Genome-wide association study of body fat distribution traits in Hispanics/Latinos from the HCHS/SOL

Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos: A 10-year retrospective review

The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a multicenter, longitudinal cohort study designed to evaluate environmental, lifestyle, and genetic risk factors as they relate to cardiometabolic and other chronic diseases among Hispanic/Latino populations in the United States. Since the study's inception in 2008, as a result of the study's robust genetic measures, HCHS/SOL has facilitated major contributions to the field of genetic research. This 10-year retrospective review highlights the major findings for genotype-phenotype relationships and advancements in statistical methods owing to the HCHS/SOL. Furthermore, we discuss the ethical and societal challenges of genetic research, especially among Hispanic/Latino adults in the United States. Continued genetic research, ancillary study expansion, and consortia collaboration through HCHS/SOL will further drive knowledge and advancements in human genetics research.

Genome-wide association study reveals shared and distinct genetic architecture of fatty acids and oxylipins in the Hispanic Community Health Study/Study of Latinos

Bioactive fatty acid-derived oxylipin molecules play key roles mediating inflammation and oxidative stress. Circulating levels of fatty acids and oxylipins are influenced by environmental and genetic factors; characterizing the genetic architecture of bioactive lipids could yield new insights into underlying biology. We performed a genome-wide association study (GWAS) of 81 fatty acids and oxylipins in 11,584 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants with genetic and lipidomic data measured at study baseline (58.6% female, mean age = 46.1 years (standard deviation 13.8)). Additionally, given the effects of central obesity on inflammation, we examined interactions with waist circumference using two-degree-of-freedom joint tests. Thirty-three of the 81 oxylipins and fatty acids were significantly heritable (heritability range: 0-32.7%). Forty (49.4%) oxylipins and fatty acids had at least one genome-wide significant (p < 6.94E-11) variant resulting in 19 independent genetic loci. Six loci (lead variant minor allele frequency [MAF] range: 0.08-0.50), including desaturase-encoding FADS and OATP1B1 transporter protein-encoding SLCO1B1, exhibited associations with two or more fatty acids and oxylipins. At several of these loci, there was evidence of colocalization of the top variant across fatty acids and oxylipins. The remaining loci were only associated with one oxylipin or fatty acid and included several CYP loci. We also identified an additional rare variant (MAF = 0.002) near CARS2 in two-degree-of-freedom tests. Our analyses revealed shared and distinct genetic architecture underlying fatty acids and oxylipins, providing insights into genetic factors and motivating work to characterize these compounds and elucidate their roles in disease.

Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas

Latin Americans are underrepresented in genetic studies, increasing disparities in personalized genomic medicine. Despite available genetic data from thousands of Latin Americans, accessing and navigating the bureaucratic hurdles for consent or access remains challenging. To address this, we introduce the Genetics of Latin American Diversity (GLAD) Project, compiling genome-wide information from 53,738 Latin Americans across 39 studies representing 46 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene flow across the Americas. Additionally, we developed GLAD-match, a simulated annealing-based algorithm, to match the genetic background of external samples to our database, sharing summary statistics (i.e., allele and haplotype frequencies) without transferring individual-level genotypes. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic software in the presence of admixture. By providing this resource, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.

