Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci U S A. 2010;107 Suppl 2:8954-8961. [PMID: 20445096 DOI: 10.1073/pnas.0914618107]

Prevalence of self-reported obesity among diverse Latino adult populations in New York City, 2013-2017

INTRODUCTION

Latinos in the United States represent a heterogeneous population disproportionally impacted by obesity. Yet, the prevalence of obesity by specific Latino group is unclear. Using the New York City Community Health Survey (2013-2017), this study compared self-reported obesity in the city's largest Latino adult populations (Puerto Ricans, Mexicans, Dominicans, Ecuadorians, and Colombians).

METHODS

Age-standardized prevalence using the 2000 Census and prevalence ratios (PRs) for self-reported obesity (BMI ≥30 kg/m2) by country of origin were estimated using weighted multivariable logistic regression adjusting for socio-demographic characteristics, health status, and behaviors.

RESULTS

Obesity prevalence among Mexicans (36.8%; 95% CI [31.5, 42.4]) and Puerto Ricans (36.3%; 95% CI [31.7, 41.3]) was significantly higher than that among Colombians (23.8%; 95% CI [18.8, 29.5]), Ecuadorians (24.2%; 95% CI [20.7, 28.1]), and Dominicans (27.0%; 95% CI [25.0, 29.1]). After adjusting for covariates, compared to Mexicans, the PRs of obesity remained significantly lower for Colombians (PR = 0.80; 95% CI [0.64, 1.00]), Ecuadorians (PR = 0.72; 95% CI [0.61, 0.86]) and Dominicans (PR = 0.75; 95% CI [0.65, 0.85]). There was no significant difference between Mexicans and Puerto Ricans.

CONCLUSION

Obesity prevalence differs by country of origin, suggesting that clustering of Latinos in public health research may obscure unique risks among specific groups. Despite group differences, all Latino groups exhibit high prevalence of obesity and warrant renewed efforts tailored to the specific context and culture of each group to prevent and reduce obesity.

Admixture mapping analysis reveals differential genetic ancestry associated with Chagas disease susceptibility in the Colombian population

Chagas disease is an infection caused by the parasite Trypanosoma cruzi, endemic in Latino America. Leveraging the three-way admixture between Native American (AMR), European (EUR) and African (AFR) populations in Latin Americans, we aimed to better understand the genetic basis of Chagas disease by performing an admixture mapping study in a Colombian population. A two-stage study was conducted, and subjects were classified as seropositive and seronegative for T. cruzi. In stage 1, global and local ancestries were estimated using reference data from the 1000 Genomes Project (1KGP) and local ancestry associations were performed by logistic regression models. The AMR ancestry showed a protective association with Chagas disease within the Major Histocompatibility Complex region (OR = 0.74, 95%CI = 0.66-0.83, lowest p-value = 4.53x10-8). The fine mapping assessment on imputed genotypes combining data from stage 1 and 2 from an independent Colombian cohort, revealed nominally associated variants in high linkage disequilibrium with the top signal (rs2032134, OR = 0.93, 95%CI = 0.90-0.97, p-value = 3.54x10-4) in the previously associated locus. To assess ancestry-specific adaptive signals, a selective sweep scan in an AMR reference population from 1KGP together with an in silico functional analysis highlighted the Tripartite Motif family and the Human Leukocyte Antigen (HLA) genes, with crucial role in the immune response against pathogens. Furthermore, these analyses emphasized the macrophages, neutrophils, and eosinophils, as key players in the defense against T. cruzi. This first admixture mapping study in Chagas disease provided novel insights underlying the host immune response in the pathogenesis of this neglected disease.

Facilitators, Challenges, and Messaging Strategies for Hispanic/Latino Populations Participating in Alzheimer's Disease and Related Dementias Clinical Research: A Literature Review

Alzheimer's disease and Alzheimer's disease-related dementias (AD/ADRD) disproportionally affect Hispanic and Latino populations, yet Hispanics/Latinos are substantially underrepresented in AD/ADRD clinical research. Diverse inclusion in trials is an ethical and scientific imperative, as underrepresentation reduces the ability to generalize study findings and treatments across populations most affected by a disease. This paper presents findings from a narrative literature review (N = 210) of the current landscape of Hispanic/Latino participation in clinical research, including the challenges, facilitators, and communication channels to conduct culturally appropriate outreach efforts to increase awareness and participation of Hispanics/Latinos in AD/ADRD clinical research studies. Many challenges identified were systemic in nature: lack of culturally relevant resources; staffing that does not represent participants' cultures/language; eligibility criteria that disproportionately excludes Hispanics/Latinos; and too few studies available in Hispanic/Latino communities. The paper also details facilitators and messaging strategies to improve engagement and interest among Hispanics/Latinos in AD/ADRD research, starting with approaches that recognize and address the heterogeneity of the Hispanic/Latino ethnicity, and then, tailor outreach activities and programs to address their diverse needs and circumstances. The needs identified in this article represent longstanding failures to improve engagement and interest among Hispanics/Latinos in AD/ADRD research; we discuss how the field can move forward learning from the experiences of the COVID-19 pandemic.

The presentation of Hispanic gastric cancer patients varies by location of patient ancestry

BACKGROUND AND OBJECTIVES

The clinical presentation of gastric cancer varies between racial and ethnic groups. While historically studied as a monolithic population, the Hispanic ethnicity is comprised of heterogenous groups with considerable biologic, socioeconomic, and cultural variability; therefore, intragroup differences among Hispanic gastric cancer patients may have been overlooked in past research.

METHODS

We conducted a retrospective review of the National Cancer Database (NCDB) to compare Hispanic patients with gastric adenocarcinoma diagnosed between 2004 and 2015, by NCDB-reported location of patient ancestry.

RESULTS

We identified a cohort of 3811 patients. There were higher proportions of females, patients with early disease onset, and stage 4 disease among patients of Mexican and South/Central American ancestry. Additionally, a significantly larger proportion of Mexican (15%) and South/Central American patients (11%) were diagnosed before age 40, in contrast to Cubans (2%), Dominicans (6%), and Puerto Ricans (3%; p < 0.0001). Mexican ancestry was independently associated with an increased rate of all-cause mortality at 5 years (hazard ratio: 1.34; 95% confidence interval: 1.09-1.64).

CONCLUSIONS

Significant clinical and epidemiological differences exist among Hispanic gastric cancer patients based on location of ancestry. Future data collection endeavors should strive to capture this granularity inherent to the Hispanic ethnicity.

