Detection and characterization of male sex chromosome abnormalities in the UK Biobank study

PURPOSE

The study aimed to systematically ascertain male sex chromosome abnormalities, 47,XXY (Klinefelter syndrome [KS]) and 47,XYY, and characterize their risks of adverse health outcomes.

METHODS

We analyzed genotyping array or exome sequence data in 207,067 men of European ancestry aged 40 to 70 years from the UK Biobank and related these to extensive routine health record data.

RESULTS

Only 49 of 213 (23%) of men whom we identified with KS and only 1 of 143 (0.7%) with 47,XYY had a diagnosis of abnormal karyotype on their medical records or self-report. We observed expected associations for KS with reproductive dysfunction (late puberty: risk ratio [RR] = 2.7; childlessness: RR = 4.2; testosterone concentration: RR = -3.8 nmol/L, all P < 2 × 10-8), whereas XYY men appeared to have normal reproductive function. Despite this difference, we identified several higher disease risks shared across both KS and 47,XYY, including type 2 diabetes (RR = 3.0 and 2.6, respectively), venous thrombosis (RR = 6.4 and 7.4, respectively), pulmonary embolism (RR = 3.3 and 3.7, respectively), and chronic obstructive pulmonary disease (RR = 4.4 and 4.6, respectively) (all P < 7 × 10-6).

CONCLUSION

KS and 47,XYY were mostly unrecognized but conferred substantially higher risks for metabolic, vascular, and respiratory diseases, which were only partially explained by higher levels of body mass index, deprivation, and smoking.

Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro

As the powerhouses of the eukaryotic cell, mitochondria must maintain their genomes which encode proteins essential for energy production. Mitochondria are characterized by guanine-rich DNA sequences that spontaneously form unusual three-dimensional structures known as G-quadruplexes (G4). G4 structures can be problematic for the essential processes of DNA replication and transcription because they deter normal progression of the enzymatic-driven processes. In this study, we addressed the hypothesis that mitochondrial G4 is a source of mutagenesis leading to base-pair substitutions. Our computational analysis of 2757 individual genomes from two Italian population cohorts (SardiNIA and InCHIANTI) revealed a statistically significant enrichment of mitochondrial mutations within sequences corresponding to stable G4 DNA structures. Guided by the computational analysis results, we designed biochemical reconstitution experiments and demonstrated that DNA synthesis by two known mitochondrial DNA polymerases (Pol γ, PrimPol) in vitro was strongly blocked by representative stable G4 mitochondrial DNA structures, which could be overcome in a specific manner by the ATP-dependent G4-resolving helicase Pif1. However, error-prone DNA synthesis by PrimPol using the G4 template sequence persisted even in the presence of Pif1. Altogether, our results suggest that genetic variation is enriched in G-quadruplex regions that impede mitochondrial DNA replication.

Using genetics to understand the causal influence of higher BMI on depression

BACKGROUND

Depression is more common in obese than non-obese individuals, especially in women, but the causal relationship between obesity and depression is complex and uncertain. Previous studies have used genetic variants associated with BMI to provide evidence that higher body mass index (BMI) causes depression, but have not tested whether this relationship is driven by the metabolic consequences of BMI nor for differences between men and women.

METHODS

We performed a Mendelian randomization study using 48 791 individuals with depression and 291 995 controls in the UK Biobank, to test for causal effects of higher BMI on depression (defined using self-report and Hospital Episode data). We used two genetic instruments, both representing higher BMI, but one with and one without its adverse metabolic consequences, in an attempt to 'uncouple' the psychological component of obesity from the metabolic consequences. We further tested causal relationships in men and women separately, and using subsets of BMI variants from known physiological pathways.

RESULTS

Higher BMI was strongly associated with higher odds of depression, especially in women. Mendelian randomization provided evidence that higher BMI partly causes depression. Using a 73-variant BMI genetic risk score, a genetically determined one standard deviation (1 SD) higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals [odds ratio (OR): 1.18, 95% confidence interval (CI): 1.09, 1.28, P = 0.00007) and women only (OR: 1.24, 95% CI: 1.11, 1.39, P = 0.0001). Meta-analysis with 45 591 depression cases and 97 647 controls from the Psychiatric Genomics Consortium (PGC) strengthened the statistical confidence of the findings in all individuals. Similar effect size estimates were obtained using different Mendelian randomization methods, although not all reached P < 0.05. Using a metabolically favourable adiposity genetic risk score, and meta-analysing data from the UK biobank and PGC, a genetically determined 1 SD higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals (OR: 1.26, 95% CI: 1.06, 1.50], P = 0.010), but with weaker statistical confidence.

CONCLUSIONS

Higher BMI, with and without its adverse metabolic consequences, is likely to have a causal role in determining the likelihood of an individual developing depression.

Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors

Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association signals (129 of which are novel). We used structural equation modeling to decompose the contributions of direct fetal and indirect maternal genetic effects, then applied Mendelian randomization to illuminate causal pathways. For example, both indirect maternal and direct fetal genetic effects drive the observational relationship between lower birth weight and higher later blood pressure: maternal blood pressure-raising alleles reduce offspring birth weight, but only direct fetal effects of these alleles, once inherited, increase later offspring blood pressure. Using maternal birth weight-lowering genotypes to proxy for an adverse intrauterine environment provided no evidence that it causally raises offspring blood pressure, indicating that the inverse birth weight-blood pressure association is attributable to genetic effects, and not to intrauterine programming.

