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Background: Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH)., Results: First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map., Conclusions: The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.

Heritability estimates of MetS range from approximately 10%-30%. The genetic variation that is shared among MetS features can be calculated by genetic correlation coefficients. The objective of this paper is to identify MetS feature as well as MetS related features which have much genetic variation in common, by reviewing the literature regarding genetic correlation coefficients. Identification of features, that have much genetic variation in common, may eventually facilitate the search for pleitropic genetic variants that may explain the clustering of MetS features. A PubMed search with the search terms "(metabolic syndrome OR insulin resistance syndrome) and (heritability OR genetic correlation OR pleiotropy)" was performed. Studies published before 7th July 2011, which presented genetic correlation coefficients between the different MetS features and genetic correlation coefficients of MetS and its features with adipose tissue-, pro-inflammatory and pro-thrombotic biomarkers were included. Nine twin and 19 family studies were included in the review. Genetic correlations varied, but were strongest between waist circumference and HOMA-IR (r(2): 0.36 to 0.79, median: 0.50), HDL cholesterol and triglycerides (r(2): -0.05 to -0.59, median -0.45), adiponectin and MetS (r(2): -0.32 to -0.43; median -0.38), adiponectin and insulin (r(2): -0.10 to -0.60; median -0.30) and between adiponectin and HDL-cholesterol (r(2): -0.22 to -0.51, median -0.29). In conclusion, heritability studies suggest that genetic pleiotropy exist especially between certain MetS features, as well as between MetS and adiponectin. Further research on actual genetic variants responsible for the genetic pleiotropy of these combinations will provide more insight into the etiology of MetS., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Several candidate gene studies on the metabolic syndrome (MetS) have been conducted. However, for most single nucleotide polymorphisms (SNPs) no systematic review on their association with MetS exists. A systematic electronic literature search was conducted until the 2nd of June 2010, using HuGE Navigator. English language articles were selected. Only genes of which at least one SNP-MetS association was studied in an accumulative total population ≥ 4000 subjects were included. Meta-analyses were conducted on SNPs with three or more studies available in a generally healthy population. In total 88 studies on 25 genes were reviewed. Additionally, for nine SNPs in seven genes (GNB3, PPARG, TCF7L2, APOA5, APOC3, APOE, CETP) a meta-analysis was conducted. The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3), C455T (APOC3) and 174G>C (IL6) were more prevalent in subjects with MetS, whereas the minor allele of Taq-1B (CETP) was less prevalent in subjects with the MetS. After having systematically reviewed the most studied SNP-MetS associations, we found evidence for an association with the MetS for eight SNPs, mostly located in genes involved in lipid metabolism., (© 2011 The Authors. obesity reviews © 2011 International Association for the Study of Obesity.)

Background: Our objective was to find single nucleotide polymorphisms (SNPs), within transcriptional pathways of glucose and lipid metabolism, which are related to multiple features of the metabolic syndrome (MetS)., Methods: 373 SNPs were measured in 3575 subjects of the Doetinchem cohort. Prevalence of MetS features, i.e. hyperglycemia, abdominal obesity, decreased HDL-cholesterol levels and hypertension, were measured twice in 6 years. Associations between the SNPs and the individual MetS features were analyzed by log-linear models. For SNPs related to multiple MetS features (P < 0.01), we investigated whether these associations were independent of each other., Results: Two SNPs, CETP Ile405Val and APOE Cys112Arg, were associated with both the prevalence of low HDL-cholesterol level (Ile405Val P = < .0001; Cys112Arg P = 0.001) and with the prevalence of abdominal obesity (Ile405Val P = 0.007; Cys112Arg P = 0.007). For both SNPs, the association with HDL-cholesterol was partly independent of the association with abdominal obesity and vice versa., Conclusion: Two SNPs, mainly known for their role in lipid metabolism, were associated with two MetS features i.e., low HDL-cholesterol concentration, as well as, independent of this association, abdominal obesity. These SNPs may help to explain why low HDL-cholesterol levels and abdominal obesity frequently co-occur.

Background: There is conflicting evidence regarding an association between the consumption of energy-dense snack (EDS) foods and the development of overweight., Objective: In the current study, we examined whether there was an association between the intake of EDS foods and annual weight and waist circumference changes in normal-weight and overweight Dutch adults., Design: The study population included 9383 men and women from the MORGEN-EPIC (Monitoring Project on Risk Factors for Chronic Diseases in the Netherlands-European Prospective Investigation into Cancer and Nutrition) study, which is a population-based cohort study in 3 towns in the Netherlands (Amsterdam, Maastricht, and Doetinchem), who had a body mass index (in kg/m(2)) <30 and who were not dieting. Participants were enrolled between 1993 and 1997 and followed for an average of 8.1 y (Amsterdam and Maastricht: 9.9 y; Doetinchem: 4.9 y). Intake of EDS foods (sweets, cakes and pastries, and savory snacks) was assessed at baseline by using a validated food-frequency questionnaire. Multivariate linear and multinomial logistic regression models were applied and stratified by center to examine the association between energy from EDS foods (kcal) and annual weight and waist circumference changes., Results: The mean (±SD) daily energy intake from EDS foods was 294 ± 192 kcal. In Amsterdam and Maastricht, the annual weight change was 168 ± 572 g/y, whereas in Doetinchem, the annual weight change was 444 ± 816 g/y. In the multivariate regression analysis adjusted for follow-up duration and anthropometric, dietary, and lifestyle factors, there was some, but inconsistent, evidence of an association of EDS-food consumption with annual weight change., Conclusion: Our study provides some, but inconsistent, evidence that consumption of EDS foods is positively associated with an increase in annual weight in normal- to overweight Dutch adults.

Background: Overweight develops gradually as a result of a long term surplus on the balance between energy intake and energy expenditure. Aim of this study was to quantify the positive energy balance responsible for excess body weight gain (energy gap) in young overweight children., Methods: Reported data on weight and height were used of 2190 Dutch children participating in the PIAMA birth cohort study. Accumulated body energy was estimated from the weight gain observed between age 2 and age 5-7. Energy gap was calculated as the difference in positive energy balance between children with and without overweight assuming an energy efficiency of 50%., Results: Ten percent of the children were overweight at the age of 5-7 years. For these children, median weight gain during 4-years follow-up was 13.3 kg, as compared to 8.5 kg in the group of children who had a normal weight at the end of the study. A daily energy gap of 289-320 kJ (69-77 kcal) was responsible for the excess weight gain or weight maintenance in the majority of the children who were overweight at the age of 5-7 years. The increase in daily energy requirement to maintain the 4.8 kilograms excess weight gain among overweight children at the end of the study was approximately 1371 kJ., Conclusions: An energy gap of about 289-320 kJ per day over a number of years can make the difference between normal weight and overweight in young children. Closing the energy gap in overweight children can be achieved by relatively small behavior changes. However, much more effort is required to lose the excess weight gained.

Background: Whether intake of alpha-linolenic acid (ALA), the plant-derived n-3 polyunsaturated fatty acid (PUFA), could prevent cardiovascular diseases is not yet clear. We examined the associations of ALA intake with 10-year incidence of coronary heart disease (CHD) and stroke in the Netherlands., Methods: Data were collected from a general population of 20,069 generally healthy men and women, aged 20 to 65 years. Habitual diet was assessed at baseline (1993-1997) with a validated 178-item food frequency questionnaire. Incidences of CHD and stroke were assessed through linkage with mortality and morbidity registers. Hazard ratios (HR) were calculated with multivariable Cox proportional hazards models, adjusted for age, gender, lifestyle, and dietary factors., Results: During 8-13 years of follow-up, we observed 280 incident CHD events (19% fatal) and 221 strokes (4% fatal). Intakes of energy-adjusted ALA in quintiles ranged from less than 1.0 g/d in the bottom quintile (Q1) to more than 1.9 g/d in the top quintile (Q5). ALA intake was not associated with incident CHD, with HRs varying between 0.89 and 1.01 (all p>0.05) in Q2-Q5 compared with the bottom quintile of ALA intake. For incident stroke, however, participants in Q2-Q5 had a 35-50% lower risk compared with the reference group. HRs were 0.65 (0.43-0.97), 0.49 (0.31-0.76), 0.53 (0.34-0.83), and 0.65 (0.41-1.04) for Q2-Q5 respectively., Conclusion: In this general Dutch population, ALA intake was not associated with incident CHD. The data suggested that a low intake of ALA may be a risk factor for incident stroke. These results warrant confirmation in other population-based studies and in trials.