Forensic anthropology casework performance: Assessing accuracy and trends for biological profile estimates on a comprehensive sample of identified decedent cases

The purpose of this study was to investigate the accuracy rates and trends in forensic anthropology casework concerning the estimation of the biological profile (sex, age, ancestry, and stature). Identified cases from the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA; n = 359) were analyzed to explore the following: accuracy rates per biological profile component, case-level performance in assessing the biological profile, and factors related to inaccuracy rates. Accuracy rates for the four biological profile components ranged from 83% to 98%, with sex estimation performing the best and stature performing the poorest. While the overall sex estimation inaccuracies were the lowest of any biological profile component, we found that females are missexed approximately ten times more often than males. Inaccurate age estimates were more frequently the result of overestimation than underestimation, while the trends are reversed for stature estimation. Regarding ancestry estimation performance, African American/Black and White decedents had the lowest inaccuracy rates, while Hispanic and Asian/Pacific Islander decedents demonstrated greater inaccuracy rates. When examining accuracy rates for each case, 81% of cases had no inaccurate biological profile estimates, while 17% and 2% inaccurately estimated one and two biological profile components, respectively. The demographic trends of identified forensic anthropology cases reflect the national unidentified decedent demographics. Biological profile accuracy rates were generally comparable to previous studies. The findings highlight the current status of forensic anthropologists' casework performance, with a greater amount of case-level inaccuracy rates than previously thought, and demonstrate the potential methodological and sampling strategies that could improve accuracy rates.

The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia

Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).

Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America

Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.

Leveraging genetic ancestry to study health disparities

Research to understand human genomic variation and its implications in health has great potential to contribute in the reduction of health disparities. Biological anthropology can play important roles in genomics and health disparities research using a biocultural approach. This paper argues that racial/ethnic categories should not be used as a surrogate for sociocultural factors or global genomic clusters in biomedical research or clinical settings, because of the high genetic heterogeneity that exists within traditional racial/ethnic groups. Genetic ancestry is used to show variation in ancestral genomic contributions to recently admixed populations in the United States, such as African Americans and Hispanic/Latino Americans. Genetic ancestry estimates are also used to examine the relationship between ancestry-related biological and sociocultural factors affecting health disparities. To localize areas of genomes that contribute to health disparities, admixture mapping and genome-wide association studies (GWAS) are often used. Recent GWAS have identified many genetic variants that are highly differentiated among human populations that are associated with disease risk. Some of these are population-specific variants. Many of these variants may impact disease risk and help explain a portion of the difference in disease burden among racial/ethnic groups. Genetic ancestry is also of particular interest in precision medicine and disparities in drug efficacy and outcomes. By using genetic ancestry, we can learn about potential biological differences that may contribute to the heterogeneity observed across self-reported racial groups.

Systematic Review on Local Ancestor Inference From a Mathematical and Algorithmic Perspective

Genotypic data provide deep insights into the population history and medical genetics. The local ancestry inference (LAI) (also termed local ancestry deconvolution) method uses the hidden Markov model (HMM) to solve the mathematical problem of ancestry reconstruction based on genomic data. HMM is combined with other statistical models and machine learning techniques for particular genetic tasks in a series of computer tools. In this article, we surveyed the mathematical structure, application characteristics, historical development, and benchmark analysis of the LAI method in detail, which will help researchers better understand and further develop LAI methods. Firstly, we extensively explore the mathematical structure of each model and its characteristic applications. Next, we use bibliometrics to show detailed model application fields and list articles to elaborate on the historical development. LAI publications had experienced a peak period during 2006-2016 and had kept on moving in the following years. The efficiency, accuracy, and stability of the existing models were evaluated by the benchmark. We find that phased data had higher accuracy in comparison with unphased data. We summarize these models with their distinct advantages and disadvantages. The Loter model uses dynamic programming to obtain a globally optimal solution with its parameter-free advantage. Aligned bases can be used directly in the Seqmix model if the genotype is hard to call. This research may help model developers to realize current challenges, develop more advanced models, and enable scholars to select appropriate models according to given populations and datasets.

Epidemiological and genetic features of amyotrophic lateral sclerosis in Latin America and the Caribbean: a systematic review

Introduction: Heterogeneity of amyotrophic lateral sclerosis (ALS) has been suggested in terms of epidemiology, phenotypes and genetics between geographic areas and populations. However, there is limited information in Latin America. We conducted a systematic review that aimed to describe the epidemiology, frequency of genetic mutations, clinical characteristics and survival of ALS patients in this region. Methods: We reviewed Medline, Scopus, Scielo and LILACS databases up to April 2020. The search terms "Amyotrophic Lateral Sclerosis" or "Motor Neuron Disease" were used in combination with the list of Latin American countries from the United Nations. All observational studies were included. A methodological overview was performed using the principles of descriptive epidemiology. Results: Overall, 1364 publications were identified and 36 studies were selected, covering 13 Latin American countries. According to the original reports, ALS occurrence varied among countries with a standardized incidence ranging from 0.3 per 100,000 person-years follow up (PYFU) in Ecuador to 3.6 per 100,000 PYFU in Uruguay. A low proportion of the C9orf72 repeat expansion was reported in Cuba and Brazil. We identified age at onset between 50 and 60 years. Survival time was higher than 40 months in half of the studies. Data from multiethnic populations reported a higher risk of developing ALS in Caucasians compared to admixed and Black populations. Conclusion: This review provides a perspective of ALS variability across Latin America and highlights specific differences when comparing to Europe and North America. However, we cannot draw firm conclusions because of different methodological concerns within the studies.

Kidney cancer mortality disparities among Hispanics in the US

INTRODUCTION

Kidney cancer incidence is increasing among Hispanics but rate differences by distinct group, such as Cuban, Puerto Rican, and Mexican have not been studied. To fill this knowledge gap, we use mortality data, reflecting fatal kidney cancers, to examine patterns by race-ethnicity, including detailed Hispanic groups, and correlate the mortality rates with each group's prevalence of known kidney cancer risk factors: smoking, obesity, hypertension, diabetes, and chronic kidney disease.

METHODS

We used individual-level death data for California, Florida, and New York (2008-2018), and population prevalence data from the National Health Interview Surveys (2008-2018). Age-adjusted mortality rates (AAMRs) and regression-derived mortality rate ratios (MRRs) were computed. Pearson correlation analyses assessed the extent to which group-specific risk factor prevalence explained variability in observed AAMRs.

