The Genome of the Netherlands: Design, and project goals

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project

WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary and environmental factors regulating TL are currently widely investigated, however, their relative contribution to TL variability is still understudied. We have used whole genome sequencing data of 250 family trios from the Genome of the Netherlands project to perform computational measurement of TL and a series of regression and genome-wide association analyses to reveal TL inheritance patterns and associated genetic factors. Our results confirm that TL is a largely heritable trait, primarily with mother’s, and, to a lesser extent, with father’s TL having the strongest influence on the offspring. In this cohort, mother’s, but not father’s age at conception was positively linked to offspring TL. Age-related TL attrition of 40 bp/year had relatively small influence on TL variability. Finally, we have identified TL-associated variations in ribonuclease reductase catalytic subunit M1 (RRM1 gene), which is known to regulate telomere maintenance in yeast. We also highlight the importance of multivariate approach and the limitations of existing tools for the analysis of TL as a polygenic heritable quantitative trait

The Prognostic Value of Troponin-T in Out-of-Hospital Cardiac Arrest Without ST-Segment Elevation: A COACT Substudy

Background: In out-of-hospital cardiac arrest (OHCA) without ST-elevation, predictive markers that can identify those with a high risk of acute coronary syndrome are lacking. Methods: In this post hoc analysis of the Coronary Angiography after Cardiac Arrest (COACT) trial, the baseline, median, peak, and time-concentration curves of troponin-T (cTnT) (T-AUC) in OHCA patients without ST-elevation were studied. cTnT values were obtained at predefined time points at 0, 3, 6, 12, 24, 36, 28, and 72 hours after admission. All patients who died within the measurement period were not included. The primary outcome was the association between cTnT and 90-day survival. Secondary outcomes included the association of cTnT and acute thrombotic occlusions, acute unstable lesions, and left ventricular function. Results: In total, 352 patients were included in the analysis. The mean age was 64 ± 13 years (80.4% men). All cTnT measures were independent prognostic factors for mortality after adjustment for potential confounders age, sex, history of coronary artery disease, witnessed arrest, time to BLS, and time to return of spontaneous circulation (eg, for T-AUC: hazard ratio, 1.44; 95% CI, 1.06-1.94; P = .02; P value for all variables ≤ .02). Median cTnT (odds ratio [OR], 1.58; 95% CI, 1.18-2.12; P = .002) and T-AUC (OR, 2.03; 95% CI, 1.25-3.29; P = .004) were independent predictors for acute unstable lesions. Median cTnT (OR, 1.62; 95% CI, 1.17-2.23; P = .003) and T-AUC (OR, 2.16; 95% CI, 1.27-3.68; P = .004) were independent predictors for acute thrombotic occlusions. CTnT values were not associated with the left ventricular function (eg, for T-AUC: OR, 2.01; 95% CI, 0.65-6.19; P = .22; P value for all variables ≥ .14) Conclusion: In OHCA patients without ST-segment elevation, cTnT release during the first 72 hours after return of spontaneous circulation was associated with clinical outcomes

Data on sex differences in one-year outcomes of out-of-hospital cardiac arrest patients without ST-segment elevation

Sex differences in out-of-hospital cardiac arrest (OHCA) patients are increasingly recognized. Although it has been found that post-resuscitated women are less likely to have significant coronary artery disease (CAD) than men, data on follow-up in these patients are limited. Data for this data in brief article was obtained as a part of the randomized controlled Coronary Angiography after Cardiac Arrest without ST-segment elevation (COACT) trial. The data supplements the manuscript “Sex differences in out-of-hospital cardiac arrest patients without ST-segment elevation: A COACT trial substudy” were it was found that women were less likely to have significant CAD including chronic total occlusions, and had worse survival when CAD was present. The dataset presented in this paper describes sex differences on interventions, implantable-cardioverter defibrillator (ICD) shocks and hospitalizations due to heart failure during one-year follow-up in patients successfully resuscitated after OHCA. Data was derived through a telephone interview at one year with the patient or general practitioner. Patients in this randomized dataset reflects a homogenous study population, which can be valuable to further build on research regarding long-term sex differences and to further improve cardiac care

