Primary stability with osseodensification drilling of dental implants in the posterior maxilla region in humans: A systematic review.

Currently, a new non-subtractive drilling technique, called osseodensification (OD), has been developed. It involves using specially designed drills with large negative cutting angles that rotate counterclockwise, causing expansion through plastic bone deformation, thus compacting the autologous bone to the osteotomy walls, which improves the primary stability of the implant.The present systematic review aimed to determine whether the OD technique can increase the primary stability of dental implants in the posterior maxilla region as compared to the conventional drilling (CD) technique.Five databases were searched up to June 30, 2022. The inclusion criteria embraced observational clinical studies, randomized and non-randomized controlled trials, human studies in vivo, comparing OD and CD, with the measurement of the primary stability of implants in the posterior maxilla region by means of the implant stability quotient (ISQ). The tools used to assess the risk of bias were RoB 2 and the NewcastleOttawa Scale (NOS).Seven articles met the inclusion criteria, with 4 classified as having a low risk of bias and 3 with a moderate risk of bias. The OD technique consistently demonstrated an average ISQ value of 73 KHz across all studies, whereas CD yielded an average value of 58.49 kHz (p < 0.001 for 5 articles).It can be concluded that in comparison with CD, OD improves primary stability at baseline in low-density bone, such as the maxilla.

Predicting Injuries in Elite Female Football Players With Global-Positioning-System and Multiomics Data.

PURPOSE: Injury prevention is a crucial aspect of sports, particularly in high-performance settings such as elite female football. This study aimed to develop an injury prediction model that incorporates clinical, Global-Positioning-System (GPS), and multiomics (genomics and metabolomics) data to better understand the factors associated with injury in elite female football players. METHODS: We designed a prospective cohort study over 2 seasons (2019-20 and 2021-22) of noncontact injuries in 24 elite female players in the Spanish Premiership competition. We used GPS data to determine external workload, genomic data to capture genetic susceptibility, and metabolomic data to measure internal workload. RESULTS: Forty noncontact injuries were recorded, the most frequent of which were muscle (63%) and ligament (20%) injuries. The baseline risk model included fat mass and the random effect of the player. Six genetic polymorphisms located at the DCN, ADAMTS5, ESRRB, VEGFA, and MMP1 genes were associated with injuries after adjusting for player load (P < .05). The genetic score created with these 6 variants determined groups of players with different profile risks (P = 3.1 × 10-4). Three metabolites (alanine, serotonin, and 5-hydroxy-tryptophan) correlated with injuries. The model comprising baseline variables, genetic score, and player load showed the best prediction capacity (C-index: .74). CONCLUSIONS: Our model could allow efficient, personalized interventions based on an athlete's vulnerability. However, we emphasize the necessity for further research in female athletes with an emphasis on validation studies involving other teams and individuals. By expanding the scope of our research and incorporating diverse populations, we can bolster the generalizability and robustness of our proposed model.

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2.

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people.

Impact of tobacco, alcohol, and marijuana on genome-wide DNA methylation and its relationship with hypertension.

Tobacco, alcohol, and marijuana consumption is an important public health problem because of their high use worldwide and their association with the risk of mortality and many health conditions, such as hypertension, which is the commonest risk factor for death throughout the world. A likely pathway of action of substance consumption leading to persistent hypertension is DNA methylation. Here, we evaluated the effects of tobacco, alcohol, and marijuana on DNA methylation in the same cohort (N = 3,424). Three epigenome-wide association studies (EWAS) were assessed in whole blood using the InfiniumHumanMethylationEPIC BeadChip. We also evaluated the mediation of the top CpG sites in the association between substance consumption and hypertension. Our analyses showed 2,569 CpG sites differentially methylated by alcohol drinking and 528 by tobacco smoking. We did not find significant associations with marijuana consumption after correcting for multiple comparisons. We found 61 genes overlapping between alcohol and tobacco that were enriched in biological processes involved in the nervous and cardiovascular systems. In the mediation analysis, we found 66 CpG sites that significantly mediated the effect of alcohol consumption on hypertension. The top alcohol-related CpG site (cg06690548, P-value = 5.9·10-83) mapped to SLC7A11 strongly mediated 70.5% of the effect of alcohol consumption on hypertension (P-value = 0.006). Our findings suggest that DNA methylation should be considered for new targets in hypertension prevention and management, particularly concerning alcohol consumption. Our data also encourage further research into the use of methylation in blood to study the neurological and cardiovascular effects of substance consumption.

