Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test

In recent years, genome-wide association studies (GWAS) and gene-expression profiling have generated a large number of valuable datasets for assessing how genetic variations are related to disease outcomes. With such datasets, it is often of interest to assess the overall effect of a set of genetic markers, assembled based on biological knowledge. Genetic marker-set analyses have been advocated as more reliable and powerful approaches compared with the traditional marginal approaches (Curtis and others, 2005. Pathways to the analysis of microarray data. TRENDS in Biotechnology 23, 429-435; Efroni and others, 2007. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2, 425). Procedures for testing the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63, 1079-1088; Liu and others, 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC bioinformatics 9, 292-2; Wu and others, 2010. Powerful SNP-set analysis for case-control genome-wide association studies. American Journal of Human Genetics 86, 929) have been proposed as powerful alternatives to the standard Rao score test (Rao, 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Mathematical Proceedings of the Cambridge Philosophical Society, 44, 50-57). The advantages of these EB-based tests are most apparent when the markers are correlated, due to the reduction in the degrees of freedom. In this paper, we propose an adaptive score test which up- or down-weights the contributions from each member of the marker-set based on the Z-scores of their effects. Such an adaptive procedure gains power over the existing procedures when the signal is sparse and the correlation among the markers is weak. By combining evidence from both the EB-based score test and the adaptive test, we further construct an omnibus test that attains good power in most settings. The null distributions of the proposed test statistics can be approximated well either via simple perturbation procedures or via distributional approximations. Through extensive simulation studies, we demonstrate that the proposed procedures perform well in finite samples. We apply the tests to a breast cancer genetic study to assess the overall effect of the FGFR2 gene on breast cancer risk.     

Dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes

Individuals with germline mutations in the tumor suppressor gene phosphatase and tensin homolog (PTEN), irrespective of clinical presentation, are diagnosed with PTEN hamartoma tumor syndrome (PHTS). PHTS confers a high risk of breast, thyroid, and other cancers or autism spectrum disorder (ASD) with macrocephaly. It remains unclear why mutations in one gene can lead to seemingly disparate phenotypes. Thus, we sought to identify differences in ASD vs. cancer-associated germline PTEN missense mutations by investigating putative structural effects induced by each mutation. We utilized a theoretical computational approach combining in silico structural analysis and molecular dynamics (MD) to interrogate 17 selected mutations from our patient population: six mutations were observed in patients with ASD (only), six mutations in patients with PHTS-associated cancer (only), four mutations shared across both phenotypes, and one mutation with both ASD and cancer. We demonstrate structural stability changes where all six cancer-associated mutations showed a global decrease in structural stability and increased dynamics across the domain interface with a proclivity to unfold, mediating a closed (inactive) active site. In contrast, five of the six ASD-associated mutations showed localized destabilization that contribute to the partial opening of the active site. Our results lend insight into distinctive structural effects of germline PTEN mutations associated with PTEN-ASD vs. those associated with PTEN-cancer, potentially aiding in identification of the shared and separate molecular features that contribute to autism or cancer, thus, providing a deeper understanding of genotype–phenotype relationships for germline PTEN mutations.     

Disruption of neurocognitive decision-making mechanisms in depression

To analyze the relationship of disruptions in neurocognitive decision-making mechanisms based on logic and reasoning, or in a situation of uncertainty based on emotional experience (emotional learning) with clinical indices of depression, a multidisciplinary clinical, psychological, and neurophysiological study was conducted in 28 patients suffering from depression (women aged 18–56) and 50 healthy volunteers (women aged 18–55). The intensity of depression was estimated quantitatively by the Hamilton’s Depression Rating Scale (HDRS-17) to qualitatively estimate cognitive functions, the “Ten Words” technique, the Wisconsin Card-Sorting Test (WCST), and the Iowa Gambling Task (IGT) were used; and to assess the functional brain state of all patients suffering from depression, a multichannel recording of the background electroencephalogram (EEG) was made. It was demonstrated that in depression, a neurocognitive deficiency was observed that correlates positively with the intensity of the depressive symptomatology. As well, a reduction occurs in the ability to make decisions based both on logic and reasoning (in the WCST), which is associated with EEG features of hypofrontality, and based on emotional learning (in the IGT test). Only in patients suffering from depression with a reduced ability to make rational decisions based on logic and reasoning was a “compensatory shift” observed toward decision making based on emotions, which leads to relatively higher indices of emotional learning. It is assumed that hypofrontality, which results in difficulties in making decisions requiring logical thought, leads to interruption of subcortical, including hippocampal, structures, an increase in the activation of which is related to better indices of emotional learning.     

Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

Magnesium profile in autism

The aim of the present study was to determine and compare plasma and erythrocyte concentrations of magnesium in 12 autistic children (10 boys, 2 girls), 17 children with other autistic spectrum disorders (14 boys, 3 girls), 5 girls with classic Rett syndrome, and 14 normal children (7 boys, 7 girls) of the same age. No differences in intracellular Mg were found between controls and pathological subjects; however, autistic children and children with other autistic spectrum disorders had significantly lower plasma concentrations of Mg than normal subjects (p=0.013 and p=0.02, respectively). Although our study population was small, we conclude that children with autistic spectrum disorders require special dietary management. If these cases are diagnosed at an early stage, they can be helped through diet.     

Identifying static and kinetic lipid phenotypes by high resolution UPLC-MS: unraveling diet-induced changes in lipid homeostasis by coupling metabolomics and fluxomics

A novel method to differentiate diet-induced alterations in plasma lipid phenotypes "static (concentration of lipids) and kinetic (endogenous production, e.g., denovo lipogenesis)" was employed. C57Bl6 mice were randomized into 2 groups and fed either a high-carbohydrate, low-fat (HC) or a carbohydrate-free, high-fat diet (HF) diet for 13 days; D(2)O was administered via intraperitoneal injection and then adding D(2)O to the drinking water for 96 h. Principal component analysis (PCA) revealed differences in the plasma lipid content, for example, triglycerides (TG) 50:2, 50:3, and 52:2 were up-regulated in mice fed the HC diet, whereas TG 52:4, 52:1, 54:5, 54:3, 54:4, and 54:2 were higher in animals fed the HF diet. However, although the fractional contribution of synthesis was ~10-fold lower in HF vs HC fed mice, changes in TG concentration were not entirely mediated by altered de novo lipogenesis. In addition, the ability to couple isotope labeling measurements with PCA analyses revealed cases where there were no differences in the concentration of a compound but its source was substantially altered. In summary, this strategy determined (i) the presence/absence of differences in concentration and (ii) the contribution of different pathways and synthesis that could affect lipid biology in a mouse model respectively.     

Clinical and neurocognitive outcome in symptomatic isovaleric acidemia

Background

Approximately 20% of adrenoleukodystrophy (X-ALD) female carriers may develop clinical manifestations, typically consisting of progressive spastic gait, sensory deficits and bladder dysfunctions. A skewing in X Chromosome Inactivation (XCI), leading to the preferential expression of the X chromosome carrying the mutant ABCD1 allele, has been proposed as a mechanism influencing X-linked adrenoleukodystrophy (X-ALD) carrier phenotype, but reported data so far are conflicting.

Methods

To shed light into this topic we assessed the XCI pattern in peripheral blood mononuclear cells (PBMCs) of 30 X-ALD carriers. Since a frequent problem with XCI studies is the underestimation of skewing due to an incomplete sample digestion by restriction enzymes, leading to variable results, we developed a pyrosequencing assay to identify samples completely digested, on which to perform the XCI assay. Pyrosequencing was also used to quantify ABCD1 allele-specific expression. Moreover, very long-chain fatty acid (VLCFA) levels were determined in the same patients.

Results

We found severely (??90:10) or moderately (??75:25) skewed XCI in 23 out of 30 (77%) X-ALD carriers and proved that preferential XCI is mainly associated with the preferential expression of the mutant ABCD1 allele, irrespective of the manifestation of symptoms. The expression of mutant ABCD1 allele also correlates with plasma VLCFA concentrations.

Conclusions

Our results indicate that preferential XCI leads to the favored expression of the mutant ABCD1 allele. This emerges as a general phenomenon in X-ALD carriers not related to the presence of symptoms. Our data support the postulated growth advantage of cells with the preferential expression of the mutant ABCD1 allele, but argue against the use of XCI pattern, ABCD1 allele-specific expression pattern and VLCFA plasma concentration as biomarkers to predict the development of symptoms in X-ALD carriers.     

Structural neuroimaging in autism

Structural neuroimaging studies done by means of magnetic resonance imaging (MRI) have provided important insights into the neurobiological basis for autism. The aim of this article is to review the current state of knowledge regarding structural brain abnormalities in autism. Results of MRI studies dealing with total brain volume, the volume of the cerebellum, caudate nucleus, thalamus, amygdala, hippocampus and the area of the corpus callosum are summarized. Existing research suggests that autistic individuals have larger total brain, cerebellar and caudate nucleus volumes; however, the area of the corpus callosum is reduced. Results of studies involving the amygdala and hippocampus volume in autistic subjects remain inconsistent and no changes have been detected in thalamic volume.     

Intestinal pathophysiology in autism

Autism is a life-long developmental disorder affecting as many as 1 in 500 children. The causes for this profound disorder are largely unknown. Recent research has uncovered pathology in the gastrointestinal tract of autistic children. The pathology, reported to extend from the esophagus to the colon, is described here along with other studies pointing to a connection between diet and the severity of symptoms expressed in autism. The evidence that there is impaired intestinal permeability in autism is reviewed, and various theories are discussed by which a leaky gut could develop. Lastly, some possible ways in which impaired gastrointestinal function might influence brain function are discussed.     