Background: Few studies investigated the association between smoking, alcohol consumption, or physical activity and the risk of unstable angina pectoris (UAP), while the strength of these associations may differ compared to other coronary diseases such as acute myocardial infarction (AMI). Therefore, we investigated whether the associations of these lifestyle factors with UAP differed from those with AMI. Additionally, we investigated whether these effects differed between subjects with and without a family history of myocardial infarction (MI)., Methods: The CAREMA study consists of 21,148 persons, aged 20-59 years at baseline and randomly sampled from the Maastricht region in 1987-1997. At baseline, all participants completed a self-administered questionnaire. After follow-up of maximally 16.9 years, 420 AMI and 274 UAP incident cases were registered. Incidence rate ratios (RRs) were estimated using Cox proportional hazards models., Results: For both diseases, smoking increased the risk while alcohol consumption was associated with a protective effect. Associations with both risk factors were stronger for AMI than UAP, although this difference was only statistically significant for smoking. In men, an inverse association was found with physical activity during leisure time which seemed to be stronger for the risk of UAP than of AMI. On the contrary, physical activity during leisure time was associated with an increased risk of both AMI and UAP in women which seemed to be weaker for UAP than for AMI. Except for occupational physical activity in women, no significant interactions on a multiplicative scale were found between the lifestyle factors and family history of MI. Nevertheless, the highest risks were found in subjects with both a positive family history and the most unfavorable level of the lifestyle factors., Conclusions: The strength of the associations with the lifestyle factors did not differ between AMI and UAP, except for smoking. Furthermore, the effects of the lifestyle factors on the risk of both coronary diseases were similar for subjects with and without a positive family history., (© 2011 Merry et al; licensee BioMed Central Ltd.)

Despite the presence of intracellular pathogen recognition receptors that allow infected cells to attract the immune system, undifferentiated keratinocytes (KCs) are the main targets for latent infection with high-risk human papilloma viruses (hrHPVs). HPV infections are transient but on average last for more than one year suggesting that HPV has developed means to evade host immunity. To understand how HPV persists, we studied the innate immune response of undifferentiated human KCs harboring episomal copies of HPV16 and 18 by genome-wide expression profiling. Our data showed that the expression of the different virus-sensing receptors was not affected by the presence of HPV. Poly(I:C) stimulation of the viral RNA receptors TLR3, PKR, MDA5 and RIG-I, the latter of which indirectly senses viral DNA through non-self RNA polymerase III transcripts, showed dampening in downstream signalling of these receptors by HPVs. Many of the genes downregulated in HPV-positive KCs involved components of the antigen presenting pathway, the inflammasome, the production of antivirals, pro-inflammatory and chemotactic cytokines, and components downstream of activated pathogen receptors. Notably, gene and/or protein interaction analysis revealed the downregulation of a network of genes that was strongly interconnected by IL-1β, a crucial cytokine to activate adaptive immunity. In summary, our comprehensive expression profiling approach revealed that HPV16 and 18 coordinate a broad deregulation of the keratinocyte's inflammatory response, and contributes to the understanding of virus persistence.

DNA methylation is a hallmark in a subset of right-sided colorectal cancers. Methylation-based screening may improve prevention and survival rate for this type of cancer, which is often clinically asymptomatic in the early stages. We aimed to discover prognostic or diagnostic biomarkers for colon cancer by comparing DNA methylation profiles of right-sided colon tumours and paired normal colon mucosa using an 8.5 k CpG island microarray. We identified a diagnostic CpG-rich region, located in the first intron of the protein-tyrosine phosphatase gamma gene (PTPRG) gene, with altered methylation already in the adenoma stage, that is, before the carcinoma transition. Validation of this region in an additional cohort of 103 sporadic colorectal tumours and 58 paired normal mucosa tissue samples showed 94% sensitivity and 96% specificity. Interestingly, comparable results were obtained when screening a cohort of Lynch syndrome-associated cancers. Functional studies showed that PTPRG intron 1 methylation did not directly affect PTPRG expression, however, the methylated region overlapped with a binding site of the insulator protein CTCF. Chromatin immunoprecipitation (ChIP) showed that methylation of the locus was associated with absence of CTCF binding. Methylation-associated changes in CTCF binding to PTPRG intron 1 could have implications on tumour gene expression by enhancer blocking, chromosome loop formation or abrogation of its insulator function. The high sensitivity and specificity for the PTPRG intron 1 methylation in both sporadic and hereditary colon cancers support biomarker potential for early detection of colon cancer., (© 2011 Macmillan Publishers Limited All rights reserved 1018-4813/11)

In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences on human longevity are expected to be much more complex. Strikingly however, beneficial metabolic and cellular features of long-lived families resemble those in animals for whom the lifespan is extended by applying genetic manipulation and, especially, dietary restriction. Candidate gene studies in humans support the notion that human orthologues from longevity genes identified in lower species do contribute to longevity but that the influence of the genetic variants involved is small. Here we discuss how an integration of novel study designs, labour-intensive biobanking, deep phenotyping and genomic research may provide insights into the mechanisms that drive human longevity and healthy ageing, beyond the associations usually provided by molecular and genetic epidemiology. Although prospective studies of humans from the cradle to the grave have never been performed, it is feasible to extract life histories from different cohorts jointly covering the molecular changes that occur with age from early development all the way up to the age at death. By the integration of research in different study cohorts, and with research in animal models, biological research into human longevity is thus making considerable progress.

Height is a classic complex trait with common variants in a growing list of genes known to contribute to the phenotype. Using a genecentric genotyping array targeted toward cardiovascular-related loci, comprising 49,320 SNPs across approximately 2000 loci, we evaluated the association of common and uncommon SNPs with adult height in 114,223 individuals from 47 studies and six ethnicities. A total of 64 loci contained a SNP associated with height at array-wide significance (p < 2.4 × 10(-6)), with 42 loci surpassing the conventional genome-wide significance threshold (p < 5 × 10(-8)). Common variants with minor allele frequencies greater than 5% were observed to be associated with height in 37 previously reported loci. In individuals of European ancestry, uncommon SNPs in IL11 and SMAD3, which would not be genotyped with the use of standard genome-wide genotyping arrays, were strongly associated with height (p < 3 × 10(-11)). Conditional analysis within associated regions revealed five additional variants associated with height independent of lead SNPs within the locus, suggesting allelic heterogeneity. Although underpowered to replicate findings from individuals of European ancestry, the direction of effect of associated variants was largely consistent in African American, South Asian, and Hispanic populations. Overall, we show that dense coverage of genes for uncommon SNPs, coupled with large-scale meta-analysis, can successfully identify additional variants associated with a common complex trait.

Background: A positive parental history of myocardial infarction (MI) is an independent risk factor for cardiovascular diseases (CVD). However, different definitions of parental history have been used. We evaluated the impact of parental gender and age of onset of MI on CVD incidence., Methods: Baseline data were collected between 1993 and 1997 in 10,524 respondents aged 40-65 years. CVD events were obtained from the National Hospital Discharge Register and Statistics Netherlands. We used proportional hazard models to calculate hazard ratios (HR) and 95% confidence intervals (CI) for CVD incidence and adjusted for lifestyle and biological risk factors., Results: At baseline, 36% had a parental history of MI. During 10-year follow-up, 914 CVD events occurred. The age and gender adjusted HR was 1.3 (95% CI 1.1-1.5) for those with a paternal MI, 1.5 (1.2-1.8) for those with a maternal MI and 1.6 (1.2-2.2) for those with both parents with an MI. With decreasing parental age of MI, HR increased from 1.2 (1.0-1.6) for age ≥70 years to 1.5 (1.2-1.8) for age <60 years for a paternal MI and from 1.1 (0.9-1.5) to 2.2 (1.6-3.0) for a maternal MI. The impact of having a mother with MI before age 60 significantly differed in women [(2.9 (1.8-4.6)] and men [1.5 (0.9-2.6)]. Adjustment only slightly influenced HRs for maternal MI., Conclusions: Respondents with a parental history of MI have an increased CVD incidence, in particular with parental onset of MI before age 70. A maternal history of MI before age 60 was the strongest predictor of CVD incidence.

