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Background Angiopoietin-like protein 3 (ANGPTL3), a liver-derived protein, plays an important role in the lipid and lipoprotein metabolism. Using data available from the DiOGenes study, we assessed the link with clinical improvements (weight, plasma lipid, and insulin levels) and changes in liver markers, alanine aminotransferase, aspartate aminotransferase (AST), adiponectin, fetuin A and B, and cytokeratin 18 (CK-18), upon low-calorie diet (LCD) intervention. We also examined the role of genetic variation in determining the level of circulating ANGPTL3 and the relation between the identified genetic markers and markers of hepatic steatosis. Methods DiOGenes is a multicenter, controlled dietary intervention where obese participants followed an 8-week LCD (800 kcal/day, using a meal replacement product). Plasma ANGPTL3 and liver markers were measured using the SomaLogic (Boulder, CO) platform. Protein quantitative trait locus (pQTL) analyses assessed the link between more than four million common variants and the level of circulating ANGPTL3 at baseline and changes in levels during the LCD intervention. Results Changes in ANGPTL3 during weight loss showed only marginal association with changes in triglycerides (nominal p = 0.02) and insulin (p = 0.04); these results did not remain significant after correcting for multiple testing. However, significant association (after multiple-testing correction) were observed between changes in ANGPTL3 and AST during weight loss (p = 0.004) and between ANGPTL3 and CK-18 (baseline p = 1.03 × 10−7, during weight loss p = 1.47 × 10−13). Our pQTL study identified two loci significantly associated with changes in ANGPTL3. One of these loci (the APOA4-APOA5-ZNF259-BUD13 gene cluster) also displayed significant association with changes in CK-18 levels during weight loss (p = 0.007). Conclusion We clarify the link between circulating levels of ANGPTL3 and specific markers of liver function. We demonstrate that changes in ANGPLT3 and CK-18 during LCD are under genetic control from trans-acting variants. Our results suggest an extended function of ANGPTL3 in the inflammatory state of liver steatosis and toward liver metabolic processes. Electronic supplementary material The online version of this article (10.1186/s12263-018-0597-3) contains supplementary material, which is available to authorized users.

Objectives: Salivary α- amylase (AMY1) is responsible for the breakdown of starch into oligosaccharides, tri and di-saccharides giving a start to the starch digestion in the oral cavity on food consumption. Several studies recently reported contradicting results regarding the link between AMY1 copy numbers (CNs) and obesity and type 2 diabetes. Objective: We investigated whether CN in the AMY1 gene was associated with differential anthropometrics and glycaemic outcomes in obese individuals who underwent a dietary plan varying in macronutrient intake, as a part of weight loss and weight maintenance program. We also investigated whether there existed an interaction between nutrient intakes and AMY1 CNs and if AMY1 CNs have influence on body weight, body composition and glycemic trajectories during dietary interventions.Methods: Using the Paralogue Ratio Test, we accurately measured the AMY1 CNs in 761 obese individuals from the Diogenes study. Subjects underwent first an 8-week low-caloric diet (LCD, at 800 kcal/d) and those achieving >8% weight loss were then randomized to a 6-month weight maintenance dietary (WMD) intervention. The association between AMY1 CNs and weight- and glycemic- parameters was tested at baseline and following each intervention phase (LCD, WMD) with the use of linear mixed effect models adjusting for gender, age, center and total energy intake.Results: At baseline, a modest association between AMY1 CN and BMI (P = 0.04) was observed. AMY1 CN was not associated with baseline glycemic variables. Additionally, AMY1 CN was not associated with anthropometric or glycemic-outcomes following either LCD or WMD. Interaction analyses between AMY1 CN and nutrient intake did not reveal significant association with any clinical parameters (at baseline and following LCD or WMD) or when testing gene x WMD interactions during the WMD phase.Conclusions: In the absence of association with weight trajectories or glycemic improvements, the AMY1 CN cannot be considered as an important biomarker for response to a clinical weight loss and weight maintenance programs in overweight/obese subjects.Funding Sources: European Commission, Food Quality and Safety Priority of the Sixth Framework Program (FP6-2005-513946), Nestlé Institute of Health Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Motivation: Current clinical and biological studies apply different biotechnologies and subsequently combine the resulting -omics data to test biological hypotheses. The plethora of -omics data and their combination generates a large number of hypotheses and apparently increases the study power. Contrary to these expectations, the wealth of -omics data may even reduce the statistical power of a study because of a large correction factor for multiple testing. Typically, this loss of power in analyzing -omics data are caused by an increased false detection rate (FDR) in measurements, like falsely detected DNA copy number changes, or falsely identified differentially expressed genes. The false detections are random and, therefore, not related to the tested conditions. Thus, a high FDR considerably decreases the discovery power of studies, especially if different -omics data are involved. Results: On a HapMap data set, where known CNVs have to be re-detected, I/NI call filtering was much more efficient than v...

