scholarly journals Recent shifts in the genomic ancestry of Mexican Americans may alter the genetic architecture of biomedical traits

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Melissa L Spear ◽  
Alex Diaz-Papkovich ◽  
Elad Ziv ◽  
Joseph M Yracheta ◽  
Simon Gravel ◽  
...  
Keyword(s):  
Complex Traits ◽  
Mexican Americans ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
The United States ◽  
European Ancestry ◽  
Risk Scores ◽  
Health Study ◽  
Complex Interactions ◽  
Hispanic Community

People in the Americas represent a diverse continuum of populations with varying degrees of admixture among African, European, and Amerindigenous ancestries. In the United States, populations with non-European ancestry remain understudied, and thus little is known about the genetic architecture of phenotypic variation in these populations. Using genotype data from the Hispanic Community Health Study/Study of Latinos, we find that Amerindigenous ancestry increased by an average of ~20% spanning 1940s-1990s in Mexican Americans. These patterns result from complex interactions between several population and cultural factors which shaped patterns of genetic variation and influenced the genetic architecture of complex traits in Mexican Americans. We show for height how polygenic risk scores based on summary statistics from a European-based genome-wide association study perform poorly in Mexican Americans. Our findings reveal temporal changes in population structure within Hispanics/Latinos that may influence biomedical traits, demonstrating a need to improve our understanding of admixed populations.

scholarly journals Recent fluctuations in Mexican American genomes have altered the genetic architecture of biomedical traits

2020 ◽  
Author(s):  
Melissa L. Spear ◽  
Alex Diaz-Papkovich ◽  
Elad Ziv ◽  
Joseph M. Yracheta ◽  
Simon Gravel ◽  
...  
Keyword(s):  
Complex Traits ◽  
Mexican Americans ◽  
Mexican American ◽  
Genetic Architecture ◽  
The United States ◽  
European Ancestry ◽  
Risk Scores ◽  
Health Study ◽  
Genome Wide ◽  
Over Time

AbstractPeople in the Americas represent a diverse group of populations with varying degrees of admixture among African, European, and Amerindigenous ancestries. In the United States, many populations with non-European ancestry remain understudied, and thus little is known about the genetic architecture of phenotypic variation in these populations. Using genome-wide genotype data from the Hispanic Community Health Study/Study of Latinos, we find that Amerindigenous ancestry has increased over time across Hispanic/Latino populations, particularly in Mexican Americans where Amerindigenous ancestry increased by an average of ∼20% over the 50-year period spanning 1940s-1990s. We find similar patterns across American cities, and replicate our observations in an independent sample of Mexican Americans. These dynamic ancestry patterns are a result of a complex interaction of several population and cultural factors, including strong ancestry-related assortative mating and subtle shifts in migration with differences in subcontinental Amerindigenous ancestry over time. These factors have shaped patterns of genetic variation, including an increase in runs of homozygosity in Amerindigenous ancestral tracts, and also influenced the genetic architecture of complex traits within the Mexican American population. We show for height, a trait correlated with ancestry, polygenic risk scores based on summary statistics from a European-based genome-wide association study perform poorly in Mexican Americans. Our findings reveal temporal changes in population structure within Hispanics/Latinos that may influence biomedical traits, demonstrating a crucial need to improve our understanding of the genetic diversity of admixed populations.

scholarly journals Findings from the Hispanic Community Health Study/Study of Latinos on the Importance of Sociocultural Environmental Interactors: Polygenic Risk Score-by-Immigration and Dietary Interactions

2021 ◽  
Vol 12 ◽  
Author(s):  
Cristin E. McArdle ◽  
Hassan Bokhari ◽  
Clinton C. Rodell ◽  
Victoria Buchanan ◽  
Liana K. Preudhomme ◽  
...  
Keyword(s):  
Community Health ◽  
Genome Wide Association Study ◽  
The United States ◽  
European Ancestry ◽  
Risk Scores ◽  
Health Study ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Hispanic Community