Genetic studies of accelerometer-based sleep measures yield new insights into human sleep behaviour

Sleep is an essential human function but its regulation is poorly understood. Using accelerometer data from 85,670 UK Biobank participants, we perform a genome-wide association study of 8 derived sleep traits representing sleep quality, quantity and timing, and validate our findings in 5,819 individuals. We identify 47 genetic associations at P < 5 × 10-8, of which 20 reach a stricter threshold of P < 8 × 10-10. These include 26 novel associations with measures of sleep quality and 10 with nocturnal sleep duration. The majority of identified variants associate with a single sleep trait, except for variants previously associated with restless legs syndrome. For sleep duration we identify a missense variant (p.Tyr727Cys) in PDE11A as the likely causal variant. As a group, sleep quality loci are enriched for serotonin processing genes. Although accelerometer-derived measures of sleep are imperfect and may be affected by restless legs syndrome, these findings provide new biological insights into sleep compared to previous efforts based on self-report sleep measures.

Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms

Being a morning person is a behavioural indicator of a person’s underlying circadian rhythm. Using genome-wide data from 697,828 UK Biobank and 23andMe participants we increase the number of genetic loci associated with being a morning person from 24 to 351. Using data from 85,760 individuals with activity-monitor derived measures of sleep timing we find that the chronotype loci associate with sleep timing: the mean sleep timing of the 5% of individuals carrying the most morningness alleles is 25 min earlier than the 5% carrying the fewest. The loci are enriched for genes involved in circadian regulation, cAMP, glutamate and insulin signalling pathways, and those expressed in the retina, hindbrain, hypothalamus, and pituitary. Using Mendelian Randomisation, we show that being a morning person is causally associated with better mental health but does not affect BMI or risk of Type 2 diabetes. This study offers insights into circadian biology and its links to disease in humans.

GWAS have previously found 24 genomic loci associated with chronotype, an individual’s preference for early or late sleep timing. Here, the authors identify 327 additional loci in a sample of 697,828 individuals and further explore the relationships of chronotype with metabolic and psychiatric diseases.

Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics

Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother–child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P < 5 × 10⁻⁸. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate that genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.

Genome-Wide and Abdominal MRI Data Provide Evidence That a Genetically Determined Favorable Adiposity Phenotype Is Characterized by Lower Ectopic Liver Fat and Lower Risk of Type 2 Diabetes, Heart Disease, and Hypertension

Recent genetic studies have identified alleles associated with opposite effects on adiposity and risk of type 2 diabetes. We aimed to identify more of these variants and test the hypothesis that such favorable adiposity alleles are associated with higher subcutaneous fat and lower ectopic fat. We combined MRI data with genome-wide association studies of body fat percentage (%) and metabolic traits. We report 14 alleles, including 7 newly characterized alleles, associated with higher adiposity but a favorable metabolic profile. Consistent with previous studies, individuals carrying more favorable adiposity alleles had higher body fat % and higher BMI but lower risk of type 2 diabetes, heart disease, and hypertension. These individuals also had higher subcutaneous fat but lower liver fat and a lower visceral-to-subcutaneous adipose tissue ratio. Individual alleles associated with higher body fat % but lower liver fat and lower risk of type 2 diabetes included those in PPARG, GRB14, and IRS1, whereas the allele in ANKRD55 was paradoxically associated with higher visceral fat but lower risk of type 2 diabetes. Most identified favorable adiposity alleles are associated with higher subcutaneous and lower liver fat, a mechanism consistent with the beneficial effects of storing excess triglycerides in metabolically low-risk depots.

A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure

Fibroblast growth factor 21 (FGF21) is a hormone that has insulin-sensitizing properties. Some trials of FGF21 analogs show weight loss and lipid-lowering effects. Recent studies have shown that a common allele in the FGF21 gene alters the balance of macronutrients consumed, but there was little evidence of an effect on metabolic traits. We studied a common FGF21 allele (A:rs838133) in 451,099 people from the UK Biobank study, aiming to use the human allele to inform potential adverse and beneficial effects of targeting FGF21. We replicated the association between the A allele and higher percentage carbohydrate intake. We then showed that this allele is more strongly associated with higher blood pressure and waist-hip ratio, despite an association with lower total body-fat percentage, than it is with BMI or type 2 diabetes. These human phenotypes of variation in the FGF21 gene will inform research into FGF21's mechanisms and therapeutic potential.

Influence of cell distribution and diabetes status on the association between mitochondrial DNA copy number and aging phenotypes in the InCHIANTI study

Mitochondrial DNA copy number (mtDNA-CN) estimated in whole blood is a novel marker of mitochondrial mass and function that can be used in large population-based studies. Analyses that attempt to relate mtDNA-CN to specific aging phenotypes may be confounded by differences in the distribution of blood cell types across samples. Also, low or high mtDNA-CN may have a different meaning given the presence of diseases associated with mitochondrial damage. We evaluated the impact of blood cell type distribution and diabetes status on the association between mtDNA-CN and aging phenotypes, namely chronologic age, interleukin-6, hemoglobin, and all-cause mortality, among 672 participants of the InCHIANTI study. After accounting for white blood cell count, platelet count, and white blood cell proportions in multivariate models, associations of mtDNA-CN with age and interleukin-6 were no longer statistically significant. Evaluation of a statistical interaction by diabetes status suggested heterogeneity of effects in the analysis of mortality (P < 0.01). The magnitude and direction of associations between mtDNA-CN estimated from blood samples and aging phenotypes are influenced by the sample cell type distribution and disease status. Therefore, accounting for these factors may aid understanding of the relevance of mitochondrial DNA copy number to health and aging.

