Multivariable clinical-genetic risk model for predicting venous thromboembolic events in patients with cancer.

BACKGROUND: Venous thromboembolism (VTE) is a leading cause of death among patients with cancer. Outpatients with cancer should be periodically assessed for VTE risk, for which the Khorana score is commonly recommended. However, it has been questioned whether this tool is sufficiently accurate at identifying patients who should receive thromboprophylaxis. The present work proposes a new index, TiC-Onco risk score to be calculated at the time of diagnosis of cancer, that examines patients' clinical and genetic risk factors for thrombosis. METHODS: We included 391 outpatients with a recent diagnosis of cancer and candidates for systemic outpatient chemotherapy. All were treated according to standard guidelines. The study population was monitored for 6 months, and VTEs were recorded. The Khorana and the TiC-Onco scores were calculated for each patient and their VTE predictive accuracy VTEs was compared. RESULTS: We recorded 71 VTEs. The TiC-Onco risk score was significantly better at predicting VTE than the Khorana score (AUC 0.73 vs. 0.58, sensitivity 49 vs. 22%, specificity 81 vs. 82%, PPV 37 vs. 22%, and NPV 88 vs. 82%). CONCLUSIONS: TiC-Onco risk score performed significantly better than Khorana score at identifying cancer patients at high risk of VTE who would benefit from personalised thromboprophylaxis.

Di-Calcium Phosphate and Phytosphingosine as an Innovative Acid-Resistant Treatment to Occlude Dentine Tubules.

The present investigation evaluated the ability of an experimental di-calcium phosphate (DCP) desensitising agent used alone or combined with phytosphingosine (PHS) to occlude dentine tubules and resist a citric acid (CA) or artificial saliva (AS) challenge. Three groups of human dentine specimens (DS) were treated with the following: (1) PHS alone, (2) DCP or (3) a combination of PHS and DCP. Dentine hydraulic conductance of DS was evaluated using a digital flow sensor at 6.9 kPa. The average fluid volume for each of the treated DS was used to calculate the total dentine permeability reduction (%P) prior to and following CA immersion for 1 min or AS immersion for 4 weeks. The treated DS were subjected to both scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy analysis. Statistically significant differences (%P) were identified between the groups by ANOVA and Fisher's multiple comparison test (p < 0.05), respectively. Interestingly, both PHS and DCP appeared to work synergistically. DS treated with DCP or PHS/DCP demonstrated a significant reduction (%P) prior to and following CA or AS challenge (p < 0.05). Both the SEM and FTIR analyses showed consistent brushite crystals occluding the dentine tubules. Conversely, the application of PHS alone failed to demonstrate any significant reduction of dentine permeability (p > 0.05) or show any evidence of occlusion of the dentine tubules. DCP can be used alone or combined with PHS to decrease the dentine permeability as well as to resist a CA and AS challenge. These results would, therefore, suggest that DCP may be a suitable treatment option for dentine hypersensitivity.

Genetic determinants of cardiometabolic risk factors in rural families in Brazil.

OBJECTIVES: The purpose of this study was to estimate the heritability of genetic and environmental correlations between cardiometabolic risk factors in extended pedigrees. METHODS: The Jequitinhonha Community Family Study Cohort (JCFSC) consists of individuals aged ≥18 years living in rural villages. Family pedigrees were constructed of the cohort. The following data were collected: demographic and socioeconomic status, lifestyle variables, anthropometrics, and lipid traits. RESULTS: The JCFSC consists of 931 individuals distributed into 69 pedigrees with 4,907 members in total. The heritabilities were 0.47 for total cholesterol (TC), 0.44 for triglycerides (TG) and 0.42 for high-density lipoprotein cholesterol (HDLc), 0.49 for metabolic syndrome, approximately 0.60 for anthropometric traits and 0.30 for blood pressure/hypertension. Significant genetic correlations (ρg ) were found mainly between TG and TC (ρg = 0.58) and hypertension and TG (ρg = 0.52). Systolic blood pressure (SBP) was correlated with TG (ρg = 0.39) and HDLc (ρg = -0.30). Diastolic blood pressures correlated with TG (ρg =0.56) and TC (ρg =0.30). Genetic correlations were also found between anthropometric traits, including: body mass index (BMI) and TG (ρg =0.34), waist circumference (WC) and TG (ρg =0.42), and WC and HDLc (ρg =-0.33). Household effects were found for HDLc (c(2) = 0.19), SBP (c(2) = 0.14) and Hypertension (c(2) = 0.14). CONCLUSIONS: To some phenotypes, including lipids, hypertension, blood pressure, and anthropometric traits, genetic contribution is important in the determination of cardiometabolic risk factors. This study provides a foundation for future studies. These will mainly focus on rare variants that could describe the genetic mechanisms influencing cardiometabolic risk. Am. J. Hum. Biol. 28:619-626, 2016. © 2016 Wiley Periodicals, Inc.