Introduction: Hispanic/Latinos experience a disproportionate burden of obesity. Acculturation to US obesogenic diet and practices may lead to an exacerbation of innate genetic susceptibility. We examined the role of gene–environment interactions to better characterize the sociocultural environmental determinants and their genome-scale interactions, which may contribute to missing heritability of obesity. We utilized polygenic risk scores (PRSs) for body mass index (BMI) to perform analyses of PRS-by-acculturation and other environmental interactors among self-identified Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).Methods: PRSs were derived using genome-wide association study (GWAS) weights from a publicly available, large meta-analysis of European ancestry samples. Generalized linear models were run using a set of a priori acculturation-related and environmental factors measured at visit 1 (2008–2011) and visit 2 (2014–2016) in an analytic subsample of 8,109 unrelated individuals with genotypic, phenotypic, and complete case data at both visits. We evaluated continuous measures of BMI and waist-to-hip ratio. All models were weighted for complex sampling design, combined, and sex-stratified.Results: Overall, we observed a consistent increase of BMI with greater PRS across both visits. We found the best-fitting model adjusted for top five principal components of ancestry, sex, age, study site, Hispanic/Latino background genetic ancestry group, sociocultural factors and PRS interactions with age at immigration, years since first arrival to the United States (p < 0.0104), and healthy diet (p < 0.0036) and explained 16% of the variation in BMI. For every 1-SD increase in PRS, there was a corresponding 1.10 kg/m2 increase in BMI (p < 0.001). When these results were stratified by sex, we observed that this 1-SD effect of PRS on BMI was greater for women than men (1.45 vs. 0.79 kg/m2, p < 0.001).Discussion: We observe that age at immigration and the adoption of certain dietary patterns may play a significant role in modifying the effect of genetic risk on obesity. Careful consideration of sociocultural and immigration-related factors should be evaluated. The role of nongenetic factors, including the social environment, should not be overlooked when describing the performance of PRS or for promoting population health in understudied populations in genomics.

scholarly journals Genomic Risk Score impact on susceptibility to systemic sclerosis

2020 ◽  
Vol 80 (1) ◽  
pp. 118-127 ◽  
Author(s):  
Lara Bossini-Castillo ◽  
Gonzalo Villanueva-Martin ◽  
Martin Kerick ◽  
Marialbert Acosta-Herrera ◽  
Elena López-Isac ◽  
...  
Keyword(s):  
Systemic Sclerosis ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
European Ancestry ◽  
Risk Scores ◽  
Immunological Parameters ◽  
Cell Counts ◽  
Best Fitting ◽  
Genomic Risk

ObjectivesGenomic Risk Scores (GRS) successfully demonstrated the ability of genetics to identify those individuals at high risk for complex traits including immune-mediated inflammatory diseases (IMIDs). We aimed to test the performance of GRS in the prediction of risk for systemic sclerosis (SSc) for the first time.MethodsAllelic effects were obtained from the largest SSc Genome-Wide Association Study (GWAS) to date (9 095 SSc and 17 584 healthy controls with European ancestry). The best-fitting GRS was identified under the additive model in an independent cohort that comprised 400 patients with SSc and 571 controls. Additionally, GRS for clinical subtypes (limited cutaneous SSc and diffuse cutaneous SSc) and serological subtypes (anti-topoisomerase positive (ATA+) and anti-centromere positive (ACA+)) were generated. We combined the estimated GRS with demographic and immunological parameters in a multivariate generalised linear model.ResultsThe best-fitting SSc GRS included 33 single nucleotide polymorphisms (SNPs) and discriminated between patients with SSc and controls (area under the receiver operating characteristic (ROC) curve (AUC)=0.673). Moreover, the GRS differentiated between SSc and other IMIDs, such as rheumatoid arthritis and Sjögren’s syndrome. Finally, the combination of GRS with age and immune cell counts significantly increased the performance of the model (AUC=0.787). While the SSc GRS was not able to discriminate between ATA+ and ACA+ patients (AUC<0.5), the serological subtype GRS, which was based on the allelic effects observed for the comparison between ACA+ and ATA+ patients, reached an AUC=0.693.ConclusionsGRS was successfully implemented in SSc. The model discriminated between patients with SSc and controls or other IMIDs, confirming the potential of GRS to support early and differential diagnosis for SSc.

scholarly journals Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data

2019 ◽  
Author(s):  
Huwenbo Shi ◽  
Kathryn S. Burch ◽  
Ruth Johnson ◽  
Malika K. Freund ◽  
Gleb Kichaev ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Empirical Bayes ◽  
Genetic Correlations ◽  
Causal Snps ◽  
European Ancestry ◽  
Risk Scores ◽  
Common Snps ◽  
Genome Wide ◽  
Summary Data

AbstractDespite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze 9 complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8x enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWAS due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.