Genome-wide association study reveals shared and distinct genetic architecture underlying fatty acid and bioactive oxylipin metabolites in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Bioactive fatty acid-derived oxylipin molecules play key roles in mediating inflammation and oxidative stress, which underlie many chronic diseases. Circulating levels of fatty acids and oxylipins are influenced by both environmental and genetic factors; characterizing the genetic architecture of bioactive lipids could yield new insights into underlying biological pathways. Thus, we performed a genome wide association study (GWAS) of n=81 fatty acids and oxylipins in n=11,584 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants with genetic and lipidomic data measured at study baseline (58.6% female, mean age = 46.1 years, standard deviation = 13.8 years). Additionally, given the effects of central obesity on inflammation, we examined interactions with waist circumference using two-degree-of-freedom joint tests. Heritability estimates ranged from 0% to 47.9%, and 48 of the 81oxylipins and fatty acids were significantly heritable. Moreover, 40 (49.4%) of the 81 oxylipins and fatty acids had at least one genome-wide significant (p< 6.94E-11) variant resulting in 19 independent genetic loci involved in fatty acid and oxylipin synthesis, as well as downstream pathways. Four loci (lead variant minor allele frequency [MAF] range: 0.08-0.50), including the desaturase-encoding FADS and the OATP1B1 transporter protein-encoding SLCO1B1, exhibited associations with four or more fatty acids and oxylipins. The majority of the 15 remaining loci (87.5%) (lead variant MAF range = 0.03-0.45, mean = 0.23) were only associated with one oxylipin or fatty acid, demonstrating evidence of distinct genetic effects. Finally, while most loci identified in two-degree-of-freedom tests were previously identified in our main effects analyses, we also identified an additional rare variant (MAF = 0.002) near CARS2, a locus previously implicated in inflammation. Our analyses revealed shared and distinct genetic architecture underlying fatty acids and oxylipins, providing insights into genetic factors and motivating future multi-omics work to characterize these compounds and elucidate their roles in disease pathways.

Determinants of obesity in Latin America

Obesity rates are increasing almost everywhere in the world, although the pace and timing for this increase differ when populations from developed and developing countries are compared. The sharp and more recent increase in obesity rates in many Latin American countries is an example of that and results from regional characteristics that emerge from interactions between multiple factors. Aware of the complexity of enumerating these factors, we highlight eight main determinants (the physical environment, food exposure, economic and political interest, social inequity, limited access to scientific knowledge, culture, contextual behaviour and genetics) and discuss how they impact obesity rates in Latin American countries. We propose that initiatives aimed at understanding obesity and hampering obesity growth in Latin America should involve multidisciplinary, global approaches that consider these determinants to build more effective public policy and strategies, accounting for regional differences and disease complexity at the individual and systemic levels.

A Bayesian method for estimating gene-level polygenicity under the framework of transcriptome-wide association study

Polygenicity refers to the phenomenon that multiple genetic variants have a nonzero effect on a complex trait. It is defined as the proportion of genetic variants with a nonzero effect on the trait. Evaluation of polygenicity can provide valuable insights into the genetic architecture of the trait. Several recent works have attempted to estimate polygenicity at the single nucleotide polymorphism level. However, evaluating polygenicity at the gene level can be biologically more meaningful. We propose the notion of gene-level polygenicity, defined as the proportion of genes having a nonzero effect on the trait under the framework of a transcriptome-wide association study. We introduce a Bayesian approach genepoly to estimate this quantity for a trait. The method is based on spike and slab prior and simultaneously estimates the subset of non-null genes. Our simulation study shows that genepoly efficiently estimates gene-level polygenicity. The method produces a downward bias for small choices of trait heritability due to a non-null gene, which diminishes rapidly with an increase in the genome-wide association study (GWAS) sample size. While identifying the subset of non-null genes, genepoly offers a high level of specificity and an overall good level of sensitivity-the sensitivity increases as the sample size of the reference panel expression and GWAS data increase. We applied the method to seven phenotypes in the UK Biobank, integrating expression data. We find height to be the most polygenic and asthma to be the least polygenic.

Weight trajectories and obesity remission among school-aged children

BACKGROUND

Many studies examining weight trajectories have used adiposity measures shown to be problematic for trajectory analysis in children with obesity, and remission of obesity remains poorly understood.

OBJECTIVES

To describe weight trajectories for school-aged children, the rate of obesity remission and factors associated.

METHODS

Children between 6 and 11 years of age with ≥3 valid height and weight measurements from an Oregon hospital-system over a minimum six-month period were included. Percent distance from the median body mass index (BMI) was used for modeling. Latent class analysis and linear mixed models were used to classify children based on their weight trajectory.

RESULTS

We included 11,247 subjects with a median of 2.1 years of follow-up, with 1,614 (14.4%) classified as overweight and 1,794 (16.0%) classified as obese. Of subjects with obesity, 1% experienced remission during follow-up, whereas 23% of those with overweight moved to within a healthy weight range. Latent class analysis identified three classes within each weight-based stratum over time. The majority of children with overweight or obesity had a flat trajectory over time. Lower socioeconomic status was associated with a worsening trajectory. Latent class models using alternate measures (BMI, BMI z-scores, tri-ponderal mass index (TMI)) differed substantially from each other.

