Novel common copy number variation for early onset extreme obesity on chromosome 11q11 identified by a genome-wide analysis

Heritability of obesity is substantial and recent meta-analyses of genome-wide association studies (GWASs) have been successful in detecting several robustly associated genomic regions for obesity using single-nucleotide polymorphisms (SNPs). However, taken together, the SNPs explain only a small proportion of the overall heritability. Copy number variations (CNVs) might contribute to the 'missing heritability'. We searched genome-wide for association between common CNVs and early-onset extreme obesity. Four hundred and twenty-four case-parents obesity trios and an independent sample of 453 extremely obese children and adolescents and 435 normal-weight and lean adult controls were genotyped by the Affymetrix Genome-Wide Human SNP Array 6.0. We detected 20 common copy number variable regions (CNVRs) which were associated with obesity. The most promising CNVRs were followed-up in an independent sample of 365 obesity trios, confirming the association for two candidate CNVRs. We identified a common CNVR exclusively covering the three olfactory receptor genes OR4P4, OR4S2 and OR4C6 to be associated with obesity (combined P-value = 0.015 in a total of 789 families; odds ratio for the obesity effect allele = 1.19; 95% confidence interval = 1.016-1.394). We also replicated two common deletions (near NEGR1 and at chromosome 10q11.22) that have previously been reported to be associated with body weight. Additionally, we support a rare CNV on chromosome 16 that has recently been reported by two independent groups. However, rare CNVs had not been the focus of our study. We conclude that common CNVs are unlikely to contribute substantially to the genetic basis of early-onset extreme obesity.

The performance of conditional tests for family data in associated regions derived from GWAS

BACKGROUND

Genome-wide association studies (GWAS) have been used successfully to identify genetic loci associated with complex diseases and phenotypes. Often this association takes the form of several significant signals (such as small p-values) in a univariate analysis at various markers within a single genetic region. Once confirmed, these associations lead to the question if a single marker tags the association signal of another, functionally relevant variant or if the single marker tags a functionally relevant haplotype. To deal with this question, methods for family data based on logistic regression, adaptations of the transmission/disequilibrium test (TDT) or weighted haplotype likelihood (WHL) methods have been proposed in the literature.

OBJECTIVES

Objectives were to examine the effect of parameters such as sample size, inheritance model, and the effects of linkage disequilibrium (LD) in the region on the ability of a selection of methods to detect an independent effect from an additional locus.

METHODS

All methods tested were applied to simulated genetic data of trios comprising a single affected offspring and two parents.

RESULTS

While regression-based methods have advantages such as model flexibility, potentially increasing power, the WHL method was more robust against increasing LD in the scenarios analyzed.

CONCLUSIONS

Simulation results suggest that the regression and WHL methods are better able with regard to statistical power than the adaptation of the TDT analyzed here to detect genetic effects at an additional locus while controlling for confounding at another locus.

Case-control genome-wide association study of attention-deficit/hyperactivity disorder

OBJECTIVE

Although twin and family studies have shown attention-deficit/hyperactivity disorder (ADHD) to be highly heritable, genetic variants influencing the trait at a genome-wide significant level have yet to be identified. Thus additional genomewide association studies (GWAS) are needed.

METHOD

We used case-control analyses of 896 cases with DSM-IV ADHD genotyped using the Affymetrix 5.0 array and 2,455 repository controls screened for psychotic and bipolar symptoms genotyped using Affymetrix 6.0 arrays. A consensus SNP set was imputed using BEAGLE 3.0, resulting in an analysis dataset of 1,033,244 SNPs. Data were analyzed using a generalized linear model.

RESULTS

No genome-wide significant associations were found. The most significant results implicated the following genes: PRKG1, FLNC, TCERG1L, PPM1H, NXPH1, PPM1H, CDH13, HK1, and HKDC1.

CONCLUSIONS

The current analyses are a useful addition to the present literature and will make a valuable contribution to future meta-analyses. The candidate gene findings are consistent with a prior meta-analysis in suggesting that the effects of ADHD risk variants must, individually, be very small and/or include multiple rare alleles.

Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder

OBJECTIVE

Although twin and family studies have shown attention-deficit/hyperactivity disorder (ADHD) to be highly heritable, genetic variants influencing the trait at a genome-wide significant level have yet to be identified. As prior genome-wide association studies (GWAS) have not yielded significant results, we conducted a meta-analysis of existing studies to boost statistical power.