Identification of a novel quantitative trait nucleotype related to iron status in a calcium channel gene.

Several iron-related parameters have been reported to show significant heritability, and thus, seemed to be genetically regulated. A genome wide family-based study revealed two regions that showed a linkage signal with transferrin receptor levels. The aim of the study was to identify genetic markers associated with iron status biomarkers. Ten SNPs selected from the literature were tested, and parameters related to iron metabolism were analysed, in a group (n=284) of Spanish women. Data were analyzed using Bayesian Model Averaging (BMA) test and decision trees. The rs1375515, located in an intronic region of the calcium channel gene CACNA2D3, showed strong associations with levels of mean corpuscular volume according to BMA test, and with levels of haemoglobin and ferritin according to decision trees. The allele G was associated to low levels of these parameters which suggests higher iron deficiency anaemia risk. This SNP along with the C282Y mutation explained significant differences in the distribution of individuals in three iron-related clinical phenotypes (normal, iron deficient and iron deficiency anaemic). In conclusion, the rs1375515, or other genetic polymorphisms in linkage, may play important roles in iron status, probably by affecting the function of a calcium channel. These findings may be useful for further investigation in the etiology of iron diseases.

Bisphosphonates-related osteonecrosis of the jaws: a preliminary study of salivary interleukins.

OBJECTIVE: The aim of this preliminary study was analyze the possible alterations in some salivary interleukins, usually associated with the inflammatory processes. MATERIAL AND METHODS: The study comprised three groups: group 1, with 26 cases with bisphosphonates-related osteonecrosis of the jaws (BRONJ). Group 2, with 29 patients who had received iBF but without BRONJ. Group 3, with 26 control patients not treated with BF and without oral lesions. We collected unstimulated whole saliva in all groups. A semiquantitative study was performed based on a cytokine array panel. We used the proteome profiler array for the study. We analyzed: Interleukin 1 alpha (IL-1α), interleukin-1 receptor antagonist (IL-1RA), and interleukin 1 beta (IL-1ß). RESULTS: We found higher salivary values for all the cytokines studied in group 1 than in group 2 and 3. IL-1ß showed the major differences compared with control group. (P < 0.05) CONCLUSIONS: This preliminary study confirms that there are alterations in these interleukins in patients with BRONJ. These results give support to further additional salivary studies on these biomarkers by quantitative measures.

Four variants in transferrin and HFE genes as potential markers of iron deficiency anaemia risk: an association study in menstruating women.

BACKGROUND: Iron deficiency anaemia is a worldwide health problem in which environmental, physiologic and genetic factors play important roles. The associations between iron status biomarkers and single nucleotide polymorphisms (SNPs) known to be related to iron metabolism were studied in menstruating women. METHODS: A group of 270 Caucasian menstruating women, a population group at risk of iron deficiency anaemia, participated in the study. Haematological and biochemical parameters were analysed and 10 selected SNPs were genotyped by minisequencing assay. The associations between genetic and biochemical data were analysed by Bayesian Model Averaging (BMA) test and decision trees. Dietary intake of a representative subgroup of these volunteers (n = 141) was assessed, and the relationship between nutrients and iron biomarkers was also determined by linear regression. RESULTS: Four variants, two in the transferrin gene (rs3811647, rs1799852) and two in the HFE gene (C282Y, H63D), explain 35% of the genetic variation or heritability of serum transferrin in menstruating women. The minor allele of rs3811647 was associated with higher serum transferrin levels and lower transferrin saturation, while the minor alleles of rs1799852 and the C282Y and H63D mutations of HFE were associated with lower serum transferrin levels. No association between nutrient intake and iron biomarkers was found. CONCLUSIONS: In contrast to dietary intake, these four SNPs are strongly associated with serum transferrin. Carriers of the minor allele of rs3811647 present a reduction in iron transport to tissues, which might indicate higher iron deficiency anaemia risk, although the simultaneous presence of the minor allele of rs1799852 and HFE mutations appear to have compensatory effects. Therefore, it is suggested that these genetic variants might potentially be used as markers of iron deficiency anaemia risk.

Antithrombin Cambridge II (A384S) supports a role for antithrombin deficiency in arterial thrombosis.