The consumption of tobacco, alcohol, and marijuana is very high worldwide and is associated with common diseases, like cardiovascular and neurological disorders.This study found that tobacco and alcohol have large effects on genome wide DNA methylation while marijuana consumption has nonsignificant effects.The genes differentially methylated were enriched in pathways related to neurodevelopment, suggesting the mediation between recreational drug consumption and neurological disorders.More remarkably, 66 alcohol related CpG sites significantly mediated the association between heavy drinking and hypertension.Our findings suggest that DNA methylation changes should be considered for new targets in disease prevention for recreational drug consumers.

Prenatal environmental exposures associated with sex differences in childhood obesity and neurodevelopment.

BACKGROUND: Obesity and neurodevelopmental delay are complex traits that often co-occur and differ between boys and girls. Prenatal exposures are believed to influence children's obesity, but it is unknown whether exposures of pregnant mothers can confer a different risk of obesity between sexes, and whether they can affect neurodevelopment. METHODS: We analyzed data from 1044 children from the HELIX project, comprising 93 exposures during pregnancy, and clinical, neuropsychological, and methylation data during childhood (5-11 years). Using exposome-wide interaction analyses, we identified prenatal exposures with the highest sexual dimorphism in obesity risk, which were used to create a multiexposure profile. We applied causal random forest to classify individuals into two environments: E1 and E0. E1 consists of a combination of exposure levels where girls have significantly less risk of obesity than boys, as compared to E0, which consists of the remaining combination of exposure levels. We investigated whether the association between sex and neurodevelopmental delay also differed between E0 and E1. We used methylation data to perform an epigenome-wide association study between the environments to see the effect of belonging to E1 or E0 at the molecular level. RESULTS: We observed that E1 was defined by the combination of low dairy consumption, non-smokers' cotinine levels in blood, low facility richness, and the presence of green spaces during pregnancy (ORinteraction = 0.070, P = 2.59 × 10-5). E1 was also associated with a lower risk of neurodevelopmental delay in girls, based on neuropsychological tests of non-verbal intelligence (ORinteraction = 0.42, P = 0.047) and working memory (ORinteraction = 0.31, P = 0.02). In line with this, several neurodevelopmental functions were enriched in significant differentially methylated probes between E1 and E0. CONCLUSIONS: The risk of obesity can be different for boys and girls in certain prenatal environments. We identified an environment combining four exposure levels that protect girls from obesity and neurodevelopment delay. The combination of single exposures into multiexposure profiles using causal inference can help determine populations at risk.

Bioavailability of Oniria®, a Melatonin Prolonged-Release Formulation, Versus Immediate-Release Melatonin in Healthy Volunteers.

BACKGROUND: Melatonin is an endogenous substance which plays a key role in sleep induction by reducing sleep onset latency; it has been approved by the European Food Safety Authority as a food supplement for exogenous administration. Oniria® is a food supplement formulated as 1.98 mg of prolonged-release melatonin tablets; it displays a dual dissolution profile in vitro. OBJECTIVES: The main objective of the present study was to evaluate the relative oral bioavailability of Oniria®, in comparison with immediate-release tablets (IRT) with a similar melatonin content as a reference. We also attempted to characterize the circadian rhythm of endogenous melatonin. METHODS: We performed an open-label, cross-over, randomized, phase I clinical study with two sequences and three periods involving 14 healthy volunteers. We characterized the endogenous melatonin circadian profile (period 1) and pharmacokinetics (PK) of both Oniria® and the reference melatonin (periods 2 and 3). RESULTS: Two phases were clearly differentiated in the PK profile of Oniria®. An initial one, from dosing up to 2 h, and a delayed one from 2 to 11 h post-administration. During the initial phase, both melatonin formulations were equivalent, with a Cmax value close to 4000 pg/mL. However, in the delayed phase, Oniria® showed significantly higher melatonin concentrations than the IRT (three times higher at 4-6 h post-administration). Moreover, Oniria® exhibited concentrations above the endogenous melatonin peak of 80 pg/mL for up to 2.5 h versus the reference formulation, potentially suggesting an effect of Oniria®, not only in the induction of sleep, but also in the maintenance. CONCLUSION: Oniria® could be a highly promising food supplement, not only for sleep induction but also for the maintenance of sleep.

The early-life exposome modulates the effect of polymorphic inversions on DNA methylation.