Background: The associations of glycemic load (GL) and glycemic index (GI) with the risk of cardiovascular diseases (CVD) are not well-established, particularly in men, and may be modified by gender., Objective: To assess whether high dietary GL and GI increase the risk of CVD in men and women., Methods: A large prospective cohort study (EPIC-MORGEN) was conducted within the general Dutch population among 8,855 men and 10,753 women, aged 21-64 years at baseline (1993-1997) and free of diabetes and CVD. Dietary intake was assessed with a validated food-frequency questionnaire and GI and GL were calculated using Foster-Powell's international table of GI. Information on morbidity and mortality was obtained through linkage with national registries. Cox proportional hazards analysis was performed to estimate hazard ratios (HRs) for incident coronary heart disease (CHD) and stroke, while adjusting for age, CVD risk factors, and dietary factors., Results: During a mean follow-up of 11.9 years, 581 CHD cases and 120 stroke cases occurred among men, and 300 CHD cases and 109 stroke cases occurred among women. In men, GL was associated with an increased CHD risk (adjusted HR per SD increase, 1.17 [95% CI, 1.02-1.35]), while no significant association was found in women (1.09 [0.89-1.33]). GI was not associated with CHD risk in both genders, while it was associated with increased stroke risk in men (1.27 [1.02-1.58]) but not in women (0.96 [0.75-1.22]). Similarly, total carbohydrate intake and starch intake were associated with a higher CHD risk in men (1.23 [1.04-1.46]; and 1.24 [1.07-1.45]), but not in women., Conclusion: Among men, high GL and GI, and high carbohydrate and starch intake, were associated with increased risk of CVD.

Background: Plasma total cholesterol (TC) levels are highly genetically determined. Although ample evidence of genetic determination of separate lipoprotein cholesterol levels has been reported, using TC level directly as a phenotype in a relatively large broad-gene based association study has not been reported to date., Methods and Results: We genotyped 361 single nucleotide polymorphisms (SNPs) across 243 genes based on pathways potentially relevant to cholesterol metabolism in 3575 subjects that were examined thrice over 11 years. Twenty-three SNPs were associated with TC levels after adjustment for multiple testing. We used 12 of them (rs7412 and rs429358 in APOE, rs646776 in CELSR2, rs1367117 in APOB, rs6756629 in ABCG5, rs662799 in APOA5, rs688 in LDLR, rs10889353 in DOCK7, rs2304130 in NCAN, rs3846662 in HMGCR, rs2275543 in ABCA1, rs7275 in SMARCA4) that were confirmed in previous candidate association or genome-wide-association studies to define a gene risk score (GRS). Average TC levels increased from 5.23 ± 0.82 mmol/L for those with 11 or less cholesterol raising alleles to 6.03 ± 1.11 mmol/L for those with 18 or more (P for trend<0.0001). The association with TC levels was slightly stronger when the weighted GRS that weighted the magnitude of allelic effects was used., Conclusion: A panel of common genetic variants in the genes pivotal in cholesterol metabolism could possibly help identify those people who are at risk of high cholesterol levels., (Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.)

Background: In high-dimensional data analysis such as differential gene expression analysis, people often use filtering methods like fold-change or variance filters in an attempt to reduce the multiple testing penalty and improve power. However, filtering may introduce a bias on the multiple testing correction. The precise amount of bias depends on many quantities, such as fraction of probes filtered out, filter statistic and test statistic used., Results: We show that a biased multiple testing correction results if non-differentially expressed probes are not filtered out with equal probability from the entire range of p-values. We illustrate our results using both a simulation study and an experimental dataset, where the FDR is shown to be biased mostly by filters that are associated with the hypothesis being tested, such as the fold change. Filters that induce little bias on the FDR yield less additional power of detecting differentially expressed genes. Finally, we propose a statistical test that can be used in practice to determine whether any chosen filter introduces bias on the FDR estimate used, given a general experimental setup., Conclusions: Filtering out of probes must be used with care as it may bias the multiple testing correction. Researchers can use our test for FDR bias to guide their choice of filter and amount of filtering in practice.

Guidelines for cardiovascular disease prevention recommend a non-pharmacological approach to reduce cardiovascular risk in those with elevated blood pressure. We assessed guideline adherence in hypertensives. This study was performed in the European Investigation into Cancer and Nutrition-NL cohort, consisting of 40,011 subjects. From 1993 to 1997, participants completed questionnaires (disease history, lifestyle and diet), a physical examination was performed and blood samples were drawn. Differences in proportions of guideline targets met between aware and unaware hypertensives were studied. Of 8779 hypertensive subjects, 90% was aware of their hypertension. They more often adhered to guidelines than unaware hypertensive subjects with respect to intake of polyunsaturated fat:saturated fat (38.6% vs 33.2%), fibres (40.6% vs 34.2%), body mass index <27 kg m(-2) (53.8% vs 46.5%) and alcohol (79.7% vs 72.6%). Despite statistical significance, the magnitude of these differences was small. Our study suggests that prevalence of a healthy lifestyle according to the recommendations in guidelines is slightly better in subjects aware of hypertension. There seems to be ample room for improvement in implementing the guidelines. Probably, patient tailored interventions and a multisiciplinary and multimodality approach can support this improvement.

Objective: To examine the associations of coffee and tea consumption with risk of morbidity and mortality of stroke and coronary heart disease (CHD) and with all-cause mortality., Methods and Results: Coffee and tea consumption were assessed with a validated food-frequency questionnaire, and 37 514 participants were observed for 13 years for the occurrence of cardiovascular morbidity and mortality. A U-shaped association between coffee and CHD was found, with the lowest hazard ratio (HR [95% CI]) for 2.1 to 3.0 cups per day (0.79 [0.65 to 0.96]; P(trend)=0.01). Tea was inversely associated with CHD, with the lowest HR (95% CI) for more than 6.0 cups per day (0.64 [0.46 to 0.90]; P(trend)=0.02). No associations between tea or coffee and stroke were found (P(trend)=0.63 and P(trend)=0.32, respectively). Although not significant, coffee slightly reduced the risk for CHD mortality (HR, 0.64; 95% CI, 0.37 to 1.11; P(trend)=0.12) for 3.1 to 6.0 cups per day. A U-shaped association between tea and CHD mortality was observed, with an HR of 0.55 (95% CI, 0.31 to 0.97; P(trend)=0.03) for 3.1 to 6.0 cups per day. Neither coffee nor tea was associated with stroke (P(trend)=0.22 and P(trend)=0.74, respectively) and all-cause mortality (P(trend)=0.33 and P(trend)=0.43, respectively)., Conclusions: High tea consumption is associated with a reduced risk of CHD mortality. Our results suggest a slight risk reduction for CHD mortality with moderate coffee consumption and strengthen the evidence on the lower risk of CHD with coffee and tea consumption.

Background: The delta-5 and delta-6 desaturases, encoded by the FADS1 and FADS2 genes, are rate-limiting enzymes in polyunsaturated fatty acid (PUFA) biosynthesis. Single nucleotide polymorphisms in the FADS gene cluster region have been associated with both PUFA concentrations in plasma or erythrocyte membrane phospholipids and cholesterol concentrations in recent genome-wide association studies., Objective: We examined whether genetic variations in the FADS gene cluster region interact with dietary intakes of n-3 (omega-3) and n-6 (omega-6) PUFAs to affect plasma total, HDL-, and non-HDL-cholesterol concentrations., Design: Dietary intakes of n-3 and n-6 PUFAs, plasma concentrations of total and HDL cholesterol, and rs174546, rs482548, and rs174570 in the FADS gene cluster region were measured in 3575 subjects in the second survey of the Doetinchem Cohort Study., Results: Significant associations between rs174546 genotypes and total and non-HDL-cholesterol concentrations were observed in the group with a high intake of n-3 PUFAs (> or =0.51% of total energy; P = 0.006 and 0.047, respectively) but not in the low-intake group (P for interaction = 0.32 and 0.51, respectively). The C allele was associated with high total and non-HDL-cholesterol concentrations. Furthermore, the C allele was significantly associated with high HDL-cholesterol concentrations in the group with a high intake of n-6 PUFAs (> or =5.26% of total energy, P = 0.004) but not in the group with a low intake (P for interaction = 0.02)., Conclusion: Genetic variation in the FADS1 gene potentially interacts with dietary PUFA intakes to affect plasma cholesterol concentrations, which should be investigated further in other studies.