RESULTS

US-born Mexican Americans and American Indians had the highest rates and MRRs compared to Whites: 1.44 (95 %CI: 1.35-1.53) and 1.51 (1.38-1.64) for Mexican American men and women, respectively, and 1.54 (95 %CI: 1.25-1.89) and 1.53 (95 %CI: 1.15-2.04) for American Indians. In contrast, non-Mexican Hispanics had lower rates than Whites. Among males, positive correlations between AAMRs and smoking, obesity, and chronic kidney disease prevalence by race-ethnicity were found.

CONCLUSION

Mexican Americans and American Indians are high-risk for fatal kidney cancer. Disparities are only partially attributable to higher smoking and obesity prevalence, and more so among men than women. A shared risk factor profile, as well as possible genetic similarities, may explain their disproportionately higher kidney cancer mortality, but further research is warranted.

Human genetic admixture

Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.

Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs

Aiming to determine their ancestry diagnostic potential, we selected two sets of nuclear deletion/insertion polymorphisms (DIPs), including 30 located on autosomal chromosomes and 33 on the X chromosome. We analysed over 200 unrelated Argentinean individuals living in urban areas of Argentina. As in most American countries, the extant Argentinean population is the result of tricontinental genetic admixture. The peopling process within the continent was characterised by mating bias involving Native American and enslaved African females and European males. Differential results were detected between autosomal DIPs and X-DIPs. The former showed that the European component was the largest (77.8%), followed by the Native American (17.9%) and African (4.2%) components, in good agreement with the previously published results. In contrast, X-DIPs showed that the European genetic contribution was also predominant but much smaller (52.9%) and considerably larger Native American and African contributions (39.6% and 7.5%, respectively). Genetic analysis revealed continental genetic contributions whose associated phenotypic traits have been mostly lost. The observed differences between the estimated continental genetic contribution proportions based on autosomal DIPs and X-DIPs reflect the effects of autosome and X-chromosome transmission behaviour and their different recombination patterns. This work shows the ability of the tested DIP panels to infer ancestry and confirm mating bias. To the best of our knowledge, this is the first study focusing on ancestry-informative autosomal DIP and X-DIP comparisons performed in a sample representing the entire Argentinean population.

Use of craniometric data to facilitate migrant identifications at the United States/Mexico border

OBJECTIVES

Thousands of migrants have died along the United States/Mexico border and many remain unidentified. The purpose of this research is to test whether estimations of population affinity, derived from craniometric data, can facilitate identification of migrant remains and provide a geographic region of origin rather than the broad label Hispanic. The appropriateness of current forensic reference data will also be assessed.

METHODS

A case study combined with craniometric data from positively identified and unidentified migrants from the Pima County Office of the Medical Examiner (n = 489) in Arizona and operation identification (n = 201) in Texas were compared to skeletal data representing Guatemalan (n = 87) and Mexican (n = 65) Mayans. Biological distance and discriminant function analyses were used to assess overall population relationships and classificatory models for forensic anthropological application.

RESULTS

The majority of evidence indicates that estimations of population affinity can assist in the facilitation identification of migrant remains, even when a broad classification is used. Biological distances among the groups suggest that positively identified Guatemalan and Mexican migrants are similar to one another but differ from Guatemalan and Mexican Mayans.

CONCLUSIONS

Population affinity estimations can aid migrant identification, and current reference data used in forensic anthropological practice should be replaced with data from positive identifications. Estimates of geographic origin may be more useful than the broad generic term Hispanic for narrowing down the search for a missing person, but more data and research is needed to achieve this goal. Although, the utility of geographic origin estimates relies on transnational data centralization and sharing, which is not always the case.

Paradoxical effect of cumulative stress exposure on information processing speed in Hispanics/Latinos with elevated heart rate variability

Chronic stress has a deleterious effect on prefrontal lobe functioning. Empirical evidence suggests elevated vagal tone, indexed by elevated heart rate variability (HRV), mitigates the effect of mental stress on frontal lobe function. Here, the mitigating effect of HRV on stress-related decrements in cognitive performance is assessed based on information processing speed (DSST), word fluency and verbal learning task performance. Artifact free electrocardiogram (ECG) data was analyzed from 1420 Hispanic/Latino adults from the Sociocultural Ancillary of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). A 12-lead ECG was used to collect short-term recordings of the root mean square of successive differences in all normal R-peak to R-peak intervals (RMSSD) and the change between adjacent beats and the standard deviation of those intervals (SDNN) as indices of total HRV. As predicted, an interaction emerged for HRV and stress on the task presumed to require the greatest prefrontal lobe involvement, i.e., the DSST. After accounting for sociodemographic factors, chronic stress was associated with better DSST performance amongst individuals at higher quartile of SDNN, but not RMSSD. The paradoxical effect for greater stress exposure on DSST performance may in part be explained by increased speed of information processing and decision making often reported in high-stress cohorts. The nature of this interaction highlights the importance of examining the relationship between stress and cognition across a spectrum of vagal tone.

A Polygenic Risk Score for Breast Cancer in US Latinas and Latin American Women

Background

More than 180 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified; these SNPs can be combined into polygenic risk scores (PRS) to predict breast cancer risk. Because most SNPs were identified in predominantly European populations, little is known about the performance of PRS in non-Europeans. We tested the performance of a 180-SNP PRS in Latinas, a large ethnic group with variable levels of Indigenous American, European, and African ancestry.

Methods

We conducted a pooled case-control analysis of US Latinas and Latin American women (4658 cases and 7622 controls). We constructed a 180-SNP PRS consisting of SNPs associated with breast cancer risk (P < 5 × 10^–8). We evaluated the association between the PRS and breast cancer risk using multivariable logistic regression, and assessed discrimination using an area under the receiver operating characteristic curve. We also assessed PRS performance across quartiles of Indigenous American genetic ancestry. All statistical tests were two-sided.

Results

Of 180 SNPs tested, 142 showed directionally consistent associations compared with European populations, and 39 were nominally statistically significant (P < .05). The PRS was associated with breast cancer risk, with an odds ratio per SD increment of 1.58 (95% confidence interval [CI = 1.52 to 1.64) and an area under the receiver operating characteristic curve of 0.63 (95% CI = 0.62 to 0.64). The discrimination of the PRS was similar between the top and bottom quartiles of Indigenous American ancestry.

Conclusions

The 180-SNP PRS predicts breast cancer risk in Latinas, with similar performance as reported for Europeans. The performance of the PRS did not vary substantially according to Indigenous American ancestry.