METHOD

We used data from four projects: a) the Children's Hospital of Philadelphia (CHOP); b) phase I of the International Multicenter ADHD Genetics project (IMAGE); c) phase II of IMAGE (IMAGE II); and d) the Pfizer-funded study from the University of California, Los Angeles, Washington University, and Massachusetts General Hospital (PUWMa). The final sample size consisted of 2,064 trios, 896 cases, and 2,455 controls. For each study, we imputed HapMap single nucleotide polymorphisms, computed association test statistics and transformed them to z-scores, and then combined weighted z-scores in a meta-analysis.

RESULTS

No genome-wide significant associations were found, although an analysis of candidate genes suggests that they may be involved in the disorder.

CONCLUSIONS

Given that ADHD is a highly heritable disorder, our negative results suggest that the effects of common ADHD risk variants must, individually, be very small or that other types of variants, e.g., rare ones, account for much of the disorder's heritability.

Disentanglement of the electronic and lattice parts of the order parameter in a 1D charge density wave system probed by femtosecond spectroscopy

We report on the high resolution studies of the temperature (T) dependence of the q=0 phonon spectrum in the quasi-one-dimensional charge density wave (CDW) compound K(0.3)MoO(3) utilizing time-resolved optical spectroscopy. Numerous modes that appear below T(c) show pronounced T dependences of their amplitudes, frequencies, and dampings. Utilizing the time-dependent Ginzburg-Landau theory we show that these modes result from linear coupling of the electronic part of the order parameter to the 2k(F) phonons, while the (electronic) CDW amplitude mode is overdamped.

PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing

MOTIVATION

In genome-wide association studies (GWAS) examining hundreds of thousands of genetic markers, the potentially high number of false positive findings requires statistical correction for multiple testing. Permutation tests are considered the gold standard for multiple testing correction in GWAS, because they simultaneously provide unbiased type I error control and high power. At the same time, they demand heavy computational effort, especially with large-scale datasets of modern GWAS. In recent years, the computational problem has been circumvented by using approximations to permutation tests, which, however, may be biased.

RESULTS

We have tackled the original computational problem of permutation testing in GWAS and herein present a permutation test algorithm one or more orders of magnitude faster than existing implementations, which enables efficient permutation testing on a genome-wide scale. Our algorithm does not rely on any kind of approximation and hence produces unbiased results identical to a standard permutation test. A noteworthy feature of our algorithm is a particularly effective performance when analyzing high-density marker sets.

AVAILABILITY

Freely available on the web at http://www.permory.org.

Calibration of optically trapped nanotools

Holographically trapped nanotools can be used in a novel form of force microscopy. By measuring the displacement of the tool in the optical traps, the contact force experienced by the probe can be inferred. In the following paper we experimentally demonstrate the calibration of such a device and show that its behaviour is independent of small changes in the relative position of the optical traps. Furthermore, we explore more general aspects of the thermal motion of the tool.

Impulsive terahertz radiation with high electric fields from an amplifier-driven large-area photoconductive antenna

We report on the generation of impulsive terahertz (THz) radiation with 36 kV/cm vacuum electric field (1.5 mW average thermal power) at 250 kHz repetition rate and a high NIR-to-THz conversion efficiency of 2 x 10(-3). This is achieved by photoexciting biased large-area photoconductive emitter with NIR fs pulses of microJ pulse energy. We demonstrate focussing of the THz beam by tailoring the pulse front of the exciting laser beam without any focussing element for the THz beam. A high dynamic range of 10(4) signal-to-noise is obtained with an amplifier based system.

Two new Loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and german study groups

Meta-analyses of population-based genome-wide association studies (GWAS) in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP) from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions) generalized to (i) the population level and (ii) to adults by genotyping another 31,182 individuals (GENERALIZATION step). Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85×10⁻⁸ in the DISCOVERY step) and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene) and MSRA (methionine sulfoxide reductase A gene; p = 4.84×10⁻⁷), the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at ∼1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial degree between children and adults.

Genome-wide association studies (GWAS) have successfully contributed to the detection of genetic variants involved in body-weight regulation. We jointly analysed two GWAS for early-onset extreme obesity in 2,258 individuals of European origin and followed-up the findings in 3,141 individuals. Evidence for association of markers in two new genetic loci was shown (SDCCAG8 on chromosome 1q43–q44 and between TNKS/MSRA on chromosome 8p23.1). We also re-identified variants in or near FTO, MC4R, and TMEM18 to be associated with extreme obesity. In addition, we assessed the effect of the markers in 31,182 obese, lean, normal weight, and unselected individuals from population-based samples and showed that the variants near FTO, MC4R, TMEM18, and SDCCAG8 were consistently associated with obesity. For variants of TNKS/MSRA, the obesity association was limited to children and adolescents. In summary, we detected two new obesity loci and confirmed that the currently known major common variants related to obesity overlap to a substantial degree between children and adults.