Red blood cell distribution width: Genetic evidence for aging pathways in 116,666 volunteers

INTRODUCTION

Variability in red blood cell volumes (distribution width, RDW) increases with age and is strongly predictive of mortality, incident coronary heart disease and cancer. We investigated inherited genetic variation associated with RDW in 116,666 UK Biobank human volunteers.

RESULTS

A large proportion RDW is explained by genetic variants (29%), especially in the older group (60+ year olds, 33.8%, <50 year olds, 28.4%). RDW was associated with 194 independent genetic signals; 71 are known for conditions including autoimmune disease, certain cancers, BMI, Alzheimer's disease, longevity, age at menopause, bone density, myositis, Parkinson's disease, and age-related macular degeneration. Exclusion of anemic participants did not affect the overall findings. Pathways analysis showed enrichment for telomere maintenance, ribosomal RNA, and apoptosis. The majority of RDW-associated signals were intronic (119 of 194), including SNP rs6602909 located in an intron of oncogene GAS6, an eQTL in whole blood.

CONCLUSIONS

Although increased RDW is predictive of cardiovascular outcomes, this was not explained by known CVD or related lipid genetic risks, and a RDW genetic score was not predictive of incident disease. The predictive value of RDW for a range of negative health outcomes may in part be due to variants influencing fundamental pathways of aging.

Quantifying the extent to which index event biases influence large genetic association studies

As genetic association studies increase in size to 100 000s of individuals, subtle biases may influence conclusions. One possible bias is 'index event bias' (IEB) that appears due to the stratification by, or enrichment for, disease status when testing associations between genetic variants and a disease-associated trait. We aimed to test the extent to which IEB influences some known trait associations in a range of study designs and provide a statistical framework for assessing future associations. Analyzing data from 113 203 non-diabetic UK Biobank participants, we observed three (near TCF7L2, CDKN2AB and CDKAL1) overestimated (body mass index (BMI) decreasing) and one (near MTNR1B) underestimated (BMI increasing) associations among 11 type 2 diabetes risk alleles (at P  <  0.05). IEB became even stronger when we tested a type 2 diabetes genetic risk score composed of these 11 variants (-0.010 standard deviations BMI per allele, P  =  5 × 10- 4), which was confirmed in four additional independent studies. Similar results emerged when examining the effect of blood pressure increasing alleles on BMI in normotensive UK Biobank samples. Furthermore, we demonstrated that, under realistic scenarios, common disease alleles would become associated at P <  5 × 10- 8 with disease-related traits through IEB alone, if disease prevalence in the sample differs appreciably from the background population prevalence. For example, some hypertension and type 2 diabetes alleles will be associated with BMI in sample sizes of  >500 000 if the prevalence of those diseases differs by >10% from the background population. In conclusion, IEB may result in false positive or negative genetic associations in very large studies stratified or strongly enriched for/against disease cases.

Gene-obesogenic environment interactions in the UK Biobank study

Background

Previous studies have suggested that modern obesogenic environments accentuate the genetic risk of obesity. However, these studies have proven controversial as to which, if any, measures of the environment accentuate genetic susceptibility to high body mass index (BMI).

Methods

We used up to 120 000 adults from the UK Biobank study to test the hypothesis that high-risk obesogenic environments and behaviours accentuate genetic susceptibility to obesity. We used BMI as the outcome and a 69-variant genetic risk score (GRS) for obesity and 12 measures of the obesogenic environment as exposures. These measures included Townsend deprivation index (TDI) as a measure of socio-economic position, TV watching, a 'Westernized' diet and physical activity. We performed several negative control tests, including randomly selecting groups of different average BMIs, using a simulated environment and including sun-protection use as an environment.

Results

We found gene-environment interactions with TDI (Pinteraction = 3 × 10 -10 ), self-reported TV watching (Pinteraction = 7 × 10 -5 ) and self-reported physical activity (Pinteraction = 5 × 10 -6 ). Within the group of 50% living in the most relatively deprived situations, carrying 10 additional BMI-raising alleles was associated with approximately 3.8 kg extra weight in someone 1.73 m tall. In contrast, within the group of 50% living in the least deprivation, carrying 10 additional BMI-raising alleles was associated with approximately 2.9 kg extra weight. The interactions were weaker, but present, with the negative controls, including sun-protection use, indicating that residual confounding is likely.

Conclusions

Our findings suggest that the obesogenic environment accentuates the risk of obesity in genetically susceptible adults. Of the factors we tested, relative social deprivation best captures the aspects of the obesogenic environment responsible.

Genome-wide associations for birth weight and correlations with adult disease

Birth weight (BW) has been shown to be influenced by both fetal and maternal factors and in observational studies is reproducibly associated with future risk of adult metabolic diseases including type 2 diabetes (T2D) and cardiovascular disease. These life-course associations have often been attributed to the impact of an adverse early life environment. Here, we performed a multi-ancestry genome-wide association study (GWAS) meta-analysis of BW in 153,781 individuals, identifying 60 loci where fetal genotype was associated with BW (P < 5 × 10-8). Overall, approximately 15% of variance in BW was captured by assays of fetal genetic variation. Using genetic association alone, we found strong inverse genetic correlations between BW and systolic blood pressure (Rg = -0.22, P = 5.5 × 10-13), T2D (Rg = -0.27, P = 1.1 × 10-6) and coronary artery disease (Rg = -0.30, P = 6.5 × 10-9). In addition, using large -cohort datasets, we demonstrated that genetic factors were the major contributor to the negative covariance between BW and future cardiometabolic risk. Pathway analyses indicated that the protein products of genes within BW-associated regions were enriched for diverse processes including insulin signalling, glucose homeostasis, glycogen biosynthesis and chromatin remodelling. There was also enrichment of associations with BW in known imprinted regions (P = 1.9 × 10-4). We demonstrate that life-course associations between early growth phenotypes and adult cardiometabolic disease are in part the result of shared genetic effects and identify some of the pathways through which these causal genetic effects are mediated.