Background: To investigate the etiology of MLH1 promoter methylation in mismatch repair (MMR) mutation-negative early onset MSI-H colon cancer. As this type of colon cancer is associated with high ages, young patients bearing this type of malignancy are rare and could provide additional insight into the etiology of sporadic MSI-H colon cancer., Methods: We studied a set of 46 MSI-H colon tumors cases with MLH1 promoter methylation which was enriched for patients with an age of onset below 50 years (n=13). Tumors were tested for CIMP marker methylation and mutations linked to methylation: BRAF, KRAS, GADD45A and the MLH1 -93G>A polymorphism. When available, normal colon and leukocyte DNA was tested for GADD45A mutations and germline MLH1 methylation. SNP array analysis was performed on a subset of tumors., Results: We identified two cases (33 and 60 years) with MLH1 germline promoter methylation. BRAF mutations were less frequent in colon cancer patients below 50 years relative to patients above 50 years (p-value: 0.044). CIMP-high was infrequent and related to BRAF mutations in patients below 50 years. In comparison with published controls the G>A polymorphism was associated with our cohort. Although similar distribution of the pathogenic A allele was observed in the patients with an age of onset above and below 50 years, the significance for the association was lost for the group under 50 years. GADD45A sequencing yielded an unclassified variant. Tumors from both age groups showed infrequent copy number changes and loss-of-heterozygosity., Conclusion: Somatic or germline GADD45A mutations did not explain sporadic MSI-H colon cancer. Although germline MLH1 methylation was found in two individuals, locus-specific somatic MLH1 hypermethylation explained the majority of sporadic early onset MSI-H colon cancer cases. Our data do not suggest an intrinsic tendency for CpG island hypermethylation in these early onset MSI-H tumors other than through somatic mutation of BRAF.

We assessed the dose-response relations within a low range of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and fish intake on fatal coronary heart disease (CHD) and nonfatal myocardial infarction (MI). In a Dutch population-based cohort study, EPA+DHA and fish intake were assessed at baseline among 21,342 participants aged 20-65 y with no history of MI or stroke. Hazard ratios were calculated with Cox proportional-hazard models. During 9-14 y of follow-up (mean 11.3 y), 647 participants (3%) died, of which 82 of CHD. Fatal CHD mainly comprised MI (64 cases). In total, 252 participants survived an MI. Median intakes in quartiles of EPA+DHA were 40, 84, 151, and 234 mg/d. Medians of fish consumption in quartiles were 1.1, 4.2, 10.7, and 17.3 g/d. Compared with the lowest quartile of EPA+DHA, participants in the top quartile had a 49% lower risk of fatal CHD (95% CI: 6-73%) and a 62% lower risk of fatal MI (95% CI: 23-81%). We observed inverse dose-response relations for EPA+DHA intake and fatal CHD (P-trend = 0.05) and fatal MI (P-trend = 0.01). Results were similar for fish consumption. Nonfatal MI was not associated with EPA+DHA or fish intake. In conclusion, in populations with a low fish consumption, EPA+DHA and fish may lower fatal CHD and MI risk in a dose-responsive manner. Low intakes of EPA+DHA or fish do not seem to protect against nonfatal MI.

The liver is currently known to be the major organ to eliminate excess cholesterol from our body. It accomplishes this function in two ways: conversion of cholesterol molecules into bile acids (BAs) and secretion of unesterified cholesterol molecules into bile. BAs are synthesized in the hepatocytes, secreted into bile and delivered to the lumen of the small intestine where they act as detergents to facilitate absorption of fats and fat-soluble vitamins. About 95% of BAs are recovered in the ileum during each cycle of the enterohepatic circulation. Five percent are lost and replaced by newly synthesized BAs, which amounts to approximately 500 mg/day in adult humans. In contrast to the efficiency of the BAs' enterohepatic circulation, 50% of the 1000 mg of cholesterol secreted daily into bile is lost in feces. It is known that rare human mutations in certain genes in bile acid and bile metabolic pathway influence blood cholesterol levels. With the recent success of genome-wide association studies, we are convinced that common genetic variants also play a role in the genetic architecture of plasma lipid traits. In this review, we summarized the current state of knowledge about genetic variations in bile acid and bile metabolic pathway, and assessed their impact on blood cholesterol levels and cholesterol metabolic kinetics in the population., (Copyright 2009 Elsevier Ireland Ltd. All rights reserved.)

Objective: Much of the genetic variation in glucose levels remains to be discovered. Especially, research on gene-environment interactions is scarce. Overweight is one of the main risk factors for hyperglycemia. As transcriptional regulation is important for both weight maintenance and glucose control, we analyzed 353 single nucleotide polymorphisms (SNPs), occurring in transcriptional pathways of glucose and lipid metabolism in interaction with body mass index (BMI) on glucose levels., Research Design and Methods: SNPs were measured in 3244 participants of the Doetichem cohort. Non-fasting glucose levels and BMI were measured twice in 6 years. SNP x BMI interactions were analyzed by mixed models and adjusted for age, sex, time since last meal, and follow-up time. False discovery rate (FDR) <0.2 was used to adjust for multiple testing., Results: Two SNPs in the PPARGC1A gene (rs8192678, FDR=0.07; rs3755863, FDR=0.17) showed a significant interaction with BMI. The rare allele of both SNPs was associated with significantly lower glucose levels in subjects with a BMI28 kg m(-2). A small intervention study (n=120) showed similar, though non-significant, results., Conclusions: Using a pathway-based approach, we found that BMI significantly modified the association between two SNPs in the PPARGC1A gene and glucose levels. The association between glucose and PPARGC1A was only present in lean subjects. This suggests that the effect of the PPARGC1A gene, which is involved both in fatty acid oxidation and glucose metabolism, is modified by BMI.

Background: In Europe, for primary prevention of cardiovascular diseases (CVD), the Systematic COronary Risk Evaluation (SCORE) risk charts for high-risk and low-risk regions (SCORE-high and SCORE-low, respectively) are used. For the Dutch 'Clinical Practice Guideline for Cardiovascular Risk Management' an adapted SCORE risk chart (SCORE-NL) was developed in collaboration with the SCORE group. We evaluated these three SCORE equations using Dutch risk factor and mortality data., Design: Prospective cohort study with 10-year follow-up., Methods: Baseline data were collected between 1987 and 1997 in 32 885 persons aged 37.5-62.5 years. Vital status was checked and causes of death were obtained from Statistics Netherlands. On the basis of the level of risk factors, the expected number of CVD deaths was calculated by applying the three SCORE equations and compared with the observed number., Results: The observed CVD mortality was three-fold higher in men (n=242; 1.6%) than in women (n=83; 0.5%). On the basis of SCORE-NL, 8.5% of the men and 0.8% of the women had a CVD mortality risk of 5% or more. The ratio of the observed-to-expected number of CVD deaths was 0.75 for men and 0.55 for women using SCORE-NL, 0.54 and 0.56 using SCORE-high, and 1.11 and 0.95 using SCORE-low., Conclusion: At the population level, SCORE-low predicts the number of CVD deaths well, whereas both SCORE-NL and SCORE-high overestimate the number of CVD deaths by a factor 1.5-2.