Unraveling autism

In this issue of AJHG, Alarcón et al.,(1) Arking et al.,(2) and Bakkaloglu et al.(3) identify a series of functional variants in the CNTNAP2 gene that unequivocally implicate this gene as causing Type 1 autism in the general population.     

Cardiopulmonary bypass and long-term neurocognitive dysfunction in the rat

Neurologic and neurocognitive complications after cardiac surgery with cardiopulmonary bypass (CPB) have been reported repeatedly. To better understand its etiology and design protective strategies, an appropriate animal model may prove useful. Although impaired short-term neurocognitive function has been recently demonstrated after CPB in rats, the demonstration of persistent long-term neurocognitive changes would be more relevant from a clinical perspective. We hypothesized that CPB results in long-term impairment of neurocognitive performance in rats. Male rats were exposed to either 60 min of normothermic non-pulsatile CPB, using a roller-pump and a neonatal membrane oxygenator, or to cannulation only (sham animals). Long-term neurocognitive function was assessed at 4 to 7 weeks after CPB (Can test), and again after 12 weeks (Morris water maze) in both operated groups and in a non-operated control group, followed by histologic evaluation of the hippocampus. In separate groups of CPB and sham animals, we also measured TNF-alpha and IL-6 in plasma. There were no significant differences in long-term neurocognitive performance or histological outcome between the three groups. Cytokine patterns were also similar in both operated groups. We conclude that CPB did not appear to cause long-term neurocognitive dysfunction in this model of CPB in young healthy rats. The lack of long-term deficits may be due to the absence of clinically important etiologic factors such as atheromatous and gaseous embolization in this model. Similar cytokine patterns in both operated groups suggest that surgical trauma rather than exposure of blood to extra-corporeal circuit was probably responsible for the inflammatory response.     

A neurocognitive model for understanding treatment action in depression

The way in which emotion is represented and processed in the human brain is an expanding area of research and has key implications for how we understand and potentially treat affective disorders such as depression. Characterizing the effects of pharmacological manipulations of key neurotransmitter systems can also help reveal the neurochemical underpinnings of emotional processing and how common antidepressant drugs may work in the treatment of depression and anxiety. This approach has revealed that depression is associated with both neural and behavioural biases towards negative over positive stimuli. Evidence from pharmacological challenge studies suggests that antidepressant treatment acts to normalize these biases early on in treatment, resulting in patients experiencing the world in a more positive way, improving their mood over time. This model is supported by evidence from both pharmacological and non-pharmacological interventions. The unique perspective on antidepressant treatment offered by this approach provides some insights into individual response to treatment, as well as novel approaches to drug development.     

Androgynic phenotypes in obese women

A sample of 521 Caucasian women from an outpatient obesity clinic were classified by androgynic design. Photographs and outline sketches were obtained and eventually characteristic body outline patterns were developed. The distinct patterns of androgynic phenotypes were useful in recording the amount, distribution and texture of fat tissue. The phenotypic patterns remained relatively constant despite weight fluctuations. In the group studied the magnitude of obesity and the age at which it first occurred were related to androgynic patterns. Early menarche and early onset of obesity were associated. Constitutional differences, as shown by the body outline drawings, are clinically useful in evaluating the kind and degree of obesity.     

Iodine in autism spectrum disorders

ObjectiveThe aim of our study was to assess the iodine status of Polish boys with severe autism compared to their healthy peers and evaluate the relationship between urinary iodine, thyroid hormones, body mass index and Autism Spectrum Disorder (ASD) symptomatology.Subjects and methodsTests were performed in 40 boys with ASD and 40 healthy boys, aged 2–17 from the same geographic region in Poland. Urinary iodine (UI), free triiodothyronine (fT3), free thyroxine (fT4), thyroid stimulating hormone (TSH), BMI, and individual symptoms measured by the Childhood Autism Rating Scale (CARS) were correlated.Validated ion chromatography method with pulsed amperometric detection was applied for the determination of urinary iodine after optimized alkaline digestion in a closed system assisted with microwaves.Results19 out of 40 children with ASD had mild to moderate iodine deficiency. Statistically significant lower levels of UI, fT3 and fT4 and higher levels of TSH were found in the autistic group when compared with the control group. Concentration of iodine in urine was negatively associated with clinician’s general impression for children between 11 and 17 years. Emotional response, adaptation to environmental change, near receptor responsiveness, verbal communication, activity level, and intellectual functioning are more associated with UI than other symptoms listed in CARS.ConclusionThe severity of certain symptoms in autism is associated with iodine status in maturing boys. Thyroid hormones were within normal reference ranges in both groups while urinary iodine was significantly lower in autistic boys suggesting that further studies into the nonhormonal role of iodine in autism are required.