Context Although calorie restriction has proven beneficial for weight loss, long-term weight control is variable between individuals. Objective To identify biomarkers of successful weight control during a dietary intervention (DI). Design, Setting, and Participants Adipose tissue (AT) transcriptomes were compared between 21 obese individuals who either maintained weight loss or regained weight during the DI. Results were validated on 310 individuals from the same study using quantitative reverse transcription polymerase chain reaction and protein levels of potential circulating biomarkers measured by enzyme-linked immunosorbent assay. Intervention Individuals underwent 8 weeks of low-calorie diet, then 6 months of ad libitum diet. Outcome Measure Weight changes at the end of the DI. Results We evaluated six genes that had altered expression during DI, encode secreted proteins, and have not previously been implicated in weight control (EGFL6, FSTL3, CRYAB, TNMD, SPARC, IGFBP3), as well as genes for which baseline expression differed between those with good and poor weight control (ASPN, USP53). Changes in plasma concentrations of EGFL6, FSTL3, and CRYAB mirrored AT messenger RNA expression; all decreased during DI in individuals with good weight control. ASPN and USP53 had higher baseline expression in individuals who went on to have good weight control. Expression quantitative trait loci analysis found polymorphisms associated with expression levels of USP53 in AT. A regulatory network was identified in which transforming growth factor β1 (TGF-β1) was responsible for downregulation of certain genes during DI in good controllers. Interestingly, ASPN is a TGF-β1 inhibitor. Conclusions We found circulating biomarkers associated with weight control that could influence weight management strategies and genes that may be prognostic for successful weight control.

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

We performed exome sequencing to detect somatic mutations in protein-coding regions in seven melanoma cell lines and donor-matched germline cells. All melanoma samples had high numbers of somatic mutations, which showed the hallmark of UV-induced DNA repair. Such a hallmark was absent in tumor sample-specific mutations in two metastases derived from the same individual. Two melanomas with non-canonical BRAF mutations harbored gain-of-function MAP2K1 and MAP2K2 (MEK1 and MEK2, respectively) mutations, resulting in constitutive ERK phosphorylation and higher resistance to MEK inhibitors. Screening a larger cohort of individuals with melanoma revealed the presence of recurring somatic MAP2K1 and MAP2K2 mutations, which occurred at an overall frequency of 8%. Furthermore, missense and nonsense somatic mutations were frequently found in three candidate melanoma genes, FAT4, LRP1B and DSC1.

While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.