Serum metabolome analysis by 1H-NMR reveals differences between chronic lymphocytic leukaemia molecular subgroups

Chronic lymphocytic leukaemia (CLL) is a heterogeneous disease exhibiting variable clinical course and survival rates. Mutational status of the immunoglobulin heavy chain variable regions (IGHVs) of CLL cells offers useful prognostic information for high-risk patients, but time and economical costs originally prevented it from being routinely used in a clinical setting. Instead, alternative markers of IGHV status, such as zeta-associated protein (ZAP70) or messenger RNA levels are often used. We report a (1)H-NMR-based metabolomics approach to examine serum metabolic profiles of early stage, untreated CLL patients (Binet stage A) classified on the basis of IGHV mutational status or ZAP70. Metabolic profiles of CLL patients (n=29) exhibited higher concentrations of pyruvate and glutamate and decreased concentrations of isoleucine compared with controls (n=9). Differences in metabolic profiles between unmutated (UM-IGHV; n=10) and mutated IGHV (M-IGHV; n=19) patients were determined using partial least square discriminatory analysis (PLS-DA; R(2)=0.74, Q(2)=0.36). The UM-IGHV patients had elevated levels of cholesterol, lactate, uridine and fumarate, and decreased levels of pyridoxine, glycerol, 3-hydroxybutyrate and methionine concentrations. The PLS-DA models derived from ZAP70 classifications showed comparatively poor goodness-of-fit values, suggesting that IGHV mutational status correlates better with disease-related metabolic profiles. Our results highlight the usefulness of (1)H-NMR-based metabolomics as a potential non-invasive prognostic tool for identifying CLL disease-state biomarkers.

Familiality and molecular genetics of attention networks in ADHD

Indices from a more elementary neuropsychological level might be useful in the search for genes for complex psychiatric disorders, such as ADHD. In this study we investigated systematically whether attentional performance as measured with the Attention Network Test (ANT) is suited for the identification of endophenotypes of ADHD. Attentional performance in affected sib pairs with ADHD (n = 181) was compared to unaffected control siblings (n = 121). Intrafamilial correlation patterns were calculated. In addition, linkage and association analyses were conducted between quantitative scores of attentional functions and dopamine receptor D4 (DRD4) and dopamine transporter (DAT1 or SLC6A3) gene variants. Only the executive attention network was significantly impaired in subjects with ADHD compared to controls (P < 0.05) and showed evidence for familiality in both affected and unaffected families. Linkage analyses revealed the highest LOD score for a severity score based on DSM-IV inattentive symptoms in the DAT1 chromosomal region (LOD score 2.6 at 15 cM). However, a SNP (rs6350) at the DAT1 locus showed a tendency for association with both alerting performance (P = 0.02) and executive attention (P = 0.01) although it did not survive alpha adjustment for multiple testing. No evidence was found for association of any of the investigated phenotypes with the VNTR in the DRD4. Thus, our data suggest that the quantitative behavioral ratings of inattentive symptoms might be more useful when searching for new genes associated with ADHD, however, among the ANT measures the executive attention network seems to be best suited for further endophenotype analyses.

Considerations on the design and financial feasibility of full-scale membrane bioreactors for municipal applications

Based on the practical experience in design and operation of three full-scale membrane bioreactors (MBR) for municipal wastewater treatment that were commissioned since 1999, an overview on the different design concepts that were applied to the three MBR plants is given. The investment costs and the energy consumption of the MBRs and conventional activated sludge (CAS) plants (with and without tertiary treatment) in the Erft river region are compared. It is found that the specific investment costs of the MBR plants are lower than those of comparable CAS with tertiary treatment. A comparison of the specific energy demand of MBRs and conventional WWTPs is given. The structure of the MBRs actual operational costs is analysed. It can be seen that energy consumption is only responsible for one quarter to one third of all operational expenses. Based on a rough design and empirical cost data, a cost comparison of a full-scale MBR and a CAS is carried out. In this example the CAS employs a sand filtration and a disinfection in order to achieve comparable effluent quality. The influence of membrane lifetime on life cycle cost is assessed.

Mutation screen and association studies for the fatty acid amide hydrolase (FAAH) gene and early onset and adult obesity

Background

The orexigenic effects of cannabinoids are limited by activation of the endocannabinoid degrading enzyme fatty acid amide hydrolase (FAAH). The aim of this study was to analyse whether FAAH alleles are associated with early and late onset obesity.