scholarly journals Genome-Wide Association Study of Opioid Cessation

2020 ◽  
Vol 9 (1) ◽  
pp. 180 ◽  
Author(s):  
Jiayi W. Cox ◽  
Richard M. Sherva ◽  
Kathryn L. Lunetta ◽  
Emma C. Johnson ◽  
Nicholas G. Martin ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Chronic Back Pain ◽  
The United States ◽  
Genome Wide Association ◽  
European Ancestry ◽  
Risk Scores ◽  
Opioid Use ◽  
Genome Wide ◽  
A Genome

The United States is experiencing an epidemic of opioid use disorder (OUD) and overdose-related deaths. However, the genetic basis for the ability to discontinue opioid use has not been investigated. We performed a genome-wide association study (GWAS) of opioid cessation (defined as abstinence from illicit opioids for >1 year or <6 months before the interview date) in 1130 African American (AA) and 2919 European ancestry (EA) participants recruited for genetic studies of substance use disorders and who met lifetime Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5) criteria for OUD. Association tests performed separately within each ethnic group were combined by meta-analysis with results obtained from the Comorbidity and Trauma Study. Although there were no genome-wide significant associations, we found suggestive associations with nine independent loci, including three which are biologically relevant: rs4740988 in PTPRD (pAA + EA = 2.24 × 10−6), rs36098404 in MYOM2 (pEA = 2.24 × 10−6), and rs592026 in SNAP25-AS1 (pEA = 6.53 × 10−6). Significant pathways identified in persons of European ancestry (EA) are related to vitamin D metabolism (p = 3.79 × 10−2) and fibroblast growth factor (FGF) signaling (p = 2.39 × 10−2). UK Biobank traits including smoking and drinking cessation and chronic back pain were significantly associated with opioid cessation using GWAS-derived polygenic risk scores. These results provide evidence for genetic influences on opioid cessation, suggest genetic overlap with other relevant traits, and may indicate potential novel therapeutic targets for OUD.

scholarly journals Genetic risk scores and hallucinations in patients with Parkinson disease

2020 ◽  
Vol 6 (5) ◽  
pp. e492 ◽  
Author(s):  
Cynthia D.J. Kusters ◽  
Kimberly C. Paul ◽  
Aline Duarte Folle ◽  
Adrienne M. Keener ◽  
Jeff M. Bronstein ◽  
...  
Keyword(s):  
Parkinson Disease ◽  
Genetic Risk ◽  
Genetic Architecture ◽  
Disease Duration ◽  
Genome Wide Association Study ◽  
Population Based ◽  
Negative Control ◽  
European Ancestry ◽  
Risk Scores ◽  
Genome Wide

ObjectiveWe examine the hypothesized overlap of genetic architecture for Alzheimer disease (AD), schizophrenia (SZ), and Parkinson disease (PD) through the use of polygenic risk scores (PRSs) with the occurrence of hallucinations in PD.MethodsWe used 2 population-based studies (ParkWest, Norway, and Parkinson's Environment and Gene, USA) providing us with 399 patients with PD with European ancestry and a PD diagnosis after age 55 years to assess the associations between 4 PRSs and hallucinations after 5 years of mean disease duration. Based on the existing genome-wide association study of other large consortia, 4 PRSs were created: one each using AD, SZ, and PD cohorts and another PRS for height, which served as a negative control.ResultsA higher prevalence of hallucinations was observed with each SD increase of the AD-PRS (odds ratio [OR]: 1.37, 95% confidence interval [CI]: 1.03–1.83). This effect was mainly driven by APOE (OR: 1.92, 95% CI: 1.14–3.22). In addition, a suggestive decrease and increase, respectively, in hallucination prevalence were observed with the SZ-PRS and the PD-PRS (OR: 0.77, 95% CI: 0.59–1.01; and OR: 1.29, 95% CI: 0.95–1.76, respectively). No association was observed with the height PRS.ConclusionsThese results suggest that mechanisms for hallucinations in PD may in part be driven by the same genetic architecture that leads to cognitive decline in AD, especially by APOE.

scholarly journals Heritability and individuality of the plasma sodium concentration: a twin study in the United States veteran population

2019 ◽  
Vol 316 (6) ◽  
pp. F1114-F1123
Author(s):  
Andrew K. Timmons ◽  
Anna M. Korpak ◽  
Jenny Tan ◽  
Kathryn P. Moore ◽  
Cindy H. Liu ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Water Balance ◽  
Plasma Glucose ◽  
Genome Wide Association Study ◽  
Sodium Concentration ◽  
The United States ◽  
European Ancestry ◽  
Plasma Sodium ◽  
Individual Level ◽  
Plasma Sodium Concentration