Polymorphic genomic inversions are chromosomal variants with intrinsic variability that play important roles in evolution, environmental adaptation, and complex traits. We investigated the DNA methylation patterns of three common human inversions, at 8p23.1, 16p11.2, and 17q21.31 in 1,009 blood samples from children from the Human Early Life Exposome (HELIX) project and in 39 prenatal heart tissue samples. We found inversion-state specific methylation patterns within and nearby flanking each inversion region in both datasets. Additionally, numerous inversion-exposure interactions on methylation levels were identified from early-life exposome data comprising 64 exposures. For instance, children homozygous at inv-8p23.1 and higher meat intake were more susceptible to TDH hypermethylation (P = 3.8 × 10-22); being the inversion, exposure, and gene known risk factors for adult obesity. Inv-8p23.1 associated hypermethylation of GATA4 was also detected across numerous exposures. Our data suggests that the pleiotropic influence of inversions during development and lifetime could be substantially mediated by allele-specific methylation patterns which can be modulated by the exposome.

teff: estimation of Treatment EFFects on transcriptomic data using causal random forest.

MOTIVATION: Causal inference on high-dimensional feature data can be used to find a profile of patients who will benefit the most from treatment rather than no treatment. However, there is a need for usable implementations for transcriptomic data. We developed teff that applies random causal forest on gene expression data to target individuals with high expected treatment effects. RESULTS: We extracted a profile of high benefit of treating psoriasis with brodalumab and observed that it was associated with higher T cell abundance in non-lesional skin at baseline and a lower response for etanercept in an independent study. Individual patient targeting with causal inference profiling can inform patients on choosing between treatments before the intervention begins. AVAILABILITY AND IMPLEMENTATION: teff is an R package available at https://teff-package.github.io. The data underlying this article are available in GEO, at https://www.ncbi.nlm.nih.gov/geo/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.

Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.

Sex Differences in the Association between Risk of Anterior Cruciate Ligament Rupture and COL5A1 Polymorphisms in Elite Footballers.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) in collagen genes are predisposing factors for anterior cruciate ligament (ACL) rupture. Although these events are more frequent in females, the sex-specific risk of reported SNPs has not been evaluated. PURPOSE: We aimed to assess the sex-specific risk of historic non-contact ACL rupture considering candidate SNPs in genes previously associated with muscle, tendon, ligament and ACL injury in elite footballers. STUDY DESIGN: This was a cohort genetic association study. METHODS: Forty-six (twenty-four females) footballers playing for the first team of FC Barcelona (Spain) during the 2020-21 season were included in the study. We evaluated the association between a history of non-contact ACL rupture before July 2022 and 108 selected SNPs, stratified by sex. SNPs with nominally significant associations in one sex were then tested for their interactions with sex on ACL. RESULTS: Seven female (29%) and one male (4%) participants had experienced non-contact ACL rupture during their professional football career before the last date of observation. We found a significant association between the rs13946 C/C genotype and ACL injury in women footballers (p = 0.017). No significant associations were found in male footballers. The interaction between rs13946 and sex was significant (p = 0.027). We found that the C-allele of rs13946 was exclusive to one haplotype of five SNPs spanning COL5A1. CONCLUSIONS: The present study suggests the role of SNPs in genes encoding for collagens as female risk factors for ACL injury in football players. CLINICAL RELEVANCE: The genetic profiling of athletes at high risk of ACL rupture can contribute to sex-specific strategies for injury prevention in footballers.

Benefits of the application of heat and pressure on peripheral venous cannulation in adults: A randomized controlled trial.