Introduction et but de l’etude Les microARNs (miRs) sont des petits ARNs endogenes qui regulent negativement l’expression des genes de facon post-transcriptionnelle. Ils auraient un role important dans la regulation de certaines voies metaboliques dans le tissu adipeux (TA). Les miRs sont particulierement stables et representent de potentiels biomarqueurs d’interet. Notamment, dans le domaine de la prise en charge de l’obesite, ils pourraient etre des marqueurs de la reponse a une intervention dietetique de restriction calorique. Le but de ce travail est d’analyser les changements du miRnome du TA de patients obeses ou en surpoids soumis a une restriction calorique, en comparant les niveaux d’expressions en basal a ceux a la fin de l’intervention. Materiel et methodes Un essai clinique randomise consistant en 8 semaines de restriction calorique a recrute 548 sujets, qui ont beneficie de multiples investigations cliniques : enquetes dietetiques, parametres anthropometriques et sanguins. Des biopsies de TA sous-cutane a l’aiguille ont ete realisees en basal et a 8 semaines. Le profil d’expression des miRs a ete determine par des puces a microARNS et valide par RTqPCR. Des modeles mixtes ont ete construits, avec la difference d’expression des miRs comme variable dependante, et ajustes sur l’âge, le sexe, le pourcentage de perte de poids et la difference d’apport energetique, le centre etant considere comme un effet aleatoire. Les calculs ont ete faits grâce au logiciel R (version 3.2.2), implemente des packages lme4 (version 1.1-11) et boot (version 1.3-17). Resultats et analyse statistique Cent cinquante huit sujets ayant a la fois des donnees disponibles d’expression des miRs et des recueils dietetiques ont ete inclus. Neuf miRs etaient differentiellement regules (p > 0,05). Tous sauf un avaient un b negatif, ce qui signifie que plus la restriction calorique est forte, plus l’expression du miR diminue. Les miRs les plus significativement regules ont ete valides par RTqPCR sur un groupe de validation de 142 sujets, selon les memes methodes. Un seul miR s’est avere proche de la significativite, miR-22-3p, (p = 0,086). Un b negatif (−0,03) indique que la diminution du niveau d’expression du miR-22-3p dans le TA est associe a une restriction calorique plus forte. Conclusion Une restriction calorique forte chez des individus obeses est associee negativement au niveau d’expression du miR-22-3p dans le TA sous-cutane. Des etudes futures determineront si ce miR est detectable dans le plasma sanguin, potentiellement produit par le TA, constituant ainsi un biomarqueur de la restriction calorique.

This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published “Golden Path,” and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self–self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.

Meta-analysis has shown a modest improvement in first-year growth response to recombinant human GH (r-hGH) for carriers of the exon 3-deleted GH receptor (GHRd3) polymorphism but with significant interstudy variability. The associations between GHRd3 and growth response to r-hGH over 3 years in relation to severity of GH deficiency (GHD) were investigated in patients from 14 countries. Treatment-naïve pre-pubertal children with GHD were enrolled from the PREDICT studies (NCT00256126 and NCT00699855), categorized by peak GH level (peak GH) during provocation test: ≤4 μg/l (severe GHD; n=45) and >4 to n=49) and genotyped for the GHRd3 polymorphism (full length (fl/fl, fl/d3, d3/d3). Gene expression (GE) profiles were characterized at baseline. Changes in growth (height (cm) and SDS) over 3 years were measured. There was a dichotomous influence of GHRd3 polymorphism on response to r-hGH, dependent on peak GH level. GH peak level (higher vs lower) and GHRd3 (fl/fl vs d3 carriers) combined status was associated with height change over 3 years (P

