Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping

Colonialism, ethnogenesis, and biogeographic ancestry in the US Southwest

OBJECTIVE

Differences between self-perceived biogeographic ancestry and estimates derived from DNA are potentially informative about the formation of ethnic identities in different sociohistorical contexts. Here, we compared self-estimates and DNA-estimates in New Mexico, where notions of shared ancestry and ethnic identity have been shaped by centuries of migration and admixture.

MATERIALS AND METHODS

We asked 507 New Mexicans of Spanish-speaking descent (NMS) to list their ethnic identity and to estimate their percentages of European and Native American ancestry. We then compared self-estimates to estimates derived from 291,917 single nucleotide polymorphisms (SNPs), and we examined how differences between the estimates varied by ethnic identity.

RESULTS

Most NMS (94%) predicted that they had non-zero percentages of European and Native American ancestry. Self-estimates and SNP-estimates were positively correlated (rEuropean  = 0.38, rNative-American  = 0.36, p < 0.001). The correlations belie systematic patterns of underestimation and overestimation based on ethnic identity. NMS with ancestral ties to 20th century immigrants, who identified as Mexican or Mexican American, often underestimated their European ancestry (self-estimate < SNP-estimate) and overestimated their Native American ancestry. The pattern was reversed for NMS who emphasized deep connections to colonial New Mexico and identified as Spanish or Spanish American.

DISCUSSION

While NMS accurately predicted that they had European and Native American ancestry, they predicted ancestry percentages with only moderate accuracy. Differences between self-estimated and SNP-estimated ancestry were associated with ethnic identities that were shaped by migration to the region over the past 400 years. We connect ethnic identities and patterns of ancestry estimation to resistance to colonial hegemony and discuss the implications of our results for the construction of ethnic identities, now and in the past.

Behavioral and Psychological Outcomes Associated with Skin Cancer Genetic Testing in Albuquerque Primary Care

Simple Summary

Genetic information is publicly available but research examining the best use of such information has not engaged diverse members of the public. We examined public reactions to melanoma genetic testing (using the melanocortin-1 receptor [MC1R] gene) in a study randomizing (like the flip of a coin) 600 diverse primary care patients to a MC1R test offer or usual care. We found that testing did not improve sun protection and skin cancer screening, nor did it lead worry to increase. However, groups less aware of their skin cancer risk, including those who thought their risk was “unlikely” at the start of the study, showed significant improvements in sun protection at three months. In conclusion, testing might be very helpful for certain people who have the most to learn about their risk, who may become motivated to protect themselves from the damaging effects of the sun as a result of skin cancer genetic testing.

Abstract

Public availability of genetic information is increasing; thus, efforts to improve diversity in basic and translational research in genomics is a top priority. Given the increasing U.S. incidence and mortality of melanoma, and the prevalence of common melanocortin-1 receptor (MC1R) gene melanoma risk variants in the general population, we examined genomic testing of MC1R for skin cancer risk in a randomized controlled trial in Albuquerque, New Mexico primary care. Participants were 48% Hispanic and were randomized 5:1 to a MC1R test invitation or usual care. We assessed 3 month sun protection, skin cancer screening, and skin cancer worry outcomes associated with testing, and key effect moderators (e.g., cancer risk perceptions, and skin cancer risk factors). Our findings indicate that the primary outcomes were unchanged by the MC1R test offer, test acceptance, and level of risk feedback. Moderator analyses showed that those with lower risk perception, and those with skin that readily tans, significantly increased their sun protection in response to higher than average risk feedback. Risk feedback did not prompt cancer worry, and average risk feedback did not erode existing sun protection. This study paves the way for the development of tailored strategies to address low skin cancer risk awareness in this understudied context of public health genomics.

Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases

Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.

Admixture mapping identifies African and Amerindigenous local ancestry loci associated with fetal growth

Fetal growth is an important determinant of cardiometabolic disease risk during childhood and adulthood. The genetic architecture of fetal growth remains largely understudied in ancestrally diverse populations. We conducted genome-wide admixture mapping scan and analysis of genetic ancestry among Hispanic American, African American, European American, and Asian American pregnant women to identify genetic loci associated with fetal growth measures across 13-40 weeks gestation. Fetal growth measures were associated with genome-wide average African, European, Amerindigenous and East Asian ancestry proportions (P ranged from10^-3 to 4.8 × 10^-2). Admixture mapping analysis identified ten African ancestry loci and three Amerindigenous ancestry loci significantly associated with fetal growth measures at Bonferroni-corrected levels of significance (P ranged from 2.18 × 10^-8 to 3.71 × 10^-6). At the chr2q23.3-24.2 locus in which higher African ancestry was associated with long bone (femur and humerus) lengths, the T allele of rs13030825 (GALNT13) was associated with longer humerus length in African Americans (β = 0.44, P = 6.25 × 10^-6 at week 27; β = 0.39, P = 7.72 × 10^-5 at week 40). The rs13030825 SNP accounted for most of the admixture association at the chr2q23.3-24.2 locus and has substantial allele frequency difference between African and European reference samples (F_ST = 0.55, P = 0.03). Regulatory annotation shows that rs13030825 overlaps with the serum response factor (SRF) transcription factor previously implicated in postnatal bone development of mice. Overall, we identified ancestry-related maternal genetic loci that influence fetal growth, shedding light on molecular pathways that regulate fetal growth and potential effects on health across the lifespan.Clinical trials registration ClinicalTrials.gov, NCT00912132.