Little is known about the population genetics of water balance. A recent meta-genome-wide association study on plasma sodium concentration identified novel loci of high biological plausibility, yet heritability of the phenotype has never been convincingly shown in European ancestry. The present study linked the Vietnam Era Twin Registry with the Department of Veterans Affairs VistA patient care clinical database. Participants ( n = 2,370, 59.6% monozygotic twins and 40.4% dizygotic twins) had a median of seven (interquartile range: 3−14) plasma sodium determinations between October 1999 and March 2017. Heritability of the mean plasma sodium concentration among all twins was 0.41 (95% confidence interval: 0.35−0.46) and 0.49 (95% confidence interval: 0.43−0.54) after exclusion of 514 twins with only a single plasma sodium determination. Heritability among Caucasian ( n = 1,958) and African-American ( n = 268) twins was 0.41 (95% confidence interval: 0.34−0.47) and 0.36 (95% confidence interval: 0.17−0.52), respectively. Exclusion of data from twins who had been prescribed medications known to impact systemic water balance had no effect. The ability of the present study to newly detect substantial heritability across multiple racial groups was potentially a function of the cohort size and relatedness, exclusion of sodium determinations confounded by elevated plasma glucose and/or reduced glomerular filtration rate, transformation of plasma sodium for the independent osmotic effect of plasma glucose, and use of multiple laboratory determinations per individual over a period of years. Individual-level plasma sodium concentration exhibited longitudinal stability (i.e., individuality); the degree to which individual-level means differed from the population mean was substantial, irrespective of the number of determinations. In aggregate, these data establish the heritability of plasma sodium concentration in European ancestry and corroborate its individuality.

scholarly journals Empirically Derived Dietary Patterns Using Robust Profile Clustering in the Hispanic Community Health Study/Study of Latinos

2020 ◽  
Vol 150 (10) ◽  
pp. 2825-2834
Author(s):  
Briana J K Stephenson ◽  
Daniela Sotres-Alvarez ◽  
Anna-Maria Siega-Riz ◽  
Yasmin Mossavar-Rahmani ◽  
Martha L Daviglus ◽  
...  
Keyword(s):  
United States ◽  
Community Health ◽  
Dietary Patterns ◽  
Latent Class ◽  
The United States ◽  
Ethnic Background ◽  
Latent Class Models ◽  
Nutrition Intervention ◽  
Health Study ◽  
Hispanic Community

ABSTRACT Background Latent class models (LCMs) have been used in exploring dietary behaviors over a wide set of foods and beverages in a given population, but are prone to overgeneralize these habits in the presence of variation by subpopulations. Objectives This study aimed to highlight unique dietary consumption differences by both study site and ethnic background of Hispanic/Latino populations in the United States, that otherwise might be missed in a traditional LCM of the overall population. This was achieved using a new model-based clustering method, referred to as robust profile clustering (RPC). Methods A total of 11,320 individuals aged 18–74 y from the Hispanic Community Health Study/Study of Latinos (2008–2011) with complete diet data were classified into 9 subpopulations, defined by study site (Bronx, Chicago, Miami, San Diego) and ethnic background. At baseline, dietary intake was ascertained using a food propensity questionnaire. Dietary patterns were derived from 132 food groups using the RPC method to identify patterns of the general Hispanic/Latino population and those specific to an identified subpopulation. Dietary patterns derived from the RPC were compared to those identified from an LCM. Results The LCM identified 48 shared consumption behaviors of foods and beverages across the entire cohort, whereas significant consumption differences in subpopulations were identified in the RPC model for these same foods. Several foods were common within study site (e.g., chicken, orange juice, milk), ethnic background (e.g., papayas, plantain, coffee), or both (e.g., rice, tomatoes, seafood). Post hoc testing revealed an improved model fit in the RPC model [Deviance Information Criterion DICRPC = 2.3 × 104, DICLCM  = 9.5 × 106]. Conclusions Dietary pattern behaviors of Hispanics/Latinos in the United States tend to align by ethnic background for some foods and by location for other foods. Consideration of both factors is imperative to better understand their contributions to population health and developing targeted nutrition intervention studies.

scholarly journals Incident Chronic Kidney Disease Risk among Hispanics/Latinos in the United States: The Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