s / Osteoarthritis and Cartilage 21 (2013) S63–S312 S77 most strongly associated with activated macrophages in the capsule of the tibiofemoral (TF) compartments (p1⁄40.0063) and the whole joint synovium (p1⁄40.0017). sCD163 was also associated with severity of radiographic OA, specifically joint space narrowing (p1⁄40.0554), but not osteophyte severity. The use of the markers in combination improved the prediction of activated macrophages in the capsule of the PF knee compartment (p1⁄40.013) and joint space narrowing (p1⁄40.0099) independent of osteophyte severity. Conclusions: These findings suggest that cell-surface markers shed from activated macrophages may be used as biomarkers to identify a subtype of OA patients with an active inflammatory disease state. The combined analysis of both CD14 and CD163 indicate synergism between the markers for identifying the presence of activated macrophages in the capsule of the PF knee and joint space narrowing. Furthermore, these results contribute to a growing literature identifying macrophages and macrophage-activation pathways as potential targets for new OA therapies. Acknowledgements: Samples were obtained with support of a grant from Lilly USA, Inc; support for the assays was provided by laboratory research funds of the PI (VBK), and support for personnel was provide by NIH 5T32AI007217-30 (HND) and P01 AR050245. 127 CHONDROCYTE HYPERTROPHY, MEASURED BY THE SECRETION OF COLLAGEN TYPE X, IS A HALLMARK OF PATHOLOGICAL CHANGES IN OSTEOARTHRITIS Y. He y, N. Urik Brndt-Hansena y, J. Wang z, D. Su z, Q. Zheng z, O. Simonsen x, K. Petersen k, M. Karsdal y, A.-C. Bay-Jensena y. yNordic BioSci., Herlev, Denmark; zNordic BioSci. China, Beijing, China; xDept. Orthopedic Surg, Aalborg Univ. Hosp., Aalborg, Denmark; kCtr. for Sensory-Motor Interaction, Dept. of Hlth.Sci. and Technology, Aalborg Univ., Aalborg, Denmark Purpose: Collagen type X (Col X) is a short chain and network-forming collagen, which is specifically synthesized by hypertrophic chondrocyte in the growth plate during endochondral ossification, the calcified cartilage in normal adult or the deep zone of osteoarthritic (OA) cartilage; thus Col Xmay play an important role in cartilage calcification. The aim of the study was to measure serum levels Col X in OA patients as well characterize the presence of the ColX in OA cartilage section. Methods:Amonoclonal antibody (mAb)was raised against the 10aa at Cterminus of NC1 domain of Col X. ThismAbwas characterized bywestern blot using U2-OS osteosarcoma cell as positive control, and by immunohistochemistry on 5 human OA knee cartilages sections. A solid-phase competitive ELISAwas developed applying the mAb and tested in a small cohort including: 47 OA patients undergoing total knee replacement surgery (mean age SD: 64 15), and 13 controls with knee problems having arthroscopy (mean age SD: 34 21), all women. Mann-Whitney test was applied to compare the serum Col X levels in TKR and control group. Pearson correlationwas done on log transformed data. Results: The mAb, NB509-11G8, was specific for the immunogen; it did not recognize truncated or nonsense peptides when tested in the ELISA. The mAb detected the monomeric Col X (59KDa) and dimeric Col X (120KDa) in the U2-OS cell lysate. Moreover, these bands were blocked by the specific peptide. NB509-11G8 stained the extracellular matrix of chondrocytes in the deep zone and calcified cartilage of human OA samples but not the middle or upper zone (fig. A). The competitive ELISA had a measuring range of 0.02-5 ng/ml, with intraand interassay CVs of 4.19% and 10.62%. The mean serum Col X level was significantly higher in the TKR than the control group (P1⁄40.017, fig. B). Serum Col X level did not correlate with age (R21⁄40.055), but weak Ă relationwith BMI (R21⁄40.17). The AUC for serum Col X for discriminating TKR from controls was 0.72 (P1⁄40.017). Conclusions: Secretion of Col X as a marker of cartilage hypertrophy may serve as an early biomarker for OA burden of disease. 