Methods

We initially assessed association of five single nucleotide polymorphisms (SNPs) in FAAH with early onset extreme obesity in up to 521 German obese children and both parents. SNPs with nominal p-values ≤ 0.1 were subsequently analysed in 235 independent German obesity families. SNPs associated with childhood obesity (p-values ≤ 0.05) were further analysed in 8,491 adult individuals of a population-based cohort (KORA) for association with adult obesity. One SNP was further analysed in 985 German obese adults and 588 normal and underweight controls. In parallel, we screened the FAAH coding region for novel sequence variants in 92 extremely obese children using single-stranded-conformation-polymorphism-analysis and denaturing HPLC and assessed the implication of the identified new variants for childhood obesity.

Results

The trio analysis revealed some evidence for an association of three SNPs in FAAH (rs324420 rs324419 and rs873978) with childhood obesity (two-sided p-values between 0.06 and 0.10). Although analyses of these variants in 235 independent obesity families did not result in statistically significant effects (two-sided p-values between 0.14 and 0.75), the combined analysis of all 603 obesity families supported the idea of an association of two SNPs in FAAH (rs324420 and rs2295632) with early onset extreme obesity (p-values between 0.02 and 0.03). No association was, however, found between these variants and adult obesity. The mutation screen revealed four novel variants, which were not associated with early onset obesity (p > 0.05).

Conclusions

As we observed some evidence for an association of the FAAH variants rs2295632 rs324420 with early onset but not adult obesity, we conclude that the FAAH variants analyzed here at least do not seem to play a major role in the etiology of obesity within our samples.

Optimal robust two-stage designs for genome-wide association studies

Optimal robust two-stage designs for genome-wide association studies are proposed using the maximum of the recessive, additive and dominant linear trend test statistics. These designs combine cost-saving two-stage genotyping with robustness against misspecification of the genetic model and are much more efficient than designs based on a single model specific test statistic in detecting multiple loci with different modes of inheritance. For given power of 90%, typical cost savings of 34% can be realised by increasing the total sample size by about 13% but genotyping only about half of the sample for the full marker set in the first stage and carrying forward about 0.06% of the markers to the second stage analysis. We also present robust two-stage designs providing optimal allocation of a limited budget for pre-existing samples. If a sample is available which would yield a power of 90% when fully genotyped, genotyping only half of the sample due to a limited budget will typically cause a loss of power of more than 55%. Using an optimal two-stage approach in the same sample under the same budget restrictions will limit the loss of power to less than 10%. In general, the optimal proportion of markers to be followed up in the second stage strongly depends on the cost ratio for chips and individual genotyping, while the design parameters of the optimal designs (total sample size, first stage proportion, first and second stage significance limit) do not much depend on the genetic model assumptions.

Necrotizing lymphadenitis: Kikuchi--Fujimoto disease alias lupus lymphadenitis?

Differentiation between lymphadenopathy in potentially life-threatening systemic lupus erythematosus (SLE) and self-limiting necrotizing lymphadenitis, also called Kikuchi- Fujimoto disease (KFD), is difficult. In the past, co-occurrence of SLE and KFD has been described repeatedly in case reports. Here, we report a case of necrotizing lymphadenitis, describe the clinical and histopathologic features in detail and discuss the current literature. KFD may in fact be a histopathologic characteristic of SLE supporting the hypothesis that KFD is a rare manifestation of SLE. To clarify whether KFD is the same entity as lupus lymphadenitis, more cases with SLE and lymphadenopathy should be examined in detail.

Suppression of Map Kinases Inhibits Microglial Activation and Attenuates Neuronal Cell Death Induced by α-Synuclein Protofibrils

α-Synuclein (α-Syn) accounts, as a major component of Lewy bodies (LB), for the filamentous deposits in many cases of neurodegenerative diseases. Yet, little is known about the molecular mechanisms of neuronal loss in these diseases. The correlation between α-Syn oligomerization/aggregation and pathologies raises the key question of which molecular form of α-Syn (i.e. monomeric α-Syn, protofibrils or mature fibrils) represents the damage-inducing culprit in the scenario of synucleinopathies. We show that human α-Syn protofibrils (PFs) are potent activators of parallel proinflammatory signalling pathways (p38 and ERK1/2 MAP kinases and NF-κB) in microglial cells in vitro. Furthermore, stereotactic injection of α-Syn PFs into the substantia nigra of adult rats leads to a profound activation of microglia and adjacent neuronal cell loss, which can be attenuated by the MAP kinase inhibitor semapimod. We propose that the neurodegenerative process of α-synucleinopathies involves microglial activation through α-Syn released or extruded from cells with pathogenic α-Syn metabolism. Compounds that inhibit the MAPK/NF-κB pathways might be a promising pharmacological strategy for the treatment of the inflammatory component of synucleinopathies including PD.