Aim: This study investigated the relation between alcohol consumption and the risk of cardiovascular disease (CVD) among 10 530-hypertensive women from the EPIC-NL cohort., Methods and Results: Alcohol consumption was assessed using a validated food-frequency questionnaire and participants were followed for occurrence of CVD. During 9.4 years follow-up, we documented 580 coronary heart disease (CHD) events and 254 strokes, 165 of which were ischemic. An inverse association (Ptrend=0.009) between alcohol consumption and risk of CHD was observed with a multivariate-adjusted hazard ratio of 0.72 (95% confidence interval: 0.52-1.01) for those consuming 70-139.9 g alcohol/week compared to lifetime abstainers. Of different beverages, only red wine consumption was associated with a reduced risk of CHD. A U-shaped relation (P=0.08) was observed for total stroke with a hazard ratio of 0.65 (0.44-0.95) for consuming 5-69.9 g alcohol/week compared with lifetime abstainers. Similar results were observed for ischemic stroke with a hazard ratio of 0.56 (0.35-0.89) for consuming of 5-69.9 g alcohol/week., Conclusion: We conclude that moderate alcohol consumption is associated with a reduced risk of CHD among hypertensive women. Light alcohol consumption tended to be related to a lower risk of stroke. Current guidelines for alcohol consumption in the general population also apply to hypertensive women.

The human proteins ciliary neurotrophic factor (CNTF) and interleukin-6 (IL6) and their receptors share structural homology with leptin and its receptor. In addition, uncoupling protein-2 (UCP2) has been shown to participate the regulation of leptin on food intake. All three proteins are active in the hypothalamus. Experiments have shown that CNTF and IL6, like leptin, can influence body weight in humans and animals, while the effect of UCP2 is not consistent. In a Dutch general population (n=545) we investigated associations of CNTF (null G/A, rs1800169), IL6 (174 G/C, rs1800795) and UCP2 (A55V, rs660339 and del/ins) polymorphisms with weight gain using interaction graphs and logistic regression analysis. The average follow-up period was 6.9 years. Individuals who gained weight (n=264) were compared with individuals who remained stable in weight (n=281). In women the CNTF polymorphism (odds ratio (OR)=2.15, 95%CI: 1.27-3.64, p=0.004) and in men the IL6 polymorphism by itself (OR=2.26, 95%CI: 1.08-4.75, p=0.03) or in combination with the CNTF polymorphism, were associated with weight gain. Furthermore, CNTF and IL6 polymorphisms in interaction with UCP2 polymorphisms had similar strong effects on weight gain in women and men, respectively. All observed effects were statistically shown to be independent of serum leptin level. These results are incorporated in a biological model for weight regulation with upstream effects of CNTF and IL6, and downstream effects of UCP2. The results of this study suggest a novel mechanism for weight regulation that is active in both women and men, but strongly influenced by sex.

MLL-rearranged infant acute lymphoblastic leukemia (ALL) remains the most aggressive type of childhood leukemia, displaying a unique gene expression profile. Here we hypothesized that this characteristic gene expression signature may have been established by potentially reversible epigenetic modifications. To test this hypothesis, we used differential methylation hybridization to explore the DNA methylation patterns underlying MLL-rearranged ALL in infants. The obtained results were correlated with gene expression data to confirm gene silencing as a result of promoter hypermethylation. Distinct promoter CpG island methylation patterns separated different genetic subtypes of MLL-rearranged ALL in infants. MLL translocations t(4;11) and t(11;19) characterized extensively hypermethylated leukemias, whereas t(9;11)-positive infant ALL and infant ALL carrying wild-type MLL genes epigenetically resembled normal bone marrow. Furthermore, the degree of promoter hypermethylation among infant ALL patients carrying t(4;11) or t(11;19) appeared to influence relapse-free survival, with patients displaying accentuated methylation being at high relapse risk. Finally, we show that the demethylating agent zebularine reverses aberrant DNA methylation and effectively induces apoptosis in MLL-rearranged ALL cells. Collectively these data suggest that aberrant DNA methylation occurs in the majority of MLL-rearranged infant ALL cases and guides clinical outcome. Therefore, inhibition of aberrant DNA methylation may be an important novel therapeutic strategy for MLL-rearranged ALL in infants.

Aims/hypothesis: The aim of this study was to examine the association of consumption of coffee and tea, separately and in total, with risk of type 2 diabetes and which factors mediate these relations., Methods: This research was conducted as part of the Dutch Contribution to the European Prospective Investigation into Cancer and Nutrition, which involves a prospective cohort of 40,011 participants with a mean follow-up of 10 years. A validated food-frequency questionnaire was used to assess coffee and tea consumption and other lifestyle and dietary factors. The main outcome was verified incidence of type 2 diabetes. Blood pressure, caffeine, magnesium and potassium were examined as possible mediating factors., Results: During follow-up, 918 incident cases of type 2 diabetes were documented. After adjustment for potential confounders, coffee and tea consumption were both inversely associated with type 2 diabetes, with hazard ratios of 0.77 (95% CI 0.63-0.95) for 4.1-6.0 cups of coffee per day (p for trend = 0.033) and 0.63 (95% CI: 0.47-0.86) for >5.0 cups of tea per day (p for trend = 0.002). Total daily consumption of at least three cups of coffee and/or tea reduced the risk of type 2 diabetes by approximately 42%. Adjusting for blood pressure, magnesium, potassium and caffeine did not attenuate the associations., Conclusions/interpretation: Drinking coffee or tea is associated with a lowered risk of type 2 diabetes, which cannot be explained by magnesium, potassium, caffeine or blood pressure effects. Total consumption of at least three cups of coffee or tea per day may lower the risk of type 2 diabetes.

Aims: Body mass index (BMI) and waist circumference (WC) are both predictors of cardiovascular diseases (CVD). We compared absolute risk, hazard ratio (HR), and population attributable risk of nonfatal and fatal CVD for BMI and WC in a large prospective cohort study with an average follow-up of 10 years., Methods and Results: Anthropometric data were measured between 1993 and 1997 in a general population sample of over 20,000 men and women aged 20-65 years in the Netherlands. All risks were adjusted for age and sex. Absolute risk of nonfatal CVD was on average 10 times higher than that of fatal CVD. In obese respondents (BMI >or=30 kg/m2), relative risk of fatal CVD was four-fold higher [HR=4.0 95% confidence interval (CI)=2.4-6.6], whereas risk of nonfatal CVD was two-fold higher (HR=1.8 95% CI=1.6-2.2) than in normal-weight respondents. Similar associations were observed for WC (>or=88 vs. <80 cm in women and >or=102 vs. 94 cm in men). In persons with overweight or obesity (BMI >or=25 kg/m2), half of all fatal CVD (attributable risk=54%, 95% CI=30-70) and a quarter of nonfatal CVD was ascribed to their overweight. On the population level, one-third of all fatal CVD cases could be attributed to overweight and obesity (population attributable risk=35%, 95% CI=14-52), and about one in seven of nonfatal CVD cases., Conclusion: The associations of BMI and WC with CVD risk were equally strong. Overweight and obesity had a stronger impact on fatal CVD than on nonfatal CVD.

Objectives: To assess the contribution of out-of-home (OH) energy and nutrient intake to total dietary intake, and to compare out- versus in-home nutrient patterns among 27 centres in 10 countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) study., Methods: Between 1995 and 2000, 36,034 participants aged between 35-74 years completed a standardized 24-h dietary recall using a software programme (EPIC-Soft) that recorded the place of food/drink consumption. Eating OH was defined as the consumption of foods and beverages anywhere other than in household premises, irrespective of the place of purchase/preparation. Nutrient intakes were estimated using a standardized nutrient database. Mean intakes were adjusted for age and weighted by season and day of recall., Results: Among women, OH eating contributed more to total fat intake than to intakes of protein and carbohydrates. Among both genders, and particularly in southern Europe, OH eating contributed more to sugar and starch intakes and less to total fibre intake. The contribution of OH eating was also lower for calcium and vitamin C intakes. The composition of diet at home was different from that consumed out of home in southern countries, but was relatively similar in the north., Conclusions: In northern Europe, OH and in-home eating are homogeneous, whereas southern Europeans consider OH eating as a distinctive occasion. In most centres, women selected more fat-rich items when eating out.