AIM: To evaluate the effectiveness of the application of topical heat, high pressure or a combination of both on antebrachial venous cannulation. DESIGN: A cross-over clinical trial blinded for haemolysis analysis. METHODS: This cross-over clinical trial with two periods was performed in the Clinical Trial Unit of Hospital Universitario de La Princesa (Madrid) during June-July of 2017 in 59 healthy adults who were randomly allocated to one of three interventions: (1) Using dry topical heat for 7 min produced by two hot seed bags (N = 21), (2) Applying controlled pressure from a sphygmomanometer inflated to 100 mmHg (N = 18) and (3) combining heat and pressure (N = 20) in one period out of two. All interventions were contrasted to standard clinical practice in the other period. The comparator involved a standard tourniquet around the upper arm to restrict venous blood flow. The primary outcome was effectiveness measured as vein cannulation at first attempt. Secondary outcomes were vein perception, pain, haemolysis in blood samples and adverse events. RESULTS: All the interventions were more effective than comparator. Vein perception was optimized in about all individuals. Moreover, pain relief was significantly higher when high pressure was applied. Haemolysis was not affected in any of the three interventions. In addition, no serious adverse events appeared. CONCLUSION: High pressure is determined to be the most effective in vein catheterization, pain relief, vein perception and quality of blood sample inalterability. Moreover, it is safe considering that only one adverse event appeared. IMPACT: Vein cannulation is a very common invasive technique, where repeated failures have been registered. Thus, we consider it relevant to develop interventions to achieve venous catheterization at first attempt to alleviate the pain and anxiety associated with this technique. We advocate using high pressure intervention for emergency, due to swiftest method and feasible in case of lacking resources, such as sphygmomanometers in the ambulance. Interventions can be extrapolated to healthy young adults, adults and patients who have healthy vein status perception. Pressure intervention could be an alternative to heat intervention when performing vein cannulation due to its lower risk of transient paresthesia for older people who often suffer from arterial hypertension.

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits.

Recombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different recombination histories in these regions that significantly associated with the differential expression of ANKRD35 in whole blood and that were in high linkage with variants previously associated with hypertension. By detecting differences in historic recombination, our method opens a way to assess the influence of recombination variation in phenotypic traits.

MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data.

BACKGROUND: Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. However, discrepancies of reported findings can be due to the uncertainty and variability of the methods used for mLOY detection and to the differences in the tissue-matrix used. RESULTS: We created a publicly available software tool called MADloy (Mosaic Alteration Detection for LOY) that incorporates existing methods and includes a new robust approach, allowing efficient calling in large studies and comparisons between methods. MADloy optimizes mLOY calling by correctly modeling the underlying reference population with no-mLOY status and incorporating B-deviation information. We observed improvements in the calling accuracy to previous methods, using experimentally validated samples, and an increment in the statistical power to detect associations with disease and mortality, using simulation studies and real dataset analyses. To understand discrepancies in mLOY detection across different tissues, we applied MADloy to detect the increment of mLOY cellularity in blood on 18 individuals after 3 years and to confirm that its detection in saliva was sub-optimal (41%). We additionally applied MADloy to detect the down-regulation genes in the chromosome Y in kidney and bladder tumors with mLOY, and to perform pathway analyses for the detection of mLOY in blood. CONCLUSIONS: MADloy is a new software tool implemented in R for the easy and robust calling of mLOY status across different tissues aimed to facilitate its study in large epidemiological studies.

Female-specific risk of Alzheimer's disease is associated with tau phosphorylation processes: A transcriptome-wide interaction analysis.

The levels of tau phosphorylation differ between sexes in Alzheimer's disease (AD). Transcriptome-wide associations of sex by disease interaction could indicate whether specific genes underlie sex differences in tau pathology; however, no such study has been reported yet. We report the first analysis of the effect of the interaction between disease status and sex on differential gene expression, meta-analyzing transcriptomic data from the 3 largest publicly available case-control studies (N = 785) in the brain to date. A total of 128 genes, significantly associated with sex-AD interactions, were enriched in phosphoproteins (false discovery rate (FDR) = 0.001). High and consistent associations were found for the overexpressions of NCL (FDR = 0.002), whose phosphorylated protein generates an epitope against neurofibrillary tangles and KIF2A (FDR = 0.005), a microtubule-associated motor protein gene. Transcriptome-wide interaction analyses suggest sex-modulated tau phosphorylation, at sites like Thr231, Ser199, or Ser202 that could increase the risk of women to AD and indicate sex-specific strategies for intervention and prevention.

Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases.

The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic correlations among these disorders remain largely unknown. We investigated whether common polymorphic inversions underlie the shared genetic influence of these disorders. We performed an inversion association analysis including 21 inversions and 25 obesity-related traits on a total of 408,898 Europeans and validated the results in 67,299 independent individuals. Seven inversions were associated with multiple diseases while inversions at 8p23.1, 16p11.2, and 11q13.2 were strongly associated with the co-occurrence of obesity with other common diseases. Transcriptome analysis across numerous tissues revealed strong candidate genes for obesity-related traits. Analyses in human pancreatic islets indicated the potential mechanism of inversions in the susceptibility of diabetes by disrupting the cis-regulatory effect of SNPs from their target genes. Our data underscore the role of inversions as major genetic contributors to the joint susceptibility to common complex diseases.