Genome-Wide Association Analyses in 128,266 Individuals Identifies New Morningness and Sleep Duration Loci

Disrupted circadian rhythms and reduced sleep duration are associated with several human diseases, particularly obesity and type 2 diabetes, but until recently, little was known about the genetic factors influencing these heritable traits. We performed genome-wide association studies of self-reported chronotype (morning/evening person) and self-reported sleep duration in 128,266 white British individuals from the UK Biobank study. Sixteen variants were associated with chronotype (P<5x10^-8), including variants near the known circadian rhythm genes RGS16 (1.21 odds of morningness, 95% CI [1.15, 1.27], P = 3x10^-12) and PER2 (1.09 odds of morningness, 95% CI [1.06, 1.12], P = 4x10^-10). The PER2 signal has previously been associated with iris function. We sought replication using self-reported data from 89,283 23andMe participants; thirteen of the chronotype signals remained associated at P<5x10^-8 on meta-analysis and eleven of these reached P<0.05 in the same direction in the 23andMe study. We also replicated 9 additional variants identified when the 23andMe study was used as a discovery GWAS of chronotype (all P<0.05 and meta-analysis P<5x10^-8). For sleep duration, we replicated one known signal in PAX8 (2.6 minutes per allele, 95% CI [1.9, 3.2], P = 5.7x10^-16) and identified and replicated two novel associations at VRK2 (2.0 minutes per allele, 95% CI [1.3, 2.7], P = 1.2x10^-9; and 1.6 minutes per allele, 95% CI [1.1, 2.2], P = 7.6x10^-9). Although we found genetic correlation between chronotype and BMI (rG = 0.056, P = 0.05); undersleeping and BMI (rG = 0.147, P = 1x10^-5) and oversleeping and BMI (rG = 0.097, P = 0.04), Mendelian Randomisation analyses, with limited power, provided no consistent evidence of causal associations between BMI or type 2 diabetes and chronotype or sleep duration. Our study brings the total number of loci associated with chronotype to 22 and with sleep duration to three, and provides new insights into the biology of sleep and circadian rhythms in humans.

Numerous studies have identified links between too little or too much sleep and circadian misalignment with metabolic disorders such as obesity and type 2 diabetes. However, cause-and-effect is not easily determined, because of multiple confounding factors affecting both sleep patterns and disease risk. Using the first release of the UK Biobank study, which combines detailed measurements and questionnaire data with genetic data, we investigate the genetics of two self-report sleep measures, chronotype and average sleep duration, in 128,266 white British individuals. We replicate previous genetic associations and identify seven and two novel genetic variants influencing chronotype and sleep duration, respectively. Associated variants are located near genes implicated in circadian rhythm regulation (RGS16, PER2), near a serotonin receptor gene (HTR6) and another gene (INADL) encoding a protein thought to be important in photosensitive retinal cells, cells known to communicate with the brain’s primary circadian pacemaker. Using the genetic risk factors, we estimate the unconfounded causal associations of BMI and type 2 diabetes on sleep patterns (and vice versa) through Mendelian Randomisation. However, we find no evidence for causal associations in either direction. The full UK Biobank release of 500,000 individuals will boost our power to detect causal associations.

Genetic Evidence for a Link Between Favorable Adiposity and Lower Risk of Type 2 Diabetes, Hypertension, and Heart Disease

Recent genetic studies have identified some alleles that are associated with higher BMI but lower risk of type 2 diabetes, hypertension, and heart disease. These "favorable adiposity" alleles are collectively associated with lower insulin levels and higher subcutaneous-to-visceral adipose tissue ratio and may protect from disease through higher adipose storage capacity. We aimed to use data from 164,609 individuals from the UK Biobank and five other studies to replicate associations between a genetic score of 11 favorable adiposity variants and adiposity and risk of disease, to test for interactions between BMI and favorable adiposity genetics, and to test effects separately in men and women. In the UK Biobank, the 50% of individuals carrying the most favorable adiposity alleles had higher BMIs (0.120 kg/m(2) [95% CI 0.066, 0.174]; P = 1E-5) and higher body fat percentage (0.301% [0.230, 0.372]; P = 1E-16) compared with the 50% of individuals carrying the fewest alleles. For a given BMI, the 50% of individuals carrying the most favorable adiposity alleles were at lower risk of type 2 diabetes (odds ratio [OR] 0.837 [0.784, 0.894]; P = 1E-7), hypertension (OR 0.935 [0.911, 0.958]; P = 1E-7), and heart disease (OR 0.921 [0.872, 0.973]; P = 0.003) and had lower blood pressure (systolic -0.859 mmHg [-1.099, -0.618]; P = 3E-12 and diastolic -0.394 mmHg [-0.534, -0.254]; P = 4E-8). In women, these associations could be explained by the observation that the alleles associated with higher BMI but lower risk of disease were also associated with a favorable body fat distribution, with a lower waist-to-hip ratio (-0.004 cm [95% CI -0.005, -0.003] 50% vs. 50%; P = 3E-14), but in men, the favorable adiposity alleles were associated with higher waist circumference (0.454 cm [0.267, 0.641] 50% vs. 50%; P = 2E-6) and higher waist-to-hip ratio (0.0013 [0.0003, 0.0024] 50% vs. 50%; P = 0.01). Results were strengthened when a meta-analysis with five additional studies was conducted. There was no evidence of interaction between a genetic score consisting of known BMI variants and the favorable adiposity genetic score. In conclusion, different molecular mechanisms that lead to higher body fat percentage (with greater subcutaneous storage capacity) can have different impacts on cardiometabolic disease risk. Although higher BMI is associated with higher risk of diseases, better fat storage capacity could reduce the risk.