Environmental and socio-cultural impacts on global DNA methylation in the indigenous Huichol population of Nayarit, Mexico

Alterations of global DNA methylation have been evaluated in several studies worldwide; however, Long Interspersed Nuclear Elements-1 (LINE-1) methylation in genetically conserved populations such as indigenous communities have not, to our knowledge, been reported. The aim of this study was to evaluate the relationship between LINE-1 methylation patterns and factors such as pesticide exposure and socio-cultural characteristics in the Indigenous Huichol Population of Nayarit, Mexico. A cross-sectional study was conducted in 140 Huichol indigenous individuals. A structured questionnaire was used to determine general and anthropometric characteristics, diet, harmful habits, and pesticide exposure. DNA methylation was determined by pyrosequencing of bisulfite-treated DNA. A lower level of LINE-1 methylation was found in the indigenous population when compared to a Mestizo population previously studied by our group. This difference might be due to the influence of the genetic admixture and differing dietary and lifestyle habits. The males in the indigenous population exhibited increased LINE-1 methylation in comparison to the females. Sex and alcohol consumption showed positive associations with LINE-1 methylation, while weight, current work in the field, current pesticide usage, and folate intake exhibited negative associations with LINE-1 methylation. The results suggest that ethnicity, as well as other internal and environmental factors, might influence LINE-1 methylation.

Effect of EGLN1 Genetic Polymorphisms on Hemoglobin Concentration in Andean Highlanders

The physiological characteristics of Andean natives living at high altitudes have been investigated extensively, with many studies reporting that Andean highlanders have a higher hemoglobin (Hb) concentration than other highlander populations. It has previously been reported that positive natural selection has acted independently on the egl-9 family hypoxia inducible factor 1 (EGLN1) gene in Tibetan and Andean highlanders and is related to Hb concentration in Tibetans. However, no study has yet revealed the genetic determinants of Hb concentration in Andeans even though several single-nucleotide polymorphisms (SNPs) in EGLN1 have previously been examined. Therefore, we explored the relationship between hematological measurements and tag SNPs designed to cover the whole EGLN1 genomic region in Andean highlanders living in Bolivia. Our findings indicated that haplotype frequencies estimated from the EGLN1 SNPs were significantly correlated with Hb concentration in the Bolivian highlanders. Moreover, we found that an Andean-dominant haplotype related to high Hb level may have expanded rapidly in ancestral Andean highlander populations. Analysis of genotype data in an ~436.3 kb genomic region containing EGLN1 using public databases indicated that the population structure based on EGLN1 genetic markers in Andean highlanders was largely different from that in other human populations. This finding may be related to an intrinsic or adaptive physiological characteristic of Andean highlanders. In conclusion, the high Hb concentrations in Andean highlanders can be partly characterized by EGLN1 genetic variants.

Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities

Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

PopInf: An Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin

Germline genetic variation contributes to cancer etiology, but self-reported race is not always consistent with genetic ancestry, and samples may not have identifying ancestry information. In this study, we describe a flexible computational pipeline, PopInf, to visualize principal component analysis output and assign ancestry to samples with unknown genetic ancestry, given a reference population panel of known origins. PopInf is implemented as a reproducible workflow in Snakemake with a tutorial on GitHub. We provide a preprocessed reference population panel that can be quickly and efficiently implemented in cancer genetics studies. We ran PopInf on The Cancer Genome Atlas (TCGA) liver cancer data and identify discrepancies between reported race and inferred genetic ancestry. The PopInf pipeline facilitates visualization and identification of genetic ancestry across samples, so that this ancestry can be accounted for in studies of disease risk.

Population structure and pharmacogenomic risk stratification in the United States

BACKGROUND

Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black (African-American), and Hispanic (Latino). Our approach to the question of PGx risk stratification entailed the integration of two distinct methodologies: population genetics and evidence-based medicine. This integrated approach allowed us to consider the clinical implications for the observed patterns of PGx variation found within and between population groups.

RESULTS

Whole genome genotypes were used to characterize individuals' continental ancestry fractions-European, African, and Native American-and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals' SIRE with > 96% accuracy, and accordingly, GA provides only a marginal increase in resolution for PGx risk stratification. In light of the concordance between SIRE and GA, taken together with the fact that information on SIRE is readily available to clinicians, we evaluated PGx variation between SIRE groups to explore the potential clinical utility of race and ethnicity. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. The vast majority of PGx variation is found within rather than between groups, a well-established fact for almost all genetic variants, which is often taken to argue against the clinical utility of population stratification. Nevertheless, analysis of highly differentiated PGx variants illustrates how SIRE partitions PGx variation based on groups' characteristic ancestry patterns. These cases underscore the extent to which SIRE carries clinically valuable information for stratifying PGx risk among populations, albeit with less utility for predicting individual-level PGx alleles (genotypes), supporting the concept of population pharmacogenomics.

CONCLUSIONS

Perhaps most interestingly, we show that individuals who identify as Black or Hispanic stand to gain far more from the consideration of race/ethnicity in treatment decisions than individuals from the majority White population.

Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades

The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.

Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations

A key aim for current genome-wide association studies (GWAS) is to interrogate the full spectrum of genetic variation underlying human traits, including rare variants, across populations. Deep whole-genome sequencing is the gold standard to fully capture genetic variation, but remains prohibitively expensive for large sample sizes. Array genotyping interrogates a sparser set of variants, which can be used as a scaffold for genotype imputation to capture a wider set of variants. However, imputation quality depends crucially on reference panel size and genetic distance from the target population. Here, we consider sequencing a subset of GWAS participants and imputing the rest using a reference panel that includes both sequenced GWAS participants and an external reference panel. We investigate how imputation quality and GWAS power are affected by the number of participants sequenced for admixed populations (African and Latino Americans) and European population isolates (Sardinians and Finns), and identify powerful, cost-effective GWAS designs given current sequencing and array costs. For populations that are well-represented in existing reference panels, we find that array genotyping alone is cost-effective and well-powered to detect common- and rare-variant associations. For poorly represented populations, sequencing a subset of participants is often most cost-effective, and can substantially increase imputation quality and GWAS power.

Native American gene flow into Polynesia predating Easter Island settlement

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1-6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around AD 1200) contemporaneous with the settlement of remote Oceania13-15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.

Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations

Background

Hispanic/Latino (HL) populations bear a disproportionately high burden of type 2 diabetes (T2D). The ability to predict T2D genetic risk using polygenic risk scores (PRS) offers great promise for improved screening and prevention. However, there are a number of complications related to the accurate inference of genetic risk across HL populations with distinct ancestry profiles. We investigated how ancestry affects the inference of T2D genetic risk using PRS in diverse HL populations from Colombia and the United States (US). In Colombia, we compared T2D genetic risk for the Mestizo population of Antioquia to the Afro-Colombian population of Chocó, and in the US, we compared European-American versus Mexican-American populations.