Purpose: The interaction between programmed cell death 1 (PD-1), expressed by activated effector or regulatory T cells, and B7-H1 (PD-L1) and B7-DC (PD-L2) results in the inhibition of T-cell function. The aim of this study was to determine B7-H1, B7-DC, and PD-1 expression in cervical carcinoma., Experimental Design: A tissue microarray of a well-defined group of 115 patients was stained with antibodies against B7-H1 and B7-DC. Three-color fluorescent immunohistochemistry was used to study the number and phenotype of tumor-infiltrating T cells expressing PD-1. Additional analyses consisted of in vitro T-cell suppression assays., Results: B7-H1 was expressed in 19%, and B7-DC was expressed by 29% of the 115 tumors. PD-1 was expressed by more than half of both the infiltrating CD8+ T cells and CD4+Foxp3+ T cells, irrespective of B7-H1 or B7-DC expression by tumors. The expression of B7-H1 did not show a direct impact on patient survival. However, subgroup analysis revealed that patients with a relative excess of infiltrating regulatory T cells displayed a better survival when the tumor was B7-H1 positive (P = 0.033). Additional studies showed that the presence of B7-H1 during the activation of CD4+Foxp3+ regulatory T cells impaired their suppressive function in a functional in vitro assay., Conclusions: B7-H1 is expressed on only a minority of cervical cancers and does not influence the survival of patients with cervical cancer. PD-1 is expressed by a vast number of infiltrating CD8 T cells, suggesting that blocking of PD-1 could have therapeutic potential in cervical cancer patients.

Background: As nuclear receptors and transcription factors have an important regulatory function in adipocyte differentiation and fat storage, genetic variation in these key regulators and downstream pathways may be involved in the onset of obesity., Objective: To explore associations between single nucleotide polymorphisms (SNPs) in candidate genes from regulatory pathways that control fatty acid and glucose metabolism, and repeated measurements of body mass index (BMI) and waist circumference in a large Dutch study population., Methods: Data of 327 SNPs across 239 genes were analyzed for 3575 participants of the Doetinchem cohort, who were examined three times during 11 years, using the Illumina Golden Gate assay. Adjusted random coefficient models were used to analyze the relationship between SNPS and obesity phenotypes. False discovery rate q-values were calculated to account for multiple testing. Significance of the associations was defined as a q-value < or = 0.20., Results: Two SNPs (in NR1H4 and SMARCA2 in women only) were significantly associated with both BMI and waist circumference. In addition, two SNPs (in SIRT1 and SCAP in women only) were associated with BMI alone. A functional SNP, in IL6, was strongly associated with waist., Conclusion: In this explorative study among participants of a large population-based cohort, five SNPs, mainly located in transcription mediator genes, were strongly associated with obesity phenotypes. The results from whole genome and candidate gene studies support the potential role of NR1H4, SIRT1, SMARCA2 and IL6 in obesity. Although replication of our findings and further research on the functionality of these SNPs and underlying mechanism is necessary, our data indirectly suggest a role of GATA transcription factors in weight control.

Objective: The ATP-binding cassette transporter ABCC1 [i.e. multidrug resistance-associated protein 1 (MRP1)] is a membrane-bound pump excreting a variety of xenobiotics from the cell, and thus ABCC1 may play an important role in smoking-related lung function loss and development of chronic obstructive pulmonary disease (COPD). We earlier showed that bronchial epithelium of COPD patients have lower ABCC1 expression than that of healthy controls, with even further decrements in more severe COPD stages. In line with these results, we now aimed to assess effects of ABCC1 single nucleotide polymorphisms (SNPs) on both the level and the longitudinal course of lung function in the general population., Methods: All 51 prevalent (minor allele frequency >5%) and noncorrelated (r<0.8) ABCC1 SNPs were analyzed in two independent, prospective, population-based cohorts, that is, Doetinchem (n = 1152) and Vlagtwedde-Vlaardingen (n = 1390) studies (three and seven median lung function measurements, respectively, per patient), using linear regression and linear mixed-effect models., Results: SNPs rs4148382 and rs212093 in the 3'-ABCC1 region were significantly associated with a higher and lower forced expiratory volume in 1 s (FEV1), respectively, in both the cohorts. Another rs35621 SNP (intron 14) was significantly associated with a highly excessive FEV1 decline in both cohorts. All replicated associations were additionally confirmed by permutation testing., Conclusion: This is the first study showing a significant relationship between ABCC1 SNPs and lung function in two independent cohorts. These SNPs are therefore putative candidates for studies aiming to prevent COPD and investigating pharmacogenetics in established COPD.

Background: Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes., Results: We propose to analyse copy number and expression array data using gene sets, rather than individual genes. The proposed model is robust and sensitive. We re-analysed two publicly available datasets as illustration. These two independent breast cancer datasets yielded similar patterns of association between gene dosage and gene expression levels, in spite of different platforms having been used. Our comparisons show a clear advantage to using sets of genes' expressions to detect associations with long-spanning, low-amplitude copy number aberrations. In addition, our model allows for using additional explanatory variables and does not require mapping between copy number and expression probes., Conclusion: We developed a general and flexible tool for integration of multiple microarray data sets, and showed how the identification of genes whose expression is affected by copy number aberrations provides a powerful approach to prioritize putative targets for functional validation.

In this study, we applied the multivariate statistical tool Partial Least Squares (PLS) to analyze the relative importance of 83 plasma proteins in relation to coronary heart disease (CHD) mortality and the intermediate end points body mass index, HDL-cholesterol and total cholesterol. From a Dutch monitoring project for cardiovascular disease risk factors, men who died of CHD between initial participation (1987-1991) and end of follow-up (January 1, 2000) (N = 44) and matched controls (N = 44) were selected. Baseline plasma concentrations of proteins were measured by a multiplex immunoassay. With the use of PLS, we identified 15 proteins with prognostic value for CHD mortality and sets of proteins associated with the intermediate end points. Subsequently, sets of proteins and intermediate end points were analyzed together by Principal Components Analysis, indicating that proteins involved in inflammation explained most of the variance, followed by proteins involved in metabolism and proteins associated with total-C. This study is one of the first in which the association of a large number of plasma proteins with CHD mortality and intermediate end points is investigated by applying multivariate statistics, providing insight in the relationships among proteins, intermediate end points and CHD mortality, and a set of proteins with prognostic value.

Plant lignans present in foods such as whole grains, seeds and nuts, fruits and vegetables, and beverages. Plant lignans are converted by intestinal bacteria into the enterolignans enterodiol and enterolactone. Up to now, epidemiological evidence for a protective role of enterolignans on cardiovascular diseases is limited and inconsistent. We investigated the association between plasma enterodiol and enterolactone and nonfatal myocardial infarction risk in a prospective study. During follow-up (1987-1998) of 15,107 subjects, aged 20-59 years, 236 incident nonfatal myocardial infarction cases were diagnosed. Controls (n=283) were frequency matched to the cases on age, sex, and study center. No statistically significant associations between plasma enterodiol and enterolactone and risk of nonfatal myocardial infarction were detected. The odds ratio for the highest versus the lowest quartile of enterodiol was 1.21 (95% confidence interval (CI): 0.70, 2.12; p for trend=0.74), and that of enterolactone 1.51 (95% CI: 0.87, 2.61; p for trend=0.12) after adjustment for known dietary risk factors for coronary heart disease. No effect modification was observed for sex, menopausal status, or smoking status. Our results do not support the hypothesis that high plasma enterodiol or enterolactone concentrations are associated with a reduced risk of nonfatal myocardial infarction.

