in residual volume; 95% confidence interval, 2.2–12; P =0.004) and was similar in magnitude to that of systolic blood pressure (7.6 g per 1-SD increase in systolic blood pressure; 95% confidence interval, 4.3–11; P <0.001). Similar results were observed for the ratio of LV mass to end-diastolic volume ( P =0.02) and with hyperinflation measured as residual volume to total lung capacity ratio ( P =0.009). Conclusions— Pulmonary hyperinflation, as measured by residual lung volume or residual lung volume to total lung capacity ratio, is associated with greater LV mass. # Clinical Perspective {#article-title-62}Background— Left ventricular (LV) mass is an important predictor of heart failure and cardiovascular mortality, yet determinants of LV mass are incompletely understood. Pulmonary hyperinflation in chronic obstructive pulmonary disease (COPD) may contribute to changes in intrathoracic pressure that increase LV wall stress. We therefore hypothesized that residual lung volume in COPD would be associated with greater LV mass. Methods and Results— The Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited smokers 50 to 79 years of age who were free of clinical cardiovascular disease. LV mass was measured by cardiac magnetic resonance. Pulmonary function testing was performed according to guidelines. Regression models were used to adjust for age, sex, body size, blood pressure, and other cardiac risk factors. Among 119 MESA COPD Study participants, the mean age was 69±6 years, 55% were male, and 65% had COPD, mostly of mild or moderate severity. Mean LV mass was 128±34 g. Residual lung volume was independently associated with greater LV mass (7.2 g per 1-SD increase in residual volume; 95% confidence interval, 2.2–12; P=0.004) and was similar in magnitude to that of systolic blood pressure (7.6 g per 1-SD increase in systolic blood pressure; 95% confidence interval, 4.3–11; P<0.001). Similar results were observed for the ratio of LV mass to end-diastolic volume (P=0.02) and with hyperinflation measured as residual volume to total lung capacity ratio (P=0.009). Conclusions— Pulmonary hyperinflation, as measured by residual lung volume or residual lung volume to total lung capacity ratio, is associated with greater LV mass.