Methods

Whole genome sequences and genotypes from the 1000 Genomes Project and the ChocoGen Research Project were used for genetic ancestry inference and for T2D polygenic risk score (PRS) calculation. Continental ancestry fractions for HL genomes were inferred via comparison with African, European, and Native American reference genomes, and PRS were calculated using T2D risk variants taken from multiple genome-wide association studies (GWAS) conducted on cohorts with diverse ancestries. A correction for ancestry bias in T2D risk inference based on the frequencies of ancestral versus derived alleles was developed and applied to PRS calculations in the HL populations studied here.

Results

T2D genetic risk in Colombian and US HL populations is positively correlated with African and Native American ancestry and negatively correlated with European ancestry. The Afro-Colombian population of Chocó has higher predicted T2D risk than Antioquia, and the Mexican-American population has higher predicted risk than the European-American population. The inferred relative risk of T2D is robust to differences in the ancestry of the GWAS cohorts used for variant discovery. For trans-ethnic GWAS, population-specific variants and variants with same direction effects across populations yield consistent results. Nevertheless, the control for bias in T2D risk prediction confirms that explicit consideration of genetic ancestry can yield more reliable cross-population genetic risk inferences.

Conclusions

T2D associations that replicate across populations provide for more reliable risk inference, and modeling population-specific frequencies of ancestral and derived risk alleles can help control for biases in PRS estimation.

Breast Cancer Health Disparities in Hispanics/Latinas

Purpose of the review

Breast cancer incidence and mortality rates are lower in some Hispanic/Latino subpopulations compared to Non-Hispanic White women. However, studies suggest that the risk of breast cancer-specific mortality is higher in US Hispanics/Latinas. In this review we summarized current knowledge on factors associated with breast cancer incidence and risk of mortality in women of Hispanic/Latino origin.

Recent findings

Associative studies have proposed a multiplicity of factors likely contributing to differences in breast cancer incidence and survival between population groups, including socioeconomic/sociodemographic factors, lifestyle choices as well as access to and quality of care. Reports of association between global genetic ancestry overall as well as subtype-specific breast cancer risk among Hispanic/Latinas suggest that incidence and subtype distribution could result from differential exposure to environmental and lifestyle related factors correlated with genetic ancestry as well as germline genetic variation.

Summary

Hispanic/Latino in the United States have been largely underrepresented in cancer research. It is important to implement inclusive programs that facilitate the access of this population to health services and that also include education programs for the community on the importance of screening. In addition, it is important to continue promoting the inclusion of Hispanics/Latinos in genomic studies that allow understanding the biological behavior of this disease in the context of all human genetic diversity.

Choices, attitudes, and experiences of genetic screening in Latino/a and Ashkenazi Jewish individuals

Genetic screening to inform personal risk has only recently become an option as the cost of sequencing decreases, and our ability to interpret sequence variants improves. Studies have demonstrated that people want to learn about their genetic information and do well after learning it, but minorities are underrepresented in these studies. We surveyed Ashkenazi Jewish (AJ) and Latino/a participants in a genetic screening study to solicit choices about genetic results to return, as well as their experience with learning these results and attitudes about genetic information secrecy and security. Participants had the option to proceed through the study self-guided, and few elected to have traditional pre-test genetic education and counseling. Despite this, the majority were satisfied with the process of selecting and receiving genetic results and felt that they understood their results. Concerns about privacy and confidentiality of genetic data were minimal, though some participants expressed modest concerns about keeping any potential results secret or the confidentiality of their genetic information. Our results support the feasibility of the option of self-guided genetic screening. Additional care will need to be taken when designing population-based screening studies to meet the needs of participants who come from communities with different experiences with genetics.

Nutritional and socio-economic predictors of adult height in 152 world populations

Height is one of the most sensitive indicators of well-being because it combines the external influences of nutrition, economic wealth, health care, social equality, and other important socio-economic factors. The aim of this ecological study was to compare actual values of male and female height from 152 populations (except sub-Saharan Africa) with the mean supply of 47 food items from the FAOSTAT database (1995-2013) and mean values of seven socio-economic indicators (1995-2013). This comparison shows that economic wealth at the country level is only a mediocre correlate of physical growth because it is only loosely associated with the quality of nutrition and it does not reflect the social distribution of wealth. In a multiple regression model, the best predictors of stature are protein sources of the best and worst quality, and total fertility (which critically influences the amount of resources expended per child). In summary, these findings indicate that irrespective of crude economic statistics, the choice of specific nutrient sources and small family size are crucial factors determining the optimal physical development of children. Based on our data, we also believe that current international dietary recommendations regarding protein intake and protein quality would deserve serious re-evaluation.

Origin and Health Status of First-Generation Africans from Early Colonial Mexico

The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16^th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ¹³C and δ¹⁵N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events.

Genetic polymorphisms of IL17A associated with Chagas disease: results from a meta-analysis in Latin American populations

Genetic factors and the immunologic response have been suggested to determine the susceptibility against the infection and the outcome of Chagas disease. In the present study, we analysed three IL17A genetic variants (rs4711998, rs8193036 and rs2275913) regarding the predisposition to Trypanosoma cruzi infection and the development of chronic Chagas cardiomyopathy (CCC) in different Latin American populations. A total of 2,967 individuals from Colombia, Argentina, Bolivia and Brazil, were included in this study. The individuals were classified as seronegative and seropositive for T. cruzi antigens, and this last group were divided into asymptomatic and CCC. For T. cruzi infection susceptibility, the IL17A rs2275913*A showed a significant association in a fixed-effect meta-analysis after a Bonferroni correction (P = 0.016, OR = 1.21, 95%CI = 1.06–1.41). No evidence of association was detected when comparing CCC vs. asymptomatic patients. However, when CCC were compared with seronegative individuals, it showed a nominal association in the meta-analysis (P = 0.040, OR = 1.20, 95%CI = 1.01–1.45). For the IL17A rs4711998 and rs8193036, no association was observed. In conclusion, our results suggest that IL17A rs2275913 plays an important role in the susceptibility to T. cruzi infection and could also be implicated in the development of chronic cardiomyopathy in the studied Latin American population.

Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry

After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.