A cytogenetic map has been developed for diploid potato (Solanum tuberosum), in which the arms of the 12 potato bivalents can be identified in pachytene complements using multicolor fluorescence in situ hybridization (FISH) with a set of 60 genetically anchored bacterial artificial chromosome (BAC) clones from the RHPOTKEY BAC library. This diagnostic set of selected BACs (five per chromosome) hybridizes to euchromatic regions and corresponds to well-defined loci in the ultradense genetic map, and with these probes a new detailed and reliable pachytene karyotype could be established. Chromosome size has been estimated both from microscopic length measurements and from 4',6-diamidino-2-phenylindole fluorescence-based DNA content measurements. In both approaches, chromosome 1 is the largest (100-115 Mb) and chromosome 11 the smallest (49-53 Mb). Detailed measurements of mega-base-pair to micrometer ratios have been obtained for chromosome 5, with average values of 1.07 Mb/mum for euchromatin and 3.67 Mb/mum for heterochromatin. In addition, our FISH results helped to solve two discrepancies in the potato genetic map related to chromosomes 8 and 12. Finally, we discuss the significance of the potato cytogenetic map for extended FISH studies in potato and related Solanaceae, which will be especially beneficial for the potato genome-sequencing project.

Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma, is a malignancy of mature, skin-homing T cells. Sézary syndrome (Sz) is often considered to represent a leukemic phase of MF. In this study, the pattern of numerical chromosomal alterations in MF tumor samples was defined using array-based comparative genomic hybridization (CGH); simultaneously, gene expression was analyzed using microarrays. Highly recurrent chromosomal alterations in MF include gain of 7q36, 7q21-7q22 and loss of 5q13 and 9p21. The pattern characteristic of MF differs markedly from chromosomal alterations observed in Sz. Integration of data from array-based CGH and gene-expression analysis yielded several candidate genes with potential relevance in the pathogenesis of MF. We confirmed that the FASTK and SKAP1 genes, residing in loci with recurrent gain, demonstrated increased expression. The RB1 and DLEU1 tumor suppressor genes showed diminished expression associated with loss. In addition, it was found that the presence of chromosomal alterations on 9p21, 8q24, and 1q21-1q22 was associated with poor prognosis in patients with MF. This study provides novel insight into genetic alterations underlying MF. Furthermore, our analysis uncovered genomic differences between MF and Sz, which suggest that the molecular pathogenesis and therefore therapeutic requirements of these cutaneous T-cell lymphomas may be distinct.

Incidence rates of cardiovascular diseases are often estimated by linkage to hospital discharge and mortality registries. The validity depends on the quality of the registries and the linkage. Therefore, we validated incidence rates of coronary heart disease (CHD), acute myocardial infarction, unstable angina pectoris, and heart failure, estimated by this method, against the disease registry of the cardiovascular registry Maastricht cohort study. The cohort consists of 21,148 persons, born between 1927 and 1977, who were randomly sampled from Maastricht and surrounding communities in 1987-1997. Incident cases were identified by linkage to the Netherlands causes of death registry and either the hospital discharge registry (HDR) or the cardiology information system (CIS) of the University Hospital Maastricht. Sensitivities and positive predictive values were calculated using the CIS-based registry as gold standard. Relatively high sensitivities and positive predictive values were found for CHD (72 and 91%, respectively) and acute myocardial infarction (84 and 97%, respectively). These values were considerably lower for unstable angina pectoris (53 and 78%, respectively) and heart failure (43 and 80%, respectively). A substantial number of cases (14-47%) were found only in the CIS-based registry, because they were missed or miscoded in the HDR-based registry. As a consequence, the incidence rates in the HDR-based registry were considerably lower than in the CIS-based registry, especially for unstable angina pectoris and heart failure. Incidence rates based on hospital discharge and mortality data may underestimate the true incidence rates, especially for unstable angina pectoris and heart failure.

The hippocampal expression profiles of wild-type mice and mice transgenic for deltaC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained approximately 2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and microarrays was most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observed by microarrays or quantitative PCR. Relevant processes such as calmodulin-dependent protein kinase activity and vesicle transport along microtubules were found affected by deep sequencing but not by microarrays. While undetectable by microarrays, antisense transcription was found for 51% of all genes and alternative polyadenylation for 47%. We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies.

The known genetic variants determining plasma HDL cholesterol (HDL-C) levels explain only part of its variation. Three hundred eighty-four single nucleotide polymorphisms (SNPs) across 251 genes based on pathways potentially relevant to HDL-C metabolism were selected and genotyped in 3,575 subjects from the Doetinchem cohort, which was examined thrice over 11 years. Three hundred fifty-three SNPs in 239 genes passed the quality-control criteria. Seven SNPs [rs1800777 and rs5882 in cholesteryl ester transfer protein (CETP); rs3208305, rs328, and rs268 in LPL; rs1800588 in LIPC; rs2229741 in NRIP1] were associated with plasma HDL-C levels with false discovery rate (FDR) adjusted q values (FDR&#95;q) < 0.05. Five other SNPs (rs17585739 in SC4MOL, rs11066322 in PTPN11, rs4961 in ADD1, rs6060717 near SCAND1, and rs3213451 in MBTPS2 in women) were associated with plasma HDL-C levels with FDR&#95;q between 0.05 and 0.2. Two less well replicated associations (rs3135506 in APOA5 and rs1800961 in HNF4A) known from the literature were also observed, but their significance disappeared after adjustment for multiple testing (P = 0.008, FDR&#95;q = 0.221 for rs3135506; P = 0.018, FDR&#95;q = 0.338 for rs1800961, respectively). In addition to replication of previous results for candidate genes (CETP, LPL, LIPC, HNF4A, and APOA5), we found interesting new candidate SNPs (rs2229741 in NRIP1, rs3213451 in MBTPS2, rs17585739 in SC4MOL, rs11066322 in PTPN11, rs4961 in ADD1, and rs6060717 near SCAND1) for plasma HDL-C levels that should be evaluated further.

Objective: To establish whether the Finnish diabetes risk score for predicting the incidence of diabetes (FINDRISK) is also valid in the Netherlands, and to choose cut-off points suitable for the Dutch situation., Design: . Descriptive., Method: The FINDRISK was validated in 3 Dutch cohort studies by means of repeated glucose measurements: the Hoorn study (n=5434), the PREVEND study (n=2713) and part of the Maastricht cohort from the MORGEN study (n=863). The predictive value was evaluated using receiver operating characteristic (ROC) analyses. The risk categories were defined on the basis of sensitivity, specificity and positive predictive value., Results: The predictive value of the FINDRISK was best in the PREVEND cohort (area under the ROC curve 0.77) and was lower for the Hoorn study and the Maastricht cohort (area under the ROC-curve 0.71 for both). The scores were divided into three risk categories: low risk (score lower than 7), slightly increased risk (score 7-9) and increased risk (score so or higher). The percentage of persons with incident diabetes within about 5 years was < 6 in the low risk category, 6-14 in the category with slightly increased risk and 12-26 in the category with increased risk. 16-28% of the Dutch population studied had a score of 10 or higher., Conclusion: The FINDRISK is a reasonably good predictor for incident diabetes in the Netherlands.

Background: Whether mutations in the hemochromatosis (HFE) gene increase cardiovascular disease risk is still undetermined. The main reason is the low frequency of the mutations, in particular of the compound C282Y/H63D genotype. We combined the data of 11 observational studies for an individual patient data meta-analysis., Methods and Results: Individual patient data were obtained from published as well as unpublished studies that had information available on the C282Y mutation as well as the H63D mutation in relation to coronary heart disease risk. Individual records were provided on each of the 53 880 participants in 11 studies. In total, 10 541 patients with coronary events were documented, of whom 5724 had an acute myocardial infarction. The crude and adjusted association between HFE genotypes and coronary events was examined by logistic regression analysis. We explored potential effect modification of the association between traditional cardiovascular risk factors and coronary events by HFE genotypes. After full adjustment, the odds ratio for coronary heart disease was 1.12 (95% CI, 0.92 to 1.37) for subjects with the compound heterozygous (C282Y/H63D) genotype relative to those with the wild-type/wild-type genotype. The odds ratios for C282Y/C282Y, C282Y/wild-type, H63D/H63D, and H63D/wild-type were 0.78 (95% CI, 0.49 to 1.26), 0.98 (95% CI, 0.90 to 1.07), 1.16 (95% CI, 0.97 to 1.38), and 1.07 (95% CI, 1.00 to 1.14), respectively. There was no evidence for effect modification., Conclusions: The results of this large individual patient data meta-analysis do not support the view that HFE gene mutations are associated with an increased risk of coronary heart disease or acute myocardial infarction.