128 CTX-II IS A MARKER OF CARTILAGE DEGRADATION BUT NOT OF BONE TURNOVER J. Catterall y, S. Dewitt Parr z, K. Fagerlund x, B. Caterson z. yDuke Univ., Durham, NC, USA; zCardiff Univ., Cardiff, United Kingdom; x Pharmatest Services Ltd, Turku, Finland Purpose: The CTx-II biomarker has been widely investigated and used to determine the status of cartilage turnover in osteoarthritis and rheumatoid arthritis. Recent publications have discussed the possibility that CTx-II release may partially reflect bone turnover rather than being a specific marker of cartilage turnover. As CTx-II has been used so widely, it is clear that the specificity of CTx-II for cartilage needed to be re-evaluated. To this end, we decided to investigate the specificity of CTx-II for cartilage in comparison to the gold standard CTx-I bone degradation marker. We investigated the specificity of the ELISAs for their respective epitopes, release of CTx-I and CTx-II from bone and cartilage explant cultures, and levels of CTx-II and CTx-I in a small acute injury and osteoarthritis (OA) cohort. Methods: ELISA specificity for CTx-I and CTx-II was determined by depletion of the epitopes from urine and by affinity purification of the epitopes. Release of CTx-I and CTx-II from bone and cartilage was investigated by digesting both cartilage and bone with either cathepsin K or matrix metalloproteinases, and release of CTx-I and CTx-II determined by ELISA. We also investigated the release of CTx-I and CTx-II in explant culture from both bone by osteoclasts mediated bone degradation and from pro-inflammatory cytokine-stimulated cartilage explant cultures. Finally, we investigated the changes in CTx-I and CTxII in patient cohorts. Results: In vitro, cathepsin K digestion of bone released CTx-I alone while digestion of bone with activated MMPs was unable to release either CTx-I or CTx-II from bone. Only digestion of cartilage by activated MMPs released CTx-II, while digestion of cartilage by either MMPs or cathepsin K was unable to release detectable CTx-I. Osteoclast digestion of bone slices released only CTx-I and no detectable CTx-II, while the reverse was true in chondrocyte-mediated cartilage degradation, with high CTx-II release and no detectable CTx-I. In our OA patient cohorts we observed an increase in CTx-II levels when compared to healthy controls but no change in CTx-I, while acute injury patients demonstrated a reduction in CTx-I levels after injury and no change in CTx-II. Conclusions: Our data strongly suggest that CTx-I reflects bone degradation and CTx-II reflects cartilage degradation, and that in acute injury and in osteoarthritis, bone turnover and cartilage degradation/ repair processes differ. As CTx-II reflects cartilage degradation, it is a valid biomarker of cartilage breakdown and not a biomarker of bone turnover, although in some cases it may reflect the connected pathology of bone and cartilage in joint diseases. 129 CTX-II LEVELS ARE ASSOCIATED WITH PERIPHERAL BONE DENSITY, SUGGESTING CTX-II EPITOPE RELEASE FROM BONE: DATA FROM COHORT HIP AND COHORT KNEE (CHECK) W.E. van Spil, K.L. Vincken, W.F. Lems, F.P. Lafeber. Univ. Med. Ctr. Utrecht, Utrecht, The Netherlands Purpose: Recent data have suggested that CTX-II (C-terminal telopeptide of collagen type II) may not only originate from articular cartilage but also from bone changes. Therefore, the purpose of this study was to look for cross-sectional associations between urinary CTX-II levels and bone density distant from the subchondral bone area. Methods: This study was performed in 366 subjects with early-stage symptomatic knee and/or hip osteoarthritis from Cohort Hip and Cohort Knee (CHECK). In urine (u-) and serum (s-) samples from these subjects, uCTX-II, the cartilage markers sCOMP, sPIIANP, and sCS846 (cartilage oligomeric matrix protein, N-terminal propeptide of procollagen type IIA, and chondroitin sulphate 846), and the bone markers uNTX-I, uCTX-I, sPINP, and sOC (N and C-terminal telopeptides of collagen type I, N-terminal propeptide of procollagen type I, and osteocalcin) were assessed by enzyme-linked immunosorbent assay or radioactive immunoassay. Bone density was determined at the tibia and