The effects of aripiprazole and olanzapine on pupillary light reflex and its relationship with pharmacogenetics in a randomized multiple-dose trial.

AIMS: Pupillography is a noninvasive and cost-effective method to determine autonomic nerve activity. Genetic variants in cytochrome P450 (CYP), dopamine receptor (DRD2, DRD3), serotonin receptor (HTR2A, HTR2C) and ATP-binding cassette subfamily B (ABCB1) genes, among others, were previously associated with the pharmacokinetics and pharmacodynamics of antipsychotic drugs. Our aim was to evaluate the effects of aripiprazole and olanzapine on pupillary light reflex related to pharmacogenetics. METHODS: Twenty-four healthy volunteers receiving 5 oral doses of 10 mg aripiprazole and 5 mg olanzapine tablets were genotyped for 46 polymorphisms by quantitative polymerase chain reaction. Pupil examination was performed by automated pupillometry. Aripiprazole, dehydro-aripiprazole and olanzapine plasma concentrations were measured by high-performance liquid chromatography-tandem mass spectrometry. RESULTS: Aripiprazole affected pupil contraction: it caused dilatation after the administration of the first dose, then caused constriction after each dosing. It induced changes in all pupillometric parameters (P < .05). Olanzapine only altered minimum pupil size (P = .046). Polymorphisms in CYP3A, HTR2A, UGT1A1, DRD2 and ABCB1 affected pupil size, the time of onset of constriction, pupil recovery and constriction velocity. Aripiprazole, dehydro-aripiprazole and olanzapine pharmacokinetics were significantly affected by polymorphisms in CYP2D6, CYP3A, CYP1A2, ABCB1 and UGT1A1 genes. CONCLUSIONS: In conclusion, aripiprazole and its main metabolite, dehydro-aripiprazole altered pupil contraction, but olanzapine did not have such an effect. Many polymorphisms may influence pupillometric parameters and several polymorphisms had an effect on aripiprazole, dehydro-aripiprazole and olanzapine pharmacokinetics. Pupillography could be a useful tool for the determination of autonomic nerve activity during antipsychotic treatment.

Extreme downregulation of chromosome Y and Alzheimer's disease in men.

Research has revealed scarcely any biological factors of Alzheimer's disease (AD) that are specific to men. Here, we found that the extreme downregulation of chromosome Y (EDY) increases the age-related risk of AD in men. We considered that EDY was a possible male-specific pathway toward AD because EDY is the most likely consequence of the mosaic loss of chromosome Y, which has been recently associated with AD. We studied EDY in the undiseased brain of 371 individuals and observed that it co-occurred across multiple brain regions (p < 10-4) and associated with rs114241159 (p = 1.53 × 10-7) within ACSS3/PPFIA2, previously linked to amyloid beta concentrations. We also analyzed the 5 largest transcriptomic case-control studies, publicly available to date on AD (cases/controls = 556/462) and found a significant interaction with age (OREDY × age = 1.22, p = 0.0038). Our analyses suggest that aging men who live longer by avoiding EDY are more resilient to AD than those who do not.

Extreme Downregulation of Chromosome Y and Cancer Risk in Men.

BACKGROUND: Understanding the biological differences between sexes in cancer is essential for personalized treatment and prevention. We hypothesized that the extreme downregulation of chromosome Y gene expression (EDY) is a signature of cancer risk in men and the functional mediator of the reported association between the mosaic loss of chromosome Y (LOY) and cancer. METHODS: We advanced a method to measure EDY from transcriptomic data. We studied EDY across 47 nondiseased tissues from the Genotype Tissue-Expression Project (n = 371) and its association with cancer status across 12 cancer studies from The Cancer Genome Atlas (n = 1774) and seven other studies (n = 7562). Associations of EDY with cancer status and presence of loss-off function mutations in chromosome X were tested with logistic regression models, and a Fisher's test was used to assess genome-wide association of EDY with the proportion of copy number gains. All statistical tests were two-sided. RESULTS: EDY was likely to occur in multiple nondiseased tissues (P < .001) and was statistically significantly associated with the EGFR tyrosine kinase inhibitor resistance pathway (false discovery rate = 0.028). EDY strongly associated with cancer risk in men (odds ratio [OR] = 3.66, 95% confidence interval [CI] = 1.58 to 8.46, P = .002), adjusted by LOY and age, and its variability was largely explained by several genes of the nonrecombinant region whose chromosome X homologs showed loss-of-function mutations that co-occurred with EDY during cancer (OR = 2.82, 95% CI = 1.32 to 6.01, P = .007). EDY associated with a high proportion of EGFR amplifications (OR = 5.64, 95% CI = 3.70 to 8.59, false discovery rate < 0.001) and EGFR overexpression along with SRY hypomethylation and nonrecombinant region hypermethylation, indicating alternative causes of EDY in cancer other than LOY. EDY associations were independently validated for different cancers and exposure to smoking, and its status was accurately predicted from individual methylation patterns. CONCLUSIONS: EDY is a male-specific signature of cancer susceptibility that supports the escape from X-inactivation tumor suppressor hypothesis for genes that protect women compared with men from cancer risk.