CONCLUSIONS

Obesity remission was uncommon using the adiposity metric of distance from the median though transition from overweight to healthy weight was more common. Children with low socioeconomic status have worse trajectories overall. The choice of adiposity metric may have a substantial effect on the outcomes.

Factors Associated with Normal-Weight Abdominal Obesity Phenotype in a Representative Sample of the Peruvian Population: A 4-Year Pooled Cross-Sectional Study

To examine factors associated with abdominal obesity among normal-weight individuals from the Demographic and Health Survey of Peru (2018-2021). Cross-sectional analytical study. The outcome variable was abdominal obesity defined according to JIS criteria. Crude (cPR) and adjusted prevalence ratios (aPR) were estimated for the association between sociodemographic and health-related variables and abdominal obesity using the GLM Poisson distribution with robust variance estimates. A total of 32,109 subjects were included. The prevalence of abdominal obesity was 26.7%. The multivariate analysis showed a statistically significant association between abdominal obesity and female sex (aPR: 11.16; 95% CI 10.43-11.94); categorized age 35 to 59 (aPR: 1.71; 95% CI 1.65-1.78); 60 to 69 (aPR: 1.91; 95% CI 1.81-2.02); and 70 or older(aPR: 1.99; 95% CI 1.87-2.10); survey year 2019 (aPR: 1.22; 95% CI 1.15-1.28); 2020 (aPR: 1.17; 95% CI 1.11-1.24); and 2021 (aPR: 1.12; 95% CI 1.06-1.18); living in Andean region (aPR: 0.91; 95% CI 0.86-0.95); wealth index poor (aPR: 1.26; 95% CI 1.18-1.35); middle (aPR: 1.17; 95% CI 1.08-1.26); rich (aPR: 1.26; 95% CI 1.17-1.36); and richest (aPR: 1.25; 95% CI 1.16-1.36); depressive symptoms (aPR: 0.95; 95% CI 0.92-0.98); history of hypertension (aPR: 1.08; 95% CI 1.03-1.13), type 2 diabetes (aPR: 1.13; 95% CI 1.07-1.20); and fruit intake 3 or more servings/day (aPR: 0.92; 95% CI 0.89-0.96). Female sex, older ages, and low and high income levels increased the prevalence ratio for abdominal obesity, while depressive symptoms, living in the Andean region, and fruit intake of 3 or more servings/day decreased it.

Evolving Science on Cardiovascular Disease Among Hispanic/Latino Adults: JACC International

The landmark, multicenter HCHS/SOL (Hispanic Community Health Study/Study of Latinos) is the largest, most comprehensive, longitudinal community-based cohort study to date of diverse Hispanic/Latino persons in the United States. The HCHS/SOL aimed to address the dearth of comprehensive data on risk factors for cardiovascular disease (CVD) and other chronic diseases in this population and has expanded considerably in scope since its inception. This paper describes the aims/objectives and data collection of the HCHS/SOL and its ancillary studies to date and highlights the critical and sizable contributions made by the study to understanding the prevalence of and changes in CVD risk/protective factors and the burden of CVD and related chronic conditions among adults of diverse Hispanic/Latino backgrounds. The continued follow-up of this cohort will allow in-depth investigations on cardiovascular and pulmonary outcomes in this population, and data from the ongoing ancillary studies will facilitate generation of new hypotheses and study questions.

Wrestling with Social and Behavioral Genomics: Risks, Potential Benefits, and Ethical Responsibility

In this consensus report by a diverse group of academics who conduct and/or are concerned about social and behavioral genomics (SBG) research, the authors recount the often-ugly history of scientific attempts to understand the genetic contributions to human behaviors and social outcomes. They then describe what the current science-including genomewide association studies and polygenic indexes-can and cannot tell us, as well as its risks and potential benefits. They conclude with a discussion of responsible behavior in the context of SBG research. SBG research that compares individuals within a group according to a "sensitive" phenotype requires extra attention to responsible conduct and to responsible communication about the research and its findings. SBG research (1) on sensitive phenotypes that (2) compares two or more groups defined by (a) race, (b) ethnicity, or (c) genetic ancestry (where genetic ancestry could easily be misunderstood as race or ethnicity) requires a compelling justification to be conducted, funded, or published. All authors agree that this justification at least requires a convincing argument that a study's design could yield scientifically valid results; some authors would additionally require the study to have a socially favorable risk-benefit profile.