Congenital heart defect (CHD) occurs in 40% of Down syndrome (DS) cases. While carrying three copies of chromosome 21 increases the risk for CHD, trisomy 21 itself is not sufficient to cause CHD. Thus, additional genetic variation and/or environmental factors could contribute to the CHD risk. Here we report genomic variations that in concert with trisomy 21, determine the risk for CHD in DS. This case-control GWAS includes 187 DS with CHD (AVSD = 69, ASD = 53, VSD = 65) as cases, and 151 DS without CHD as controls. Chromosome 21–specific association studies revealed rs2832616 and rs1943950 as CHD risk alleles (adjusted genotypic P-values

The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the 'missing heritability'. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10(-4) (95% confidence interval [9.6×10(-5)-3.1×10(-4)]); accounts overall for 0.5% [0.19%-0.82%] of severe childhood obesity cases (P = 3.8×10(-10); odds ratio = 25.0 [9.9-60.6]); and results in a mean body mass index (BMI) increase of 5.8 kg.m(-2) [1.8-10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.

Differences between genomes can be due to single nucleotide variants, translocations, inversions, and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 500 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease. Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs. While a link between a given CNV and a disease may have often been established, the relative CNV contribution to disease progression and impact on drug response is not necessarily understood. In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification of recurrent CNVs to the association with phenotypes. We emphasize the importance of germline CNVs and propose strategies to aid clinicians to better interpret structural variations and assess their clinical implications.

Item does not contain fulltext The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency >0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P < 5 x 10(-8)) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across approximately 115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits.

To access publisher full text version of this article. Please click on the hyperlink in Additional Links field. Both obesity and being underweight have been associated with increased mortality. Underweight, defined as a body mass index (BMI) ≤ 18.5 kg per m(2) in adults and ≤ -2 standard deviations from the mean in children, is the main sign of a series of heterogeneous clinical conditions including failure to thrive, feeding and eating disorder and/or anorexia nervosa. In contrast to obesity, few genetic variants underlying these clinical conditions have been reported. We previously showed that hemizygosity of a ∼600-kilobase (kb) region on the short arm of chromosome 16 causes a highly penetrant form of obesity that is often associated with hyperphagia and intellectual disabilities. Here we show that the corresponding reciprocal duplication is associated with being underweight. We identified 138 duplication carriers (including 132 novel cases and 108 unrelated carriers) from individuals clinically referred for developmental or intellectual disabilities (DD/ID) or psychiatric disorders, or recruited from population-based cohorts. These carriers show significantly reduced postnatal weight and BMI. Half of the boys younger than five years are underweight with a probable diagnosis of failure to thrive, whereas adult duplication carriers have an 8.3-fold increased risk of being clinically underweight. We observe a trend towards increased severity in males, as well as a depletion of male carriers among non-medically ascertained cases. These features are associated with an unusually high frequency of selective and restrictive eating behaviours and a significant reduction in head circumference. Each of the observed phenotypes is the converse of one reported in carriers of deletions at this locus. The phenotypes correlate with changes in transcript levels for genes mapping within the duplication but not in flanking regions. The reciprocal impact of these 16p11.2 copy-number variants indicates that severe obesity and being underweight could have mirror aetiologies, possibly through contrasting effects on energy balance. Leenaards Foundation Jerome Lejeune Foundation Telethon Action Suisse Foundation Swiss National Science Foundation European Commission 037627 QLG1-CT-2000-01643 Ludwig Institute for Cancer Research Swiss Institute of Bioinformatics Imperial College Department of Medicine Comprehensive Biomedical Research Centre Imperial College Healthcare NHS Trust National Institute for Health Research Wellcome Trust Medical Research Council Instituto de Salud Carlos III (ISCIII)-FIS German Mental Retardation Network German Federal Ministry of Education and Research NGFNplus 01GS08160 European Union PI081714 PS09/01778 201413 245536 info:eu-repo/grantAgreement/EC/FP7/223423 Belgian National Fund for Scientific Research, Flanders Dutch Organisation for Health Research and Development (ZON-MW) 917-86-319 Hersenstichting Nederland (B.B.A.d.V.) Chinese National Natural Science Foundation 81000346 Simons Foundation Autism Research Initiative Autism Speaks NIH GM061354 MH071425 Oesterreichische Nationalbank (OENB) 13059 Children's Tumor Foundation Harvard Medical School Fudan University Chinese National '973' project on Population and Health 2010CB529601 Science and Technology Council of Shanghai 09JC1402400 Michael Smith Foundation for Health CIHR MOP 74502 Estonian Government SF0180142s08 SF0180026s09 SF0180027s10 Helmholtz Zentrum Munich State of Bavaria German National Genome Research Network 01GS0823 German Federal Ministry of Education and Research (BMBF) Munich Center of Health Sciences (MC Health, LMUinnovativ) Genome Canada McLaughlin Centre Academy of Finland 104781 120315 129269 1114194 University Hospital Oulu Biocenter University of Oulu, Finland 75617 NHLBI 5R01HL087679-02 1RL1MH083268-01 NIH/NIMH 5R01MH63706:02 ENGAGE project Medical Research Council, UK G0500539 G0600705 Academy of Finland Biocentrum Helsinki SAF2008-02278 HEALTH-F4-2007-201413

Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) >or= 40 kg m(-2) or BMI standard deviation score >or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.

Contains fulltext : 88508.pdf (Publisher’s version ) (Closed access) Narcolepsy is a rare sleep disorder with the strongest human leukocyte antigen (HLA) association ever reported. Since the associated HLA-DRB1*1501-DQB1*0602 haplotype is common in the general population (15-25%), it has been suggested that it is almost necessary but not sufficient for developing narcolepsy. To further define the genetic basis of narcolepsy risk, we performed a genome-wide association study (GWAS) in 562 European individuals with narcolepsy (cases) and 702 ethnically matched controls, with independent replication in 370 cases and 495 controls, all heterozygous for DRB1*1501-DQB1*0602. We found association with a protective variant near HLA-DQA2 (rs2858884; P < 3 x 10(-8)). Further analysis revealed that rs2858884 is strongly linked to DRB1*03-DQB1*02 (P < 4 x 10(-43)) and DRB1*1301-DQB1*0603 (P < 3 x 10(-7)). Cases almost never carried a trans DRB1*1301-DQB1*0603 haplotype (odds ratio = 0.02; P < 6 x 10(-14)). This unexpected protective HLA haplotype suggests a virtually causal involvement of the HLA region in narcolepsy susceptibility. 01 september 2010

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

Summary: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. Availability: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles. Contact: brian.stevenson@licr.org Supplementary information: Supplementary data are available at http://sourceforge.net/projects/associationview/ online.

Datasets used for detecting copy number variation (CNV) are shown to be affected by a technical artifact. A novel CNV calling algorithm is presented which removes this artifact and identifies regions of CNV better than existing methods., Background Large-scale high throughput studies using microarray technology have established that copy number variation (CNV) throughout the genome is more frequent than previously thought. Such variation is known to play an important role in the presence and development of phenotypes such as HIV-1 infection and Alzheimer's disease. However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined. Results We describe the presence of a genome-wide technical artifact, spatial autocorrelation or 'wave', which occurs in a large dataset used to determine the location of CNV across the genome. By removing this artifact we are able to obtain both a more biologically meaningful clustering of the data and an increase in the number of CNVs identified by current calling methods without a major increase in the number of false positives detected. Moreover, removing this artifact is critical for the development of a novel model-based CNV calling algorithm - CNVmix - that uses cross-sample information to identify regions of the genome where CNVs occur. For regions of CNV that are identified by both CNVmix and current methods, we demonstrate that CNVmix is better able to categorize samples into groups that represent copy number gains or losses. Conclusion Removing artifactual 'waves' (which appear to be a general feature of array comparative genomic hybridization (aCGH) datasets) and using cross-sample information when identifying CNVs enables more biological information to be extracted from aCGH experiments designed to investigate copy number variation in normal individuals.