New quality measure for SNP array based CNV detection

MOTIVATION

Only a few large systematic studies have evaluated the impact of copy number variants (CNVs) on common diseases. Several million individuals have been genotyped on single nucleotide variation arrays, which could be used for genome-wide CNVs association studies. However, CNV calls remain prone to false positives and only empirical filtering strategies exist in the literature. To overcome this issue, we defined a new quality score (QS) estimating the probability of a CNV called by PennCNV to be confirmed by other software.

RESULTS

Out-of-sample comparison showed that the correlation between the consensus CNV status and the QS is twice as high as it is for any previously proposed CNV filters. ROC curves displayed an AUC higher than 0.8 and simulations showed an increase up to 20% in statistical power when using QS in comparison to other filtering strategies. Superior performance was confirmed also for alternative consensus CNV definition and through improving known CNV-trait associations.

AVAILABILITY AND IMPLEMENTATION

http://goo.gl/T6yuFM CONTACT: zoltan.kutalik@unil.ch or aurelien@mace@unil.chSupplementary information: Supplementary data are available at Bioinformatics online.

Variants in the FTO and CDKAL1 loci have recessive effects on risk of obesity and type 2 diabetes, respectively

AIMS/HYPOTHESIS

Genome-wide association (GWA) studies have identified hundreds of common genetic variants associated with obesity and type 2 diabetes. These studies have usually focused on additive association tests. Identifying deviations from additivity may provide new biological insights and explain some of the missing heritability for these diseases.

METHODS

We performed a GWA study using a dominance deviation model for BMI, obesity (29,925 cases) and type 2 diabetes (4,040 cases) in 120,286 individuals of British ancestry from the UK Biobank study. We also investigated whether single nucleotide polymorphisms previously shown to be associated with these traits showed any enrichment for departures from additivity.

RESULTS

Known obesity-associated variants in FTO showed strong evidence of deviation from additivity (p DOMDEV = 3 × 10(-5)) through a recessive effect of the allele associated with higher BMI. The average BMI of individuals carrying zero, one or two BMI-raising alleles was 27.27 (95% CI 27.22, 27.31) kg/m(2), 27.54 (95% CI 27.50, 27.58) kg/m(2) and 28.07 (95% CI 28.00, 28.14) kg/m(2), respectively. A similar effect was observed in 105,643 individuals from the GIANT Consortium (p DOMDEV = 0.003; meta-analysis p DOMDEV = 1 × 10(-7)). For type 2 diabetes, we detected a recessive effect (p DOMDEV = 5 × 10(-4)) at CDKAL1. Relative to homozygous non-risk allele carriers, homozygous risk allele carriers had an OR of 1.48 (95% CI 1.32, 1.65), while the heterozygous group had an OR of 1.06 (95% CI 0.99, 1.14), a result consistent with that of a previous study. We did not identify any novel associations at genome-wide significance.

CONCLUSIONS/INTERPRETATION

Although we found no evidence of widespread non-additive genetic effects contributing to obesity and type 2 diabetes risk, we did find robust examples of recessive effects at the FTO and CDKAL1 loci.

ACCESS TO RESEARCH MATERIALS

Summary statistics are available at www.t2diabetesgenes.org and by request (a.r.wood@exeter.ac.uk). All underlying data are available on application from the UK Biobank.

Human longevity is influenced by many genetic variants: evidence from 75,000 UK Biobank participants

Variation in human lifespan is 20 to 30% heritable in twins but few genetic variants have been identified. We undertook a Genome Wide Association Study (GWAS) using age at death of parents of middle-aged UK Biobank participants of European decent (n=75,244 with father's and/or mother's data, excluding early deaths). Genetic risk scores for 19 phenotypes (n=777 proven variants) were also tested. In GWAS, a nicotine receptor locus(CHRNA3, previously associated with increased smoking and lung cancer) was associated with fathers' survival. Less common variants requiring further confirmation were also identified. Offspring of longer lived parents had more protective alleles for coronary artery disease, systolic blood pressure, body mass index, cholesterol and triglyceride levels, type-1 diabetes, inflammatory bowel disease and Alzheimer's disease. In candidate analyses, variants in the TOMM40/APOE locus were associated with longevity, but FOXO variants were not. Associations between extreme longevity (mother >=98 years, fathers >=95 years, n=1,339) and disease alleles were similar, with an additional association with HDL cholesterol (p=5.7x10-3). These results support a multiple protective factors model influencing lifespan and longevity (top 1% survival) in humans, with prominent roles for cardiovascular-related pathways. Several of these genetically influenced risks, including blood pressure and tobacco exposure, are potentially modifiable.

Genetic evidence that lower circulating FSH levels lengthen menstrual cycle, increase age at menopause and impact female reproductive health

STUDY QUESTION

How does a genetic variant in the FSHB promoter, known to alter FSH levels, impact female reproductive health?

SUMMARY ANSWER

The T allele of the FSHB promoter polymorphism (rs10835638; c.-211G>T) results in longer menstrual cycles and later menopause and, while having detrimental effects on fertility, is protective against endometriosis.

WHAT IS KNOWN ALREADY

The FSHB promoter polymorphism (rs10835638; c.-211G>T) affects levels of FSHB transcription and, as a result, circulating levels of FSH. FSH is required for normal fertility and genetic variants at the FSHB locus are associated with age at menopause and polycystic ovary syndrome (PCOS).