Population Histories of the United States Revealed through Fine-Scale Migration and Haplotype Analysis

The population of the United States is shaped by centuries of migration, isolation, growth, and admixture between ancestors of global origins. Here, we assemble a comprehensive view of recent population history by studying the ancestry and population structure of more than 32,000 individuals in the US using genetic, ancestral birth origin, and geographic data from the National Geographic Genographic Project. We identify migration routes and barriers that reflect historical demographic events. We also uncover the spatial patterns of relatedness in subpopulations through the combination of haplotype clustering, ancestral birth origin analysis, and local ancestry inference. Examples of these patterns include substantial substructure and heterogeneity in Hispanics/Latinos, isolation-by-distance in African Americans, elevated levels of relatedness and homozygosity in Asian immigrants, and fine-scale structure in European descents. Taken together, our results provide detailed insights into the genetic structure and demographic history of the diverse US population.

A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans

We performed a hypothesis-generating phenome-wide association study (PheWAS) to identify and characterize cross-phenotype associations, where one SNP is associated with two or more phenotypes, between thousands of genetic variants assayed on the Metabochip and hundreds of phenotypes in 5,897 African Americans as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study. The PAGE I study was a National Human Genome Research Institute-funded collaboration of four study sites accessing diverse epidemiologic studies genotyped on the Metabochip, a custom genotyping chip that has dense coverage of regions in the genome previously associated with cardio-metabolic traits and outcomes in mostly European-descent populations. Here we focus on identifying novel phenome-genome relationships, where SNPs are associated with more than one phenotype. To do this, we performed a PheWAS, testing each SNP on the Metabochip for an association with up to 273 phenotypes in the participating PAGE I study sites. We identified 133 putative pleiotropic variants, defined as SNPs associated at an empirically derived p-value threshold of p<0.01 in two or more PAGE study sites for two or more phenotype classes. We further annotated these PheWAS-identified variants using publicly available functional data and local genetic ancestry. Amongst our novel findings is SPARC rs4958487, associated with increased glucose levels and hypertension. SPARC has been implicated in the pathogenesis of diabetes and is also known to have a potential role in fibrosis, a common consequence of multiple conditions including hypertension. The SPARC example and others highlight the potential that PheWAS approaches have in improving our understanding of complex disease architecture by identifying novel relationships between genetic variants and an array of common human phenotypes.

Association of IL18 genetic polymorphisms with Chagas disease in Latin American populations

Host genetic factors have been suggested to play an important role in the susceptibility to Chagas disease. Given the influence of interleukin 18 (IL-18) in the development of the disease, in the present study, we analyzed three IL18 genetic variants (rs2043055, rs1946518, rs360719) regarding the predisposition to Trypanosoma cruzi infection and the development of chronic Chagas cardiomyopathy (CCC), in different Latin America populations. Genetic data of 3,608 patients from Colombia, Bolivia, Argentina, and Brazil were meta-analyzed to validate previous findings with increased statistical power. Seropositive and seronegative individuals were compared for T. cruzi infection susceptibility. In the Colombian cohort, the allelic frequencies of the three variants showed a significant association, with adjustment for sex and age, and also after applying multiple testing adjustments. Among the Colombian and Argentinean cohorts, rs360719 showed a significant genetic effect in a fixed-effects meta-analysis after a Bonferroni correction (OR: 0.76, CI: 0.66-0.89, P = 0.001). For CCC, the rs2043055 showed an association with protection from cardiomyopathy in the Colombian cohort (OR: 0.79, CI: 0.64-0.99, P = 0.037), with adjustment for sex and age, and after applying multiple testing adjustments. The meta-analysis of the CCC vs. asymptomatic patients from the four cohorts showed no evidence of association. In conclusion, our results validated the association found previously in the Colombian cohort suggesting that IL18 rs360719 plays an important role in the susceptibility to T. cruzi infection and no evidence of association was found between the IL18 genetic variants and CCC in the Latin American population studied.

Craniometric variation and ancestry estimation in two contemporary Caribbean populations

Ancestry estimation of skeletonized remains by forensic anthropologists is conducted through comparative means, and a lack of population-specific data results in possible misclassifications. This is especially germane to individuals of Latin American ancestry. Generally, each country in Latin America can trace their ancestral lineage through three main parental groups: Indigenous, European, and African. However, grouping all Latin American individuals under the broad "Hispanic" category ignores the specific genetic contributions from each parental group, which is variable and dependent on the population histories and sociocultural dynamics of each country. This study analyzes the craniometric ancestry of Hispaniola (the Dominican Republic and Haiti) using 190 cranial Computed Tomography (CT) scans (f=103; m=87), along with the island's history, to explore similarities and differences between the two groups. MANOVA results indicate that 53.6% and 71.4% of the 28 cranial measurements differ between the ancestries and sexes, respectively; and intraobserver error analyses demonstrate that 85.7% of measurements from CT scans are good-excellent in reliability. Further, a total of 12 canonical discriminant function analyses produced cross-validated classification accuracies of 73.7-78.6% for females, 71.8-87.5% for males, and 72.0-77.8% for pooled sex. This study demonstrates that, despite sharing a small island, Dominican and Haitian individuals can be differentiated with a fair amount of statistical certainty, which is possible due to complex socio-cultural, -political, and -demographic factors that have produced and maintained genetic heterogeneity. Moreover, the discriminant functions provided here can be used by the international forensic science community to identify individuals living on Hispaniola.

Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic

Background

Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human.

Methods

We examined both H. pylori DNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from cultured H. pylori were analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses.

Results

H. pylori strains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both in H. pylori and in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant in H. pylori infection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) of H. pylori was not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent.

Conclusions

Genetic features of H. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy between H. pylori and the host human genotypes support the hypothesis that adaptability of hspAmerind H. pylori strains are weaker than hpEurope strains. H. pylori strains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.

Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations

Testing for Hardy-Weinberg equilibrium (HWE) is an important component in almost all analyses of population genetic data. Genetic markers that violate HWE are often treated as special cases; for example, they may be flagged as possible genotyping errors, or they may be investigated more closely for evolutionary signatures of interest. The presence of population structure is one reason why genetic markers may fail a test of HWE. This is problematic because almost all natural populations studied in the modern setting show some degree of structure. Therefore, it is important to be able to detect deviations from HWE for reasons other than structure. To this end, we extend statistical tests of HWE to allow for population structure, which we call a test of "structural HWE." Additionally, our new test allows one to automatically choose tuning parameters and identify accurate models of structure. We demonstrate our approach on several important studies, provide theoretical justification for the test, and present empirical evidence for its utility. We anticipate the proposed test will be useful in a broad range of analyses of genome-wide population genetic data.