Whole-Exome Sequencing identified Olfactory Receptor genes as a key contributor to extreme obesity with progression to nonalcoholic steatohepatitis in Mexican patients: Olfactory receptor genes in obese NASH patients

INTRODUCTION AND OBJECTIVES

Obesity is a global health problem that triggers fat liver accumulation. The prevalence of obesity and the risk of non-alcoholic steatohepatitis (NASH) among young obese Mexican is high. Furthermore, genetic predisposition is a key factor in weight gain and disrupts metabolism. Herein, we used Whole-Exome Sequencing to identify potential causal variants and the biological processes that lead to obesity with progression to NASH among Mexican patients.

MATERIALS AND METHODS

Whole-Exome Sequencing was performed in nine obese patients with NASH diagnosis with a BMI ≥30 kg/m² and one control (BMI=24.2 kg/m²) by using the Ion S5^TM platform. Genetic variants were determined by Ion Reporter software. Enriched GO biological set genes were identified by the WebGestalt tool. Genetic variants within ≥2 obese NASH patients and having scores of SIFT 0.0-0.05 and Polyphen 0.85-1.0 were categorized as pathogenic.

RESULTS

A total of 1359 variants with a probable pathogenic effect were determined in obese patients with NASH diagnosis. After several filtering steps, the most frequent pathogenic variants found were rs25640-HSD17B4, rs8105737-OR1I1, rs998544-OR5R1, and rs4916685, rs10037067, and rs2366926 in ADGRV1. Notably, the primary biological processes affected by these pathogenic variants were the sensory perception and detection of chemical stimulus pathways in which the olfactory receptor gene family was the most enriched.

CONCLUSIONS

Variants in the olfactory receptor genes were highly enriched in Mexican obese patients that progress to NASH and could be potential targets of association studies.

Genetic determinants of cardiometabolic and pulmonary phenotypes and obstructive sleep apnoea in HCHS/SOL

BACKGROUND

Obstructive Sleep Apnoea (OSA) often co-occurs with cardiometabolic and pulmonary diseases. This study is to apply genetic analysis methods to explain the associations between OSA and related phenotypes.

METHODS

In the Hispanic Community Healthy Study/Study of Latinos, we estimated genetic correlations ρ_g between the respiratory event index (REI) and 54 anthropometric, glycemic, cardiometabolic, and pulmonary phenotypes. We used summary statistics from published genome-wide association studies to construct Polygenic Risk Scores (PRSs) representing the genetic basis of each correlated phenotype (ρ_g>0.2 and p-value<0.05), and of OSA. We studied the association of the PRSs of the correlated phenotypes with both REI and OSA (REI≥5), and the association of OSA PRS with the correlated phenotypes. Causal relationships were tested using Mendelian Randomization (MR) analysis.

FINDINGS

The dataset included 11,155 participants, 31.03% with OSA. 22 phenotypes were genetically correlated with REI. 10 PRSs covering obesity and fat distribution (BMI, WHR, WHRadjBMI), blood pressure (DBP, PP, MAP), glycaemic control (fasting insulin, HbA1c, HOMA-B) and insomnia were associated with REI and/or OSA. OSA PRS was associated with BMI, WHR, DBP and glycaemic traits (fasting insulin, HbA1c, HOMA-B and HOMA-IR). MR analysis identified robust causal effects of BMI and WHR on OSA, and probable causal effects of DBP, PP, and HbA1c on OSA/REI.

INTERPRETATION

There are shared genetic underpinnings of anthropometric, blood pressure, and glycaemic phenotypes with OSA, with evidence for causal relationships between some phenotypes.

FUNDING

Described in Acknowledgments.