STUDY DESIGN, SIZE, DURATION

We used cross-sectional data from the UK Biobank to look at associations between the FSHB promoter polymorphism and reproductive traits, and performed a genome-wide association study (GWAS) for length of menstrual cycle.

PARTICIPANTS/MATERIALS, SETTING, METHODS

We included white British individuals aged 40-69 years in 2006-2010, in the May 2015 release of genetic data from UK Biobank. We tested the FSH-lowering T allele of the FSHB promoter polymorphism (rs10835638; c.-211G>T) for associations with 29, mainly female, reproductive phenotypes in up to 63 350 women and 56 608 men. We conducted a GWAS in 9534 individuals to identify genetic variants associated with length of menstrual cycle.

MAIN RESULTS AND THE ROLE OF CHANCE

The FSH-lowering T allele of the FSHB promoter polymorphism (rs10835638; MAF 0.16) was associated with longer menstrual cycles [0.16 SD (c. 1 day) per minor allele; 95% confidence interval (CI) 0.12-0.20; P = 6 × 10(-16)], later age at menopause (0.13 years per minor allele; 95% CI 0.04-0.22; P = 5.7 × 10(-3)), greater female nulliparity [odds ratio (OR) = 1.06; 95% CI 1.02-1.11; P = 4.8 × 10(-3)] and lower risk of endometriosis (OR = 0.79; 95% CI 0.69-0.90; P = 4.1 × 10(-4)). The FSH-lowering T allele was not associated with other female reproductive illnesses or conditions in our study and we did not replicate associations with male infertility or PCOS. In the GWAS for menstrual cycle length, only variants near the FSHB gene reached genome-wide significance (P < 5 × 10(-9)).

LIMITATIONS, REASONS FOR CAUTION

The data included might be affected by recall bias. Cycle length was not available for 25% of women still cycling (1% did not answer, 6% did not know and for 18% cycle length was recorded as 'irregular'). Women with a cycle length recorded were aged over 40 and were approaching menopause; however, we did not find evidence that this affected the results. Many of the groups with illnesses had relatively small sample sizes and so the study may have been under-powered to detect an effect.

WIDER IMPLICATIONS OF THE FINDINGS

We found a strong novel association between a genetic variant that lowers FSH levels and longer menstrual cycles, at a locus previously robustly associated with age at menopause. The variant was also associated with nulliparity and endometriosis risk. These findings should now be verified in a second independent group of patients. We conclude that lifetime differences in circulating levels of FSH between individuals can influence menstrual cycle length and a range of reproductive outcomes, including menopause timing, infertility, endometriosis and PCOS.

STUDY FUNDING/COMPETING INTERESTS

None.

TRIAL REGISTRATION NUMBER

Not applicable.

Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes

Initial results from sequencing studies suggest that there are relatively few low-frequency (<5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency–large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant–common phenotype associations—11 132 cis-gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (<5%), respectively, low frequency–large effect associations comprised 7% of detectable cis-gene expression traits [89 of 1314 cis-eQTLs at P < 1 × 10⁻⁰⁶ (false discovery rate ∼5%)] and one of eight biomarker associations at P < 8 × 10⁻¹⁰. Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect.

Wear in alumina-on-alumina ceramic total hip replacements: a retrieval analysis of edge loading

We analysed 54 alumina ceramic-on-ceramic bearings from total hip replacements retrieved at one centre after a mean duration of 3.5 years (0.2 to 10.6) in situ. These implants were obtained from 54 patients (16 men and 38 women) with a mean age of 67 years (33 to 88) who underwent revision for a variety of reasons. Posterior edge loading was found in the majority of these retrievals (32 out of 54). Anterosuperior edge loading occurred less often but produced a higher rate of wear. Stripe wear on the femoral heads had a median volumetric wear rate of 0.2 mm(3)/year (0 to 7.2). The wear volume on the femoral heads corresponded to the width of edge wear on the matching liner. Anteversion of the acetabular component was found to be a more important determinant than inclination for wear in ceramic bearings. Posterior edge loading may be considered to be a normal occurrence in ceramic-on-ceramic bearings, with minimal clinical consequences. Edge loading should be defined as either anterosuperior or posterior, as each edge loading mechanism may result in different clinical implications.

The tribological behaviour of different clearance MOM hip joints with lubricants of physiological viscosities

Clearance is one of the most influential parameters on the tribological performance of metal-on-metal (MOM) hip joints and its selection is a subject of considerable debate. The objective of this paper is to study the lubrication behaviour of different clearances for MOM hip joints within the range of human physiological and pathological fluid viscosities. The frictional torques developed by MOM hip joints with a 50 mm diameter were measured for both virgin surfaces and during a wear simulator test. Joints were manufactured with three different diametral clearances: 20, 100, and 200 microm. The fluid used for the friction measurements which contained different ratios of 25 percent newborn calf serum and carboxymethyl cellulose (CMC) with the obtained viscosities values ranging from 0.001 to 0.71 Pa s. The obtained results indicate that the frictional torque for the 20 microm clearance joint remains high over the whole range of the viscosity values. The frictional torque of the 100 microm clearance joint was low for the very low viscosity (0.001 Pa s) lubricant, but increased with increasing viscosity value. The frictional torque of the 200 microm clearance joint was high at very low viscosity levels, however, it reduced with increasing viscosity. It is concluded that a smaller clearance level can enhance the formation of an elastohydrodynamic lubrication (EHL) film, but this is at the cost of preventing fluid recovery between the bearing surfaces during the unloaded phase of walking. Larger clearance bearings allow a better recovery of lubricant during the unloaded phase, which is necessary for higher viscosity lubricants. The selection of the clearance value should therefore consider both the formation of the EHL film and the fluid recovery as a function of the physiological viscosity in order to get an optimal tribological performance for MOM hip joints. The application of either 25 per cent bovine serum or water in existing in vitro tribological study should also be revised to consider the relevance of clinic synovial fluid viscosities and to avoid possible misleading results.