American Ancestry Is a Risk Factor for Suspected Nonalcoholic Fatty Liver Disease in Hispanic/Latino Adults

BACKGROUND & AIMS

Nonalcoholic fatty liver disease (NAFLD) disproportionally affects Hispanic/Latino populations. However, the magnitude varies among Hispanic/Latino ethnic groups. We investigated the mechanisms of these disparities.

METHODS

We examined associations of NAFLD-associated genetic variants and continental ancestry with suspected NAFLD, levels of alanine aminotransferase (ALT), and liver fibrosis using data from the Hispanic Community Health Study/Study of Latinos-a population-based study of Hispanic/Latino adults in the United States. We evaluated data from 16,415 Hispanic/Latino adults in 4 cities from 2008 through 2011. Subjects suspected of having NAFLD or liver fibrosis were identified based on unexplained increases in levels of aminotransferases and FIB-4 score, respectively.

RESULTS

Among the 9342 participants with available genetic and aminotransferase data, the PNPLA3 G allele (odds ratio [OR], 1.53; 95% CI, 1.41-1.66), TM6SF2 T allele (OR, 1.41; 95% CI, 1.20-1.67), and PPP1R3B G allele (OR, 1.16; 95% CI, 1.06-1.28) were associated with suspected NAFLD. PNPLA3 G was also associated with increased levels of ALT, except in participants with Dominican and South American backgrounds, and with liver fibrosis. The frequency of PNPLA3 G was high (41%) and TM6SF2 T (5%) was low in Hispanic/Latinos. PNPLA3 G frequency differed among Hispanic background groups with the highest proportion in Mexicans (52%) and the lowest proportion in Dominicans (23%). After adjustment for demographic, clinical, and behavioral factors, as well as PNPLA3 G, TM6SF2 T, and PPP1R3B G, American ancestry had a positive association with level of ALT (r = 6.61%; P < .001), whereas African (r = -3.84%; P < .001) and European (r = -4.31%; P < .001) ancestry were inversely associated with level of ALT.

CONCLUSIONS

American ancestry and PNPLA3 G are independent predictors of ALT levels in US Hispanic/Latinos and may in part explain NAFLD disparities in US Hispanic/Latinos.

Racial/ethnic disparities in renal cell carcinoma: Increased risk of early-onset and variation in histologic subtypes

Background

Racial/ethnic minority groups have a higher burden of renal cell carcinoma (RCC), but RCC among Hispanic Americans (HAs) and American Indians and Alaska Natives (AIs/ANs) are clinically not well characterized. We explored variations in age at diagnosis and frequencies of RCC histologic subtypes across racial/ethnic groups and Hispanic subgroups using National Cancer Database (NCDB) and Arizona Cancer Registry Data.

Methods

Adult RCC cases with known race/ethnicity were included. Logistic regression analysis was performed to estimate odds and 95% confidence interval (CI) of early‐onset (age at diagnosis <50 years) and diagnosis with clear cell RCC (ccRCC) or papillary RCC.

Results

A total of 405 073 RCC cases from NCDB and 9751 cases from ACR were identified and included. In both datasets, patients from racial/ethnic minority groups had a younger age at diagnosis than non‐Hispanic White (NHW) patients. In the NCDB, AIs/ANs had twofold increased odds (OR, 2.21; 95% CI, 1.88‐2.59) of early‐onset RCC compared with NHWs. HAs also had twofold increased odds of early‐onset RCC (OR, 2.14; 95% CI, 1.79‐2.55) in the ACR. In NCDB, ccRCC was more prevalent in AIs (86.3%) and Mexican Americans (83.5%) than NHWs (72.5%). AIs/ANs had twofold increased odds of diagnosis with ccRCC (OR, 2.18; 95% CI, 1.85‐2.58) in the NCDB, but the association was stronger in the ACR (OR, 2.83; 95% CI, 2.08‐3.85). Similarly, Mexican Americans had significantly increased odds of diagnosis with ccRCC (OR, 2.00; 95% CI, 1.78‐2.23) in the NCDB.

Conclusions

This study reports younger age at diagnosis and higher frequencies of ccRCC histologic subtype in AIs/ANs and Hispanic subgroups. These variations across racial/ethnic groups and Hispanic subgroups may have potential clinical implications.

Native American admixture recapitulates population-specific migration and settlement of the continental United States

European and African descendants settled the continental US during the 17th-19th centuries, coming into contact with established Native American populations. The resulting admixture among these groups yielded a significant reservoir of Native American ancestry in the modern US population. We analyzed the patterns of Native American admixture seen for the three largest genetic ancestry groups in the US population: African descendants, Western European descendants, and Spanish descendants. The three groups show distinct Native American ancestry profiles, which are indicative of their historical patterns of migration and settlement across the country. Native American ancestry in the modern African descendant population does not coincide with local geography, instead forming a single group with origins in the southeastern US, consistent with the Great Migration of the early 20th century. Western European descendants show Native American ancestry that tracks their geographic origins across the US, indicative of ongoing contact during westward expansion, and Native American ancestry can resolve Spanish descendant individuals into distinct local groups formed by more recent migration from Mexico and Puerto Rico. We found an anomalous pattern of Native American ancestry from the US southwest, which most likely corresponds to the Nuevomexicano descendants of early Spanish settlers to the region. We addressed a number of controversies surrounding this population, including the extent of Sephardic Jewish ancestry. Nuevomexicanos are less admixed than nearby Mexican-American individuals, with more European and less Native American and African ancestry, and while they do show demonstrable Sephardic Jewish ancestry, the fraction is no greater than seen for other New World Spanish descendant populations.

Genomic medicine in Chagas disease

Genetic approaches have been proposed for improving the understanding of the causes of differential susceptibility to Trypanosoma cruzi infection and Chagas disease outcome. Polymorphisms in genes involved in the immune/inflammatory response are being studied in order to clarify their possible role in the occurrence or severity of the cardiac and/or gastrointestinal complications. However still today, the number of significant associated genes is limited and the pathophysiological mechanisms underlying this condition are unknown. This article review the information currently available from the published scientific literature regarding the genetic variants of molecules of the immune system and other variants that can contribute to the clinical presentation of the disease. Genomic medicine will improve our knowledge about the molecular basis of Chagas disease, will open new avenues for developing biomarkers of disease progression, new therapeutic strategies to suit the requirements of individual patients, and will contribute to the control of one of the infections with the greatest socio-economic impact in the Americas.