Skewed X-inactivation is common in the general female population

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants

On the origin of obesity and type 2 diabetes

The incidence of type 2 diabetes (T2D) is rising rapidly worldwide and there are already more than 180 million diabetic subjects. T2D risk factors include ethnic background, age, hypertension, overweight, increased abdominal fat, and lack of physical exercise. Obesity is considered to be the most important risk factor for T2D and the main one driving the current epidemic as 90% of T2D patients are obese. Worldwide obesity has also reached epidemic proportions, with 300 million adults classified as clinically obese. T2D and obesity are multifactorial disorders in which both genetic and non-genetic (environmental and lifestyle) factors play a role. The past years has witnessed substantial advances in understanding the genetic basis of obesity and T2D. To date, 17 common obesity loci and 18 common T2D loci have been identified. However, only around 10% of the genetic risk for these traits can be explained. Therefore, many more risk loci for obesity and T2D still need to be discovered. The high prevalence of T2D in many human populations poses a further evolutionary question: Why is the disease so common, when it should disappear as those genetically susceptible to it are removed by natural selection? In the present thesis we focus on (I) evaluating alternative methods to find candidate genes for T2D and obesity, (II) studying genetic and environmental risk factors for T2D and obesity, and (III) studying the origin of the high prevalence of T2D and obesity in modern societies. Both obesity and T2D are complex genetic traits but they share some non-genetic risk factors. In the introduction, chapter 2, we describe the genes recently identified for T2D and obesity by genome-wide association studies (GWAS) and evaluate their functions in an effort to determine whether there is any support for the hypothesis that T2D and obesity share some underlying mechanism(s). In the first, methodological, part of the thesis (part I), we use an alternative strategy to find candidate genes for obesity and T2D and explore alternative methods for the investigation of GWAS data to obtain valuable information on the biology and evolutionary origin of T2D. In chapter 3 we combine six tools for disease gene identification to analyse the overlapping T2D and obesity susceptibility loci to pinpoint shared candidate genes for T2D and obesity. In this study, we evaluated alternative methods to study GWAS data. Instead of focusing on the single nucleotide polymorphisms (SNPs) with the highest statistical significance, we took advantage of prior biological information and tried to detect overrepresented pathways in the GWAS data in chapter 4. We evaluated whether pathway classification analysis can help prioritize the biological pathways most likely to be involved in the disease etiology. Part II of the thesis reports on studies investigating genetic and environmental risk factors for T2D and obesity. In chapter 5 we investigated the role of variants in NPY1R, NPY2R and NPY5R genes, involved in the hypothalamic pathway, in total and nutrient-specific energy intake. In chapter 6, we investigate whether we can replicate the recently reported associations of the susceptibility loci with different obesity related phenotypes and explored the effect of variation in the currently implicated obesity genes affects on dietary energy and macronutrient intake. In chapter 7, we assessed the association between both parity and age at first full-term pregnancy with the risk of T2D in women. The studies, described in part III, aim to investigate the evolutionary explanation of obesity and T2D. In chapter 8 we tested a theory on the evolutionary origin of obesity and T2D, the thrifty gene hypothesis, by investigating whether recently identified T2D and obesity risk alleles have been under recent positive selection. In chapter 9 we investigate whether sub- or infertility predicts later-in-life T2D risk. To investigate body weight from a historical perspective, we studied weight distribution in an 18th century criminal gang (chapter 10). Chapter 11 provides a general discussion on the origin of obesity and T2D

Computational candidate gene prioritization for venous thrombosis

Thrombosis and Hemostasi

HHEX gene polymorphisms are associated with type 2 diabetes in the Dutch Breda cohort

Recently, the hematopoietically expressed homeobox ( HHEX) gene, encoding a transcription factor, was identified in a large genome-wide scan in French individuals as a type 2 diabetes ( T2D)-susceptibility locus. We aimed to check whether this finding could be replicated in a Dutch T2D cohort. Two common variants ( rs7923837 and rs1111875) located near the HHEX gene were genotyped in 501 unrelated T2D patients and in 920 healthy controls. The major alleles of both variants were overrepresented in T2D cases compared with controls ( 66.7 vs 64.1%, P = 0.16 for rs7923837 and 64.6 vs 60.4%, P = 0.027 for rs1111875). For both polymorphisms, the risk for T2D was significantly increased in carriers of the major alleles ( rs7923837: odds ratio ( OR): 1.57, 95% confidence interval ( CI): 1.08 - 2.27, P = 0.017 and rs1111875: OR: 1.68, 95% CI: 1.19 - 2.35, P = 0.003). The haplotype analysis did not reveal a risk haplotype that provided stronger evidence for association with T2D than each variant individually. Assuming a dominant genetic model, the population-attributable risks for diabetes due to the at- risk alleles of rs7923837 and rs1111875 were estimated to be 33 and 36%, respectively. These data provide evidence that variants near the HHEX gene contribute to the risk of T2D in a Dutch population

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic intro-gression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height