2020 ◽  
Vol 31 (6) ◽  
pp. 1315-1324
Author(s):  
Ana C. Ricardo ◽  
Matthew Shane Loop ◽  
Franklyn Gonzalez ◽  
Claudia M. Lora ◽  
Jinsong Chen ◽  
...  
Keyword(s):  
United States ◽  
Risk Factors ◽  
The United States ◽  
Health Study ◽  
Creatinine Ratio ◽  
Albumin Creatinine Ratio ◽  
Urine Albumin ◽  
Hispanic Community ◽  
Urine Albumin Creatinine Ratio ◽  
Rate Ratios

BackgroundAlthough Hispanics/Latinos in the United States are often considered a single ethnic group, they represent a heterogenous mixture of ancestries who can self-identify as any race defined by the U.S. Census. They have higher ESKD incidence compared with non-Hispanics, but little is known about the CKD incidence in this population.MethodsWe examined rates and risk factors of new-onset CKD using data from 8774 adults in the Hispanic Community Health Study/Study of Latinos. Incident CKD was defined as eGFR <60 ml/min per 1.73 m2 with eGFR decline ≥1 ml/min per 1.73 m2 per year, or urine albumin/creatinine ratio ≥30 mg/g. Rates and incidence rate ratios were estimated using Poisson regression with robust variance while accounting for the study’s complex design.ResultsMean age was 40.3 years at baseline and 51.6% were women. In 5.9 years of follow-up, 648 participants developed CKD (10.6 per 1000 person-years). The age- and sex-adjusted incidence rates ranged from 6.6 (other Hispanic/mixed background) to 15.0 (Puerto Ricans) per 1000 person-years. Compared with Mexican background, Puerto Rican background was associated with 79% increased risk for incident CKD (incidence rate ratios, 1.79; 95% confidence interval, 1.33 to 2.40), which was accounted for by differences in sociodemographics, acculturation, and clinical characteristics. In multivariable regression analysis, predictors of incident CKD included BP >140/90 mm Hg, higher glycated hemoglobin, lower baseline eGFR, and higher baseline urine albumin/creatinine ratio.ConclusionsCKD incidence varies by Hispanic/Latino heritage and this disparity may be in part attributed to differences in sociodemographic characteristics. Culturally tailored public heath interventions focusing on the prevention and control of risk factors might ameliorate the CKD burden in this population.

scholarly journals Polygenic Risk Scores Augment Stroke Subtyping

2021 ◽  
Vol 7 (2) ◽  
pp. e560
Author(s):  
Jiang Li ◽  
Durgesh P. Chaudhary ◽  
Ayesha Khan ◽  
Christoph Griessenauer ◽  
David J. Carey ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Genetic Correlation ◽  
Genome Wide Association Study ◽  
Low Frequency ◽  
European Ancestry ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Large Artery ◽  
Polygenic Risk ◽  
Gene Sets

ObjectiveTo determine whether the polygenic risk score (PRS) derived from MEGASTROKE is associated with ischemic stroke (IS) and its subtypes in an independent tertiary health care system and to identify the PRS derived from gene sets of known biological pathways associated with IS.MethodsControls (n = 19,806/7,484, age ≥69/79 years) and cases (n = 1,184/951 for discovery/replication) of acute IS with European ancestry and clinical risk factors were identified by leveraging the Geisinger Electronic Health Record and chart review confirmation. All Geisinger MyCode patients with age ≥69/79 years and without any stroke-related diagnostic codes were included as low risk control. Genetic heritability and genetic correlation between Geisinger and MEGASTROKE (EUR) were calculated using the summary statistics of the genome-wide association study by linkage disequilibrium score regression. All PRS for any stroke (AS), any ischemic stroke (AIS), large artery stroke (LAS), cardioembolic stroke (CES), and small vessel stroke (SVS) were constructed by PRSice-2.ResultsA moderate heritability (10%–20%) for Geisinger sample as well as the genetic correlation between MEGASTROKE and the Geisinger cohort was identified. Variation of all 5 PRS significantly explained some of the phenotypic variations of Geisinger IS, and the R2 increased by raising the cutoff for the age of controls. PRSLAS, PRSCES, and PRSSVS derived from low-frequency common variants provided the best fit for modeling (R2 = 0.015 for PRSLAS). Gene sets analyses highlighted the association of PRS with Gene Ontology terms (vascular endothelial growth factor, amyloid precursor protein, and atherosclerosis). The PRSLAS, PRSCES, and PRSSVS explained the most variance of the corresponding subtypes of Geisinger IS suggesting shared etiologies and corroborated Geisinger TOAST subtyping.ConclusionsWe provide the first evidence that PRSs derived from MEGASTROKE have value in identifying shared etiologies and determining stroke subtypes.

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