Retrieval analysis of squeaking alumina ceramic-on-ceramic bearings

This multicentre study analysed 12 alumina ceramic-on-ceramic components retrieved from squeaking total hip replacements after a mean of 23 months in situ (11 to 61). The rates and patterns of wear seen in these squeaking hips were compared with those seen in matched controls using retrieval data from 33 'silent' hip replacements with similar ceramic bearings. All 12 bearings showed evidence characteristic of edge-loading wear. The median rate of volumetric wear was 3.4 mm(3)/year for the acetabular component, 2.9 mm(3)/year on the femoral heads and 6.3 mm(3)/year for head and insert combined. This was up to 45 times greater than that of previously reported silent ceramic-on-ceramic retrievals. The rate of wear seen in ceramic components revised for squeaking hips appears to be much greater than in that seen in retrievals from 'silent' hips.

Wear and acetabular component orientation in third generation alumina-on-alumina ceramic bearings: an analysis of 33 retrievals [corrected]

We studied 33 third generation, alumina ceramic-on-ceramic bearings retrieved from cementless total hip replacements after more than six months in situ. Wear volume was measured with a Roundtest machine, and acetabular orientation from the anteroposterior pelvic radiograph. The overall median early wear rate was 0.1 mm(3)/yr for the femoral heads, and 0.04 mm(3)/yr for the acetabular liners. We then excluded hips where the components had migrated. In this stable subgroup of 22 bearings, those with an acetabular anteversion of < 15 degrees (seven femoral heads) had a median femoral head wear rate of 1.2 mm(3)/yr, compared with 0 mm(3)/yr for those with an anteversion of > or =15 degrees (15 femoral heads, p < 0.001). Even under edge loading, wear volumes with ceramic-on-ceramic bearings are small in comparison to other bearing materials. Low acetabular anteversion is associated with greater wear.

In vivo biocompatibility and mechanical study of novel bone-bioactive materials for prosthetic implantation

Two epoxy materials with or without adhesively bonded hydroxyapatite (HA) coatings were studied for their biocompatibility and mechanical pushout strength using in vivo implantation in the rabbit lower femur for a duration of 10 days to 6 months. Both were two-part epoxies cured at room temperature for 24 h, with material 1 (Ampreg 26; SP Systems Limited, Cowes, UK) postcured at 110 degrees C (Tg approximately 80 degrees C) and Material 2 (CG5052; Ciba Geigy Limited, Cambridge, UK) at 125 degrees C (Tg approximately 120 degrees C). Implantation in dead rabbit bone was performed to provide mechanical baseline levels. Polymethylmethacrylate (PMMA) and conventionally HA-coated titanium alloy (Ti-6Al-4V) were used as control materials. In the biological study, different fluorescent dyes were used to label newly formed bone. After 6 weeks of implantation, results from mechanical pushout tests showed that the interfacial shear strength (ISS) values were significantly higher than for dead bones with each of the different implants (p < .01-.001). HA-coated material 2 showed a significantly higher ISS value than the uncoated material (p < .05) after 6 weeks' implantation. However, the ISS value for the uncoated material 2 was significantly higher than for PMMA controls (p < .05). No significant differences in the ISS values were shown between HA-coated materials 1 and 2 and Ti-6Al-4V on in vivo implantation for 6 weeks. Failure points of the pushout test from the three HA-coated materials were defined by scanning electron microscopy. Specimens implanted with both HA-coated epoxies were fractured within the HA-coatings or the bone, while with HA-coated Ti-6Al-4V cracked between the coating and metal implant. The percentage of bone in contact with the implant surface was obtained by image analysis which showed that there were no significant differences between different materials after short time implantation (up to 6 week). Long-term implantation of the HA-coated material 2 showed that the percentage of bone contact had increased from 52.8+/-1.1% (6 week) to 80.0+/-0.3% (3 months) (p < .01) and remained at 81.0+/-0.8% (6 months). Measurements of bone mineralization rate (BMR) showed that after 3 weeks of implantation, there were no significant differences between PMMA and uncoated materials 1 and 2. After 6 weeks, the BMRs in animals implanted with either HA-coated material 1 or 2 were significantly higher than with HA-coated Ti-6Al-4V (p < .05-.0001 in both cases), but with HA-coated material 2 was lower than with this material uncoated (p < .05-.001). No significant differences were found between the two HA-coated epoxy materials. In addition, there were always lower BMRs during the third week of implantation than other periods regardless of biomaterial implanted. The study indicated that the adhesively bonded HA-coated novel epoxy materials were superior to conventional plasma-sprayed Ti-6Al-4V implants with respect to both BMR and bone integration with the implant surfaces. Adhesively bonded HA-coated epoxy materials had similar ISS values to HA-coated Ti-6Al-4V, but the former failed within the bone and coating, while the latter showed splitting between coating and metal.