Although the control of thrombin in the microvasculature at the endothelial cell surface is crucial to prevent atherothrombosis, the role of antithrombin in arterial thrombosis is unclear. It is widely considered that antithrombin deficiency is unlikely to contribute to arterial thrombosis, but no convincing epidemiological study has been performed because of the low frequency of this deficiency. In this study we evaluated the role in myocardial infarction (MI) of a relatively common mutation affecting antithrombin gene (A384S: Antithrombin Cambridge II) that has functional features that may impair the right control of thrombogenic events caused by injury to the vascular wall. Moreover, this deficiency, which is not detected using common methods to diagnose antithrombin deficiency, also increases the risk of venous thrombosis. We included 1,224 patients with MI (691 consecutive patients and 533 survivors of a premature event), and 1,649 controls. The mutation was identified in 0.3% of controls, but 0.8% of MI patients. After adjusting for sex and other cardiovascular risk factors, the antithrombin Cambridge II significantly increased 5.66-fold the risk of MI (95% CI: 1.53-20.88; p = 0.009). Interestingly, young patients had the highest risk of MI associated with the mutation (OR: 9.98; 95%CI: 1.60-62.24; p = 0.009). This is the first epidemiological study that supports a role for antithrombin deficiency in arterial thrombosis. These results suggest that deficiency of antithrombin may be an independent risk factor for MI that has been underestimated, but larger studies are needed to confirm the relevance of inhibitors of thrombin in arterial thrombosis.

Heritability of plasma concentrations of activated protein C in a Spanish population.

The protein C anticoagulant pathway plays a crucial role in the regulation of fibrin formation. Protein C is activated on the surface of endothelial cells by the thrombin-thrombomodulin complex with the stimulation of the endothelial protein C receptor. The levels of circulating activated protein C reflect in-vivo protein C activation, and a low level of activated protein C is a risk factor for venous thromboembolism. The objective of the study was to assess the relative contributions of genetic and environmental factors to the variation in the levels of activated protein C and protein C. Blood samples were collected from 126 individuals belonging to 19 Spanish families, and heritability and common household effect were estimated for protein C, activated protein C and its complexes with protein C and alpha1-antitrypsin. In addition, we calculated the genetic correlation between protein C and activated protein C phenotypes. Although all phenotypes showed significant heritability, activated protein C phenotype resulted in a very high heritability of 83%, which clearly shows that this phenotype is strongly influenced by the action of gene(s). Furthermore, the bivariant analyses of protein C and activated protein C phenotypes indicate that there is a high genetic correlation between them (0.74). Nevertheless, this correlation is counteracted by a negative environmental correlation (-0.54) resulting in a phenotypic correlation of 0.35. The presence of such strong genetic effects suggests that it will be possible to localize the loci that influence this phenotype and determine the contribution to the risk of thrombosis.

Investigation of the fine structure of European populations with applications to disease association studies.

An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North-South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.

A sequence variation scan of the coagulation factor VIII (FVIII) structural gene and associations with plasma FVIII activity levels.

Plasma factor VIII coagulant activity (FVIII:C) level is a highly heritable quantitative trait that is strongly correlated with thrombosis risk. Polymorphisms within only 1 gene, the ABO blood-group locus, have been unequivocally demonstrated to contribute to the broad population variability observed for this trait. Because less than 2.5% of the structural FVIII gene (F8) has been examined previously, we resequenced all known functional regions in 222 potentially distinct alleles from 137 unrelated nonhemophilic individuals representing 7 racial groups. Eighteen of the 47 variants identified, including 17 single-nucleotide polymorphisms (SNPs), were previously unknown. As the degree of linkage disequilibrium across F8 was weak overall, we used measured-genotype association analysis to evaluate the influence of each polymorphism on the FVIII:C levels in 398 subjects from 21 pedigrees known as the Genetic Analysis of Idiopathic Thrombophilia project (GAIT). Our results suggested that 92714C>G, a nonsynonymous SNP encoding the B-domain substitution D1241E, was significantly associated with FVIII:C level. After accounting for important covariates, including age and ABO genotype, the association persisted with each C-allele additively increasing the FVIII:C level by 14.3 IU dL(-1) (P = .016). Nevertheless, because the alleles of 56010G>A, a SNP within the 3' splice junction of intron 7, are strongly associated with 92714C>G in GAIT, additional studies are required to determine whether D1241E is itself a functional variant.

Searching for master regulators of transcription in a human gene expression data set.

Microarray technologies allow the measurement of the expression levels of thousands of transcripts at the same time. As part of Genetic Analysis Workshop 15 (GAW15), we analyzed a data set that measured the expression of more than 3000 genes in 14 families. Our goal was to identify genomic regions that regulate the expression of several genes at the same time. We tried two different approaches: one was maximum likelihood-based variance-component linkage analysis and the other was a new linkage regression approach. We detected some loci that were linked with the expression level of more genes than would be expected by chance. These loci are candidates for master regulators of transcription (MRT). Finally, for each candidate MRT, we did a gene ontology (GO) analysis to test whether the genes linked to it were biologically related.

Homozygosity of the T allele of the 46 C-->T polymorphism in the F12 gene is a risk factor for acute coronary artery disease in the Spanish population.

Following new guidelines that contain recommendations on the desirable features of a genetic association study, we performed a case-control study to establish the risk of acute coronary artery disease (CAD) related to the polymorphism (46 C-->T) in the F12 gene. We found a 6-fold higher risk of acute CAD associated with the homozygosity of the T allele of the F12, 46C-->T polymorphism in the Spanish population.