Cholesteryl ester transfer protein (CETP) and hepatic lipase (HL) are two HDL modifying proteins that have both pro- and anti-atherogenic properties. We hypothesized that CETP and HL synergistically affect HDL cholesterol and atherosclerotic risk. To test our hypothesis, we analysed the genotype frequencies of CETP Taq1B (rs708272) and LIPC-514C/T (rs1800588) polymorphisms in male coronary artery disease patients (CAD; n=792) and non-symptomatic controls (n=539). Cases and controls had similar allele frequencies, but the occurrence of the combined genotypes differed (p=0.027). In CAD patients, 1.3% had the CETP-B2B2/LIPC-TT genotype, with only 0.2% in controls (p=0.033). The presence of the CETP lowering B2 allele and the HL lowering LIPC-T allele synergistically increased HDL cholesterol from 0.87+/-0.19 mmol/L in the B1B1/CC (n=183) to 1.21+/-0.25 mmol/L in the B2B2/TT carriers (n=10). The B1B1/CC carriers had an increased CAD risk (OR 1.4; p=0.025). Despite their high HDL cholesterol, the B2B2/TT individuals also had an increased CAD risk (OR 3.7; p=0.033). In a 2-year follow up, the loss of coronary artery lumen diameter in these patients was higher than in all other patients combined (0.34+/-0.70 versus 0.10+/-0.29 mm; p=0.044). We conclude that a high HDL cholesterol does not protect against coronary artery disease when associated with combined CETP- and HL-lowering gene variants.

Expression profiling is a well established tool for the genome-wide analysis of human cancers. However, the high sensitivity of this approach combined with the well known cellular and molecular heterogeneity of cancer often result in extremely complex expression signatures that are difficult to interpret functionally. The majority of sporadic colorectal cancers are triggered by mutations in the adenomatous polyposis coli (APC) tumor suppressor gene, leading to the constitutive activation of the Wnt/beta-catenin signaling pathway and formation of adenomas. Despite this common genetic basis, colorectal cancers are very heterogeneous in their degree of differentiation, growth rate, and malignancy potential. Here, we applied a cross-species comparison of expression profiles of intestinal polyps derived from hereditary colorectal cancer patients carrying APC germline mutations and from mice carrying a targeted inactivating mutation in the mouse homologue Apc. This comparative approach resulted in the establishment of a conserved signature of 166 genes that were differentially expressed between adenomas and normal intestinal mucosa in both species. Functional analyses of the conserved genes revealed a general increase in cell proliferation and the activation of the Wnt/beta-catenin signaling pathway. Moreover, the conserved signature was able to resolve expression profiles from hereditary polyposis patients carrying APC germline mutations from those with bi-allelic inactivation of the MYH gene, supporting the usefulness of such comparisons to discriminate among patients with distinct genetic defects.

The human immunodeficiency virus (HIV) damages fronto-striatal regions, and is associated with deficits in executive functioning. We recently developed a semantic event sequencing task based on the Picture Arrangement subtest of the Wechsler Adult Intelligence Scale-III for use with functional magnetic resonance imaging (fMRI) and found recruitment of dorsolateral prefrontal cortex and basal ganglia in healthy participants. To assess the impact of HIV on the functioning of the basal ganglia and prefrontal cortex, we administered this task to 11 HIV+ and 11 Control participants matched for age and education. Neuropsychological evaluation demonstrated that the HIV+ group had mild impairment in memory retrieval and motor functioning, but was not demented. Morphometric measurements suggested no atrophy in basal ganglia regions. The results of the fMRI analysis revealed hypoactivation of the left caudate, left dorsolateral prefrontal cortex, and bilateral ventral prefrontal cortex in the HIV+ group. Functional connectivity analysis demonstrated less functional connectivity between the caudate and prefrontal cortex and basal ganglia regions in the HIV+ group. In contrast, the HIV+ group demonstrated increased activation of right postcentral/supramarginal gyrus, and greater connectivity between the caudate and this same anterior parietal region. The results of this study extend previous investigations by demonstrating compromised function of the caudate and connected prefrontal regions in HIV during cognition. This disruption of fronto-striatal circuitry likely precedes the development of cognitive impairment in HIV.

In whole genome microarray studies major gene expression changes are easily identified, but it is a challenge to capture small, but biologically important, changes. Pathway-based programs can capture small effects but may have the disadvantage of being restricted to functionally annotated genes. A structured approach toward the identification of major and small changes for interpretation of biological effects is needed. We present a structured approach, a framework, that addresses different considerations in 1) the identification of informative genes in microarray data sets and 2) the interpretation of their biological relevance. The steps of this framework include gene ranking, gene selection, gene grouping, and biological interpretation. Random forests (RF), which takes gene-gene interactions into account, is examined to rank and select genes. For human, mouse, and rat whole genome arrays, less than half of the probes on the array are annotated. Consequently, pathway analysis tools ignore half of the information present in the microarray data set. The framework described takes all genes into account. RF is a useful tool to rank genes by taking interactions into account. Applying a permutation approach, we were able to define an objective threshold for gene selection. RF combined with self-organizing maps identified genes with coordinated but small gene expression responses that were not fully annotated but corresponded to the same biological process. The presented approach provides a flexible framework for biological interpretation of microarray data sets. It includes all genes in the data set, takes gene-gene interactions into account, and provides an objective threshold for gene selection.

Background: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle., Results: Gene expression profiles in the hippocampus of five wild-type and five transgenic deltaC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms., Conclusion: The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.

We report the generation of mice with an intact and functional copy of the 2.3-megabase human dystrophin gene (hDMD), the largest functional stretch of human DNA thus far integrated into a mouse chromosome. Yeast spheroplasts containing an artificial chromosome with the full-length hDMD gene were fused with mouse embryonic stem cells and were subsequently injected into mouse blastocysts to produce transgenic hDMD mice. Human-specific PCR, Southern blotting, and fluorescent in situ hybridization techniques demonstrated the intactness and stable chromosomal integration of the hDMD gene on mouse chromosome 5. Expression of the transgene was confirmed by RT-PCR and Western blotting. The tissue-specific expression pattern of the different DMD transcripts was maintained. However, the human Dp427p and Dp427m transcripts were expressed at 2-fold higher levels and human Dp427c and Dp260 transcripts were expressed at 2- and 4-fold lower levels than their endogenous counterparts. Ultimate functional proof of the hDMD transgene was obtained by crossing of hDMD mice with dystrophin-deficient mdx mice and dystrophin and utrophin-deficient mdx x Utrn-/- mice. The hDMD transgene rescued the lethal dystrophic phenotype of the mdx x Utrn-/- mice. All signs of muscular dystrophy disappeared in the rescued mice, as demonstrated by histological staining of muscle sections and gene expression profiling experiments. Currently, hDMD mice are extensively used for preclinical testing of sequence-specific therapeutics for the treatment of Duchenne muscular dystrophy. In addition, the hDMD mouse can be used to study the influence of the genomic context on deletion and recombination frequencies, genome stability, and gene expression regulation.

Genome-wide and hypothesis-based approaches to the study of ageing and longevity have been dominated by genetic investigations. To identify essential mechanisms of a complex trait such as ageing in higher species, a holistic understanding of interacting pathways is required. More information on such interactions is expected to be obtained from global gene expression analysis if combined with genetic studies. Genetic sequence variation often provides a functional gene marker for the trait, whereas a gene expression profile may provide a quantitative biomarker representing complex cellular pathway interactions contributing to the trait. Thus far, gene expression studies have associated multiple pathways to ageing including mitochondrial electron transport and the oxidative stress response. However, most of the studies are underpowered to detect small age-changes. A systematic survey of gene expression changes as a function of age in human individuals and animal models is lacking. Well designed gene expression studies, especially at the level of biological processes, will provide hypotheses on gene-environmental interactions determining biological ageing rate. Cross-sectional studies monitoring the profile as a chronological marker of ageing must be integrated with prospective studies indicating which profiles represent biomarkers preceding and predicting physiological decline and mortality. New study designs such as the Leiden Longevity Study, including two generations of subjects from longevity families, aim to achieve these combined approaches.