Wear induced by motion between bone and titanium or cobalt-chrome alloys

We studied the wear generated by motion between polished and shot-blasted titanium-alloy (Ti-6Al-4V) or cobalt-chrome alloy (Co-Cr) surfaces and cortical bone in vitro. Semicircular sections of human proximal femoral cortex were reamed to fit metal cylinders of each alloy. The cylinders were then fitted in the bone, loaded and rotated in physiological saline. Ti-alloy resulted in more wear both of the bone and of the metal than did Co-Cr alloy. Metal wear was reduced and bone wear was increased by shot-blasting, a procedure which introduces surface residual stresses and roughens the metal surface. We conclude that when there is gross motion between a metal implant and bone, Ti-alloy is likely to generate more wear debris than Co-Cr alloy. The least wear both of bone and of metal was produced by polished Co-Cr.

Wear induced by motion between bone and titanium or cobalt-chrome alloys

We studied the wear generated by motion between polished and shot-blasted titanium-alloy (Ti-6Al-4V) or cobalt-chrome alloy (Co-Cr) surfaces and cortical bone in vitro. Semicircular sections of human proximal femoral cortex were reamed to fit metal cylinders of each alloy. The cylinders were then fitted in the bone, loaded and rotated in physiological saline. Ti-alloy resulted in more wear both of the bone and of the metal than did Co-Cr alloy. Metal wear was reduced and bone wear was increased by shot-blasting, a procedure which introduces surface residual stresses and roughens the metal surface. We conclude that when there is gross motion between a metal implant and bone, Ti-alloy is likely to generate more wear debris than Co-Cr alloy. The least wear both of bone and of metal was produced by polished Co-Cr.

Evaluation of wear in an all-polymer total knee replacement. Part 2: clinical evaluation of wear in a polyethylene on polyacetal total knee

In an effort to improve the long-term result of total joint replacement arthroplasty, we have investigated the use of a polymer-on-polymer articular replacement arthroplasty. Because of their known biocompatibility and previous use in orthopedic surgery, polyethylene and polyacetal (copolymer, Hoechst) were selected. Polyethylene served in its usual role as the concave member of the articulation; polyacetal formed the convex number. Formal wear testing using a multi-channel hip simulator demonstrated superior wear characteristics of the polymer-on-polymer configuration compared to a conventional chrome-cobalt versus polymer (polyethylene) configuration. A clinical series of relatively high-activity patients having a minimum five-year follow-up (N = 26) showed no specific unfavorable reaction to this material combination in a total knee replacement. Given certain potential advantages of polymeric materials, as well as some theoretical disadvantages of metallic materials, a polymer-on-polymer design for a large joint replacement may have some merit.

Implant arthroplasty in the adult hindfoot

In patients with mild to moderate valgus deformity and localized pain due to lateral impingement, the subtalar implant has been effective in controlling position and relieving localized pain. When used in conjunction with a talonavicular resurfacing prosthesis in the absence of talonavicular subluxation, the implant has been effective in relieving pain and maintaining the foot in a normal or nearly normal position. In feet with valgus deformity and talonavicular subluxation, both the subtalar implant and the talonavicular prosthesis with a built-in stop must be used. Use of these implants requires that the foot be supple and correctable to at least neutral position at surgery. The valgus hindfoot with a subluxated but otherwise normal talonavicular joint presents a greater problem. In this condition correction can be maintained only if the subtalar implant is used in conjunction with the modified talonavicular joint with a built-in stop. External supports in the shoe have not been routinely used in all patients after operation for a variety of reasons (mostly nonmedical). It may be advisable in patients who have had correction of a deformity to continue to use some sort of support in the shoe for most ambulation. Arthroplasty early in the disease course, before severe deformities develop, may prevent progression of the disorder, but more experience is necessary to validate clinical impressions.

Development and evolution of the ICLH ankle replacement

In 1972 the original ICLH ankle was first used clinically, and since then the authors have implanted 75 ICLH ankles. The overall percentage of acceptable results in this series is about 70%. The most frequent complication seen was delayed wound healing. Talomalleolar contact with resultant pain was a significant problem early in the series. Partial collapse of the talus has occurred in five ankles. Our experience has shown that it is possible to replace the ankle and initially achieve a functioning, pain-free arthroplasty. There are many factors that may adversely influence the ultimate outcome; and thus, the procedure should be approached with caution.

The effects of proteolytic enzymes on the mechanical properties of adult human articular cartilage

The effects of the lysosomal proteinase cathepsin D on the mechanical properties of adult human articular cartilage were examined in detail in 7 joints within the age range 21 to 72 years. The results of a preliminary study on the effects of the lysosomal proteinase cathepsin B1 and clostridial collagenase on the mechanical properties of cartilage are also presented. Cartilage which had been incubated with either cathepsin D or cathepsin B1 showed increased deformation in uniaxial compression perpendicular to the articular surface. The enzyme-treated cartilage also showed decreased tensile stiffness at low values of stress. This effect was more pronounced in specimens from the deeper zone of cartilage than in specimens from the superficial zone. It was also more pronounced in specimens which were aligned perpendicular to the predominant alignment of the collagen fibres in the superficial zone than in specimens which were parallel to the collagen fibres. At higher stresses the tensile stiffness of the treated cartilage was not significantly different from that of the untreated tissue. The tensile fracture stress of the cartilage was also not significantly reduced by the action of cathepsin D. In contrast to the effects observed with the cathepsins, the preliminary results obtained by incubating cartilage for 24 h with clostridial collagenase showed that both the tensile stiffness and the fracture stress were considerably lower than the corresponding values for the untreated tissue. Biochemical analysis of the incubation media, and the specimens, revealed that a large proportion of the proteoglycans was released from the cartilage by each of the three enzymes. The proportion of the total collagen which was released from the cartilage was different for each enzyme: cathepsin D released between 0 and 1.5 per cent, cathepsin B1 released between 2.3 and 4.3 per cent and collagenase released between 5.3 and 27.8 per cent of the collagen after 24 h.