Low-frequency variants at the CYP2C9 locus among Puerto Rican patients on warfarin: in silico predictions of functionality and conservation

Aim: Perform in silico predictions of functional consequences of CYP2C9 variants identified by next-generation sequencing in Puerto Ricans. Methods: Identified low-frequency CYP2C9 variants (minor allele frequencies <2%) were evaluated using the Combined Annotation-Dependent Depletion (CADD v1.3) tools and molecular modeling/docking analysis to predict impact on CYP2C9 activity. Results: CYP2C9*5,*8,*9,*11,*12,*21 and a novel *61 induce conformational changes that affect the binding site of S-warfarin. Most of these deleterious variants occur at higher frequency among individuals with large African ancestry. Conclusion: The unfavorable distance of S-warfarin from heme group, and low-binding interactions due to these CYP2C9 variants, suggest major complications during warfarin therapy. This study contributes to the field by predicting functional alterations of rare CYP2C9 variants for the first time in Hispanics.

A genome-wide association study of prostate cancer in Latinos

Latinos represent <1% of samples analyzed to date in genome‐wide association studies of cancer. The clinical value of genetic information in guiding personalized medicine in populations of non‐European ancestry will require additional discovery and risk locus characterization efforts across populations. In the present study, we performed a GWAS of prostate cancer (PrCa) in 2,820 Latino PrCa cases and 5,293 controls to search for novel PrCa risk loci and to examine the generalizability of known PrCa risk loci in Latino men. We also conducted a genetic admixture‐mapping scan to identify PrCa risk alleles associated with local ancestry. Genome‐wide significant associations were observed with 84 variants all located at the known PrCa risk regions at 8q24 (128.484–128.548) and 10q11.22 (MSMB gene). In admixture mapping, we observed genome‐wide significant associations with local African ancestry at 8q24. Of the 162 established PrCa risk variants that are common in Latino men, 135 (83.3%) had effects that were directionally consistent as previously reported, among which 55 (34.0%) were statistically significant with p < 0.05. A polygenic risk model of the known PrCa risk variants showed that, compared to men with average risk (25th–75th percentile of the polygenic risk score distribution), men in the top 10% had a 3.19‐fold (95% CI: 2.65, 3.84) increased PrCa risk. In conclusion, we found that the known PrCa risk variants can effectively stratify PrCa risk in Latino men. Larger studies in Latino populations will be required to discover and characterize genetic risk variants for PrCa and improve risk stratification for this population.

What's new?

There is strong evidence for a genetic predisposition to prostate cancer (PrCa). Most of this information has come from European ancestry populations, with Latinos representing less than 1% of samples in cancer genome‐wide association studies (GWAS). In this study, the majority of established PrCa risk variants (83.3%) were consistently associated with PrCa risk in Latinos. A polygenic risk score comprised of GWAS‐identified risk variants could identify 10% of Latino men with a ~three‐fold increase in PrCa risk. These findings suggest that common germline variants for PrCa can stratify risk in Latino men, which has implications for targeted screening and prevention.

PAMAM: Power analysis in multiancestry admixture mapping

Admixed populations arise when two or more previously isolated populations interbreed. Admixture mapping (AM) methods are used for tracing the ancestral origin of disease-susceptibility genetic loci in the admixed population such as African American and Latinos. AM is different from genome-wide association studies in that ancestry rather than genotypes are tracked in the association process. The power and sample size of AM primarily depend on proportion of admixture and differences in the risk allele frequencies among the ancestral populations. Ensuring sufficient power to detect the effect of ancestry on disease susceptibility is critical for interpretability and reliability of studies using AM approach. However, there is no power and sample size analysis tool existing for AM studies in admixed population. In this study, we developed power analysis of multiancestry AM (PAMAM) to estimate power and sample size for two-way and three-way population admixtures. PAMAM is the first web-based bioinformatics tool developed to calculate power and sample size in admixed population under a variety of genetic and disease phenotype models. It is a valuable resource for investigators to design a cost-efficient study and develop grant application to pursue AM studies. PAMAM is built on JavaScript back-end with HTML front-end. It is accessible through any modern web browser such as Firefox, Internet Explorer, and Google Chrome regardless of operating system. It is a user-friendly tool containing links for support information including user manual and examples, and freely available at https://research.cchmc.org/mershalab/PAMAM/login.html.

The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data

The history of Ecuador was marked by the arrival of Europeans with Africans, resulting in the mixture of Native Americans with Africans and Europeans. The present study contributes to the knowledge of the Ecuadorian mestizo population by offering information about ancestry and ethnic heterogeneity. Forty-six AIM-InDels (Ancestry Informative Insertion/Deletion Markers) were used to obtain information on 240 Ecuadorian individuals from three regions (Amazonia, the Highlands, and the Coast). As a result, the population involved a significant contribution from Native Americans (values up to 51%), followed by Europeans (values up to 33%) and Africans (values up to 13%). Furthermore, we compared the data obtained with nine previously reported scientific articles on autosomal, mitochondrial DNA and Y chromosomes. The admixture results correspond to Ecuador's historical background and vary slightly between regions.

Emerging genomic biomarkers for improving kidney, prostate, and bladder cancer health disparities outcomes

BACKGROUND

Recent advances in genomic and genetic technologies have facilitated better health outcomes for urologic cancer patients. Genomic and genetic heterogeneity may contribute to differences in tumor biology and urologic cancer burden across various populations.

OBJECTIVE

To examine how emerging genomic and genetic biomarkers, self-reported race, and ancestry-informative markers are associated with kidney, prostate, and bladder cancer outcomes.

RESULTS

Genomic and genetic alterations found in African American kidney cancer patients included distinct somatic mutations, somatic copy number alterations, chromosomal instability, germ-line risk alleles, and germ-line genetic variants. These changes correlated with improved risk prediction, prognosis, and survival; and a predicted decrease in response to targeted therapies. SNP risk alleles and ancestry-informative markers were associated with improved risk prediction in prostate cancer patients of both African and European descent. AKT activation suggest differential response to AKT-targeted therapies in African American, Asian American, and Tunisian bladder cancer patients. Both self-reported race and genetic ancestry predicted urologic cancer risk prediction.

CONCLUSION

Precision medicine approaches that integrate population-specific genomic and genetic information with other known urologic cancer-specific characteristics can improve outcomes and be leveraged to reduce cancer health disparities. Further investigations are necessary to identify novel genomic biomarkers with clinical utility.