International audience; Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

Corrigendum: Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy

Cancer genomes frequently contain somatic copy number alterations (SCNA) that can significantly perturb the expression level of affected genes and thus disrupt pathways controlling normal growth. In melanoma, many studies have focussed on the copy number and gene expression levels of the BRAF, PTEN and MITF genes, but little has been done to identify new genes using these parameters at the genome-wide scale. Using karyotyping, SNP and CGH arrays, and RNA-seq, we have identified SCNA affecting gene expression ('SCNA-genes') in seven human metastatic melanoma cell lines. We showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. Since few of these alterations were recurrent across our samples, we used a protein network-guided approach to determine whether any pathways were enriched in SCNA-genes in one or more samples. From this unbiased genome-wide analysis, we identified 28 significantly enriched pathway modules. Comparison with two large, independent melanoma SCNA datasets showed less than 10% overlap at the individual gene level, but network-guided analysis revealed 66% shared pathways, including all but three of the pathways identified in our data. Frequently altered pathways included WNT, cadherin signalling, angiogenesis and melanogenesis. Additionally, our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma. Our study demonstrates the utility of network-guided approaches, for both large and small datasets, to identify pathways recurrently perturbed in cancer.

Aims/hypothesisIn islets from individuals with type 2 diabetes and in islets exposed to chronic elevated glucose, mitochondrial energy metabolism is impaired. Here, we studied early metabolic changes and mitochondrial adaptations in human beta cells during chronic glucose stress.MethodsRespiration and cytosolic ATP changes were measured in human islet cell clusters after culture for 4 days in 11.1 mmol/l glucose. Metabolomics was applied to analyse intracellular metabolite changes as a result of glucose stress conditions. Alterations in beta cell function were followed using insulin secretion assays or cytosolic calcium signalling after expression of the calcium probe YC3.6 specifically in beta cells of islet clusters.ResultsAt early stages of glucose stress, mitochondrial energy metabolism was augmented in contrast to the previously described mitochondrial dysfunction in beta cells from islets of diabetic donors. Following chronic glucose stress, mitochondrial respiration increased (by 52.4%,p p Conclusion/interpretationWe propose that metabolic changes and associated mitochondrial overactivation are early adaptations to glucose stress, and may reflect what happens as a result of poor blood glucose control. Inhibition of mitochondrial pyruvate transport reduces mitochondrial nutrient overload and allows beta cells to recover from chronic glucose stress.

The extracellular matrix (ECM) of adipocytes is important for body weight regulation. Here, we investigated whether genetic variation in ECM-related genes is associated with weight regain among participants of the European DiOGenes study. Overweight and obese subjects (n = 469, 310 females, 159 males) were on an 8-week low-calorie diet with a 6-month follow-up. Body weight was measured before and after the diet, and after follow-up. Weight maintenance scores (WMS, regained weight as percentage of lost weight) were calculated based on the weight data. Genotype data were retrieved for 2903 SNPs corresponding to 124 ECM-related genes. Regression analyses provided us with six significant SNPs associated with the WMS in males: 3 SNPs in the POSTN gene and a SNP in the LAMB1, COL23A1, and FBLN5 genes. For females, 1 SNP was found in the FN1 gene. The risk of weight regain was increased by: the C/C genotype for POSTN in a co-dominant model (OR 8.25, 95 % CI 2.85–23.88) and the T/C–C/C genotype in a dominant model (OR 4.88, 95 % CI 2.35–10.16); the A/A genotype for LAMB1 both in a co-dominant model (OR 18.43, 95 % CI 2.35–144.63) and in a recessive model (OR 16.36, 95 % CI 2.14–124.9); the G/A genotype for COL23A1 in a co-dominant model (OR 3.94, 95 % CI 1.28–12.10), or the A-allele in a dominant model (OR 2.86, 95 % CI 1.10–7.49); the A/A genotype for FBLN5 in a co-dominant model (OR 13.00, 95 % CI 1.61–104.81); and the A/A genotype for FN1 in a recessive model (OR 2.81, 95 % CI 1.40–5.63). Concluding, variants of ECM genes are associated with weight regain after weight loss in a sex-specific manner. Electronic supplementary material The online version of this article (doi:10.1007/s12263-015-0506-y) contains supplementary material, which is available to authorized users.

Background Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets. Results Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs. Conclusion Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.