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis.

BACKGROUND: Chromosomal inversions are structural genetic variants where a chromosome segment changes its orientation. While sporadic de novo inversions are known genetic risk factors for cancer susceptibility, it is unknown if common polymorphic inversions are also associated with the prognosis of common tumors, as they have been linked to other complex diseases. We studied the association of two well-characterized human inversions at 17q21.31 and 8p23.1 with the prognosis of lung, liver, breast, colorectal, and stomach cancers. RESULTS: Using data from The Cancer Genome Atlas (TCGA), we observed that inv8p23.1 was associated with overall survival in breast cancer and that inv17q21.31 was associated with overall survival in stomach cancer. In the meta-analysis of two independent studies, inv17q21.31 heterozygosity was significantly associated with colorectal disease-free survival. We found that the association was mediated by the de-methylation of cg08283464 and cg03999934, also linked to lower disease-free survival. CONCLUSIONS: Our results suggest that chromosomal inversions are important genetic factors of tumor prognosis, likely affecting changes in methylation patterns.

Genetic variability analysis in a population from Bogotá: Towards a haplotype map / Análisis de la variabilidad genética de una muestra de la población de Bogotá: hacia la constitución de un mapa de haplotipos

Introduction: The HapMap and the 1000 Genomes projects have been important for understanding the genetic component of common diseases and normal phenotypes. However, the Colombian genetic variability included in these projects is not fully representative of our country. Objective: To contribute to the knowledge of the Colombian genetic variability through the genomic study of a sample of individuals from Bogotá. Materials and methods: A total of 2,372,784 genetic markers were genotyped in 32 individuals born in Bogotá whose parents are from the same region, using the Illumina™ platform. The genetic variability levels were determined and compared with the data available from other populations of the 1000 Genomes Project. Results: The genetic variability detected in the individuals from Bogotá was similar to those with shared ancestry. However, despite the low levels of genetic differentiation between Bogotá and Medellín, populations the principal component analysis suggested a different genetic composition in them. Conclusions: Our genomic analysis of a Bogotá sample allowed us to detect similarities and differences with other American populations. The increase of the Bogotá sample and the inclusion of samples from other regions of the country will improve our understanding of the genetic variability in Colombia, essential for studies of human health and the prevention and treatment of common diseases in our country.

Introducción. Los proyectos del mapa de haplotipos (HapMap) y de los 1.000 genomas han sido fundamentales para la compresión del componente genético de las enfermedades comunes y los fenotipos normales. Sin embargo, la variabilidad genética colombiana incluida en estos proyectos no es representativa del país. Objetivo. Contribuir al conocimiento de la variabilidad genética de la población colombiana a partir del estudio genómico de una muestra de individuos de Bogotá. Materiales y métodos. Se genotipificaron 2'372.784 marcadores genéticos de 32 individuos nacidos en Bogotá y de padres originarios de la misma ciudad utilizando la plataforma Illumina™. Los niveles de variabilidad genética se determinaron y se compararon con los datos disponibles de otras poblaciones del proyecto de los 1.000 genomas. Resultados. Los individuos analizados presentaron una variabilidad genética semejante a la de poblaciones con las que comparten ancestros. No obstante, a pesar de la poca diferenciación genética detectada en la población de Bogotá y en la de Medellín, el análisis de los componentes principales sugiere una composición genética diferente en las dos poblaciones. Conclusiones. El análisis genómico de la muestra de Bogotá permitió detectar similitudes y diferencias con otras poblaciones americanas. El aumento de tamaño de la muestra bogotana y la inclusión de muestras de otras regiones del país permitirán una mejor compresión de la variabilidad genética en Colombia, lo cual es fundamental para los estudios de salud humana, y la prevención y el tratamiento de enfermedades comunes en el país.