Epistasis of polymorphisms related to the articular cartilage extracellular matrix in knee osteoarthritis: Analysis-based multifactor dimensionality reduction

Osteoarthritis (OA) is a complex disease with a multifactorial etiology. The genetic component is one of the main associated factors, resulting from interactions between genes and environmental factors. The aim of this study was to identify gene-gene interactions (epistasis) of the articular cartilage extracellular matrix (ECM) in knee OA. Ninety-two knee OA patients and 147 healthy individuals were included. Participants were genotyped in order to evaluate nine variants of eight genes associated with ECM metabolism using the OpenArray technology. Epistasis was analyzed using the multifactor dimensionality reduction (MDR) method. The MDR analysis showed significant gene-gene interactions between MMP3 (rs679620) and COL3A1 (rs1800255), and between COL3A1 (rs1800255) and VEGFA (rs699947) polymorphisms, with information gain values of 3.21% and 2.34%, respectively. Furthermore, in our study we found interactions in high-risk genotypes of the HIF1AN, MMP3 and COL3A1 genes; the most representative were [AA+CC+GA], [AA+CT+GA] and [AA+CT+GG], respectively; and low-risk genotypes [AA+CC+GG], [GG+TT+GA] and [AA+TT+GA], respectively. Knowing the interactions of these polymorphisms involved in articular cartilage ECM metabolism could provide a new tool to identify individuals at high risk of developing knee OA.

Interest and Uptake of MC1R Testing for Melanoma Risk in a Diverse Primary Care Population: A Randomized Clinical Trial

Importance

Germline variants in the MC1R gene are common and confer moderate melanoma risk in those with varied skin types. Approaches to precision skin cancer prevention that include genetic information may promote risk awareness and risk reduction in the general population, including Hispanics.

Objective

To examine prevalence of interest in and uptake of MC1R testing in the general population and examine patterns across demographic and skin cancer risk factors.

Design, Setting, and Participants

A randomized clinical trial examined interest in and uptake of MC1R testing among patients at University of New Mexico General Internal Medicine clinics. Study participants were randomized to either a usual-care condition (National Cancer Institute skin cancer pamphlet for diverse skin types) or an MC1R test offer. Participants were registered clinic patients (≥6 months) and English or Spanish fluent. Of the 600 participants recruited to the overall trial, the present study included those 499 participants randomized to the MC1R test offer.

Interventions

Participants were presented with the option to log onto the study website to read 3 educational modules presenting the rationale, benefits, and drawbacks of MC1R testing.

Main Outcomes and Measures

Main outcomes include website log on (yes vs no), saliva test kit request (yes vs no), and saliva test kit return for MC1R testing (yes vs no). Demographic and skin cancer risk factors were examined as potential predictors of test interest and uptake.

Results

Of the 499 participants (220 [44%] non-Hispanic white, 242 [48%] Hispanic, 396 [79%] female; mean [SD] age, 54 [14.3] years), 232 (46%) elected to learn about MC1R testing by logging onto the website; 204 (88%) of those who logged on decided to request testing; and 167 (82%) of those who requested testing returned the kit. The strongest predictors of website log on were race/ethnicity and education (non-Hispanic whites were more likely to log on [odds ratio for Hispanics vs non-Hispanic whites, 0.5; 95% CI, 0.3-0.7], as were more highly educated individuals [odds ratio for more than high school vs high school or less, 2.7; 95% CI, 1.7-4.3]). The strongest predictor of ordering the test was sunburn history (odds ratio, 5.4; 95% CI, 2.3-12.9 vs no sunburn history).

Conclusions and Relevance

There were moderately high levels of MC1R test interest and uptake in this diverse sample. Addressing potential barriers to testing may be warranted as genomic information becomes integrated into general population approaches to the precision prevention of skin cancer.

Trial Registration

ClinicalTrials.gov identifier: NCT03130569.

Impact of the gene-gene interactions related to the HIF-1α signaling pathway with the knee osteoarthritis development

INTRODUCTION/OBJECTIVES

Articular cartilage is the target tissue of osteoarthritis (OA), and because it lacks capillary networks, the microenvironment is hypoxic. Hypoxia inducible factor-1 alpha (HIF-1α) regulates the homeostasis of this tissue. The aim of this study was to investigate whether genetic polymorphisms of the HIF-1α signaling pathway are involved in the development of knee OA.

METHOD

We performed a case-control association study and genotyped 134 knee OA patients and 267 healthy controls. All participants were genotyped in order to evaluate 42 SNPs from 22 genes involved in the HIF-1α signaling pathway using the OpenArray technology. Gene-gene interactions (epistasis) were analyzed using the multifactor dimensionality reduction (MDR) method.

RESULTS

The MDR analysis showed epistasis between AKT2 (rs8100018) and IGF1 (rs2288377), AKT2 (rs8100018) and IGF1 (rs35767), IGF1 (rs35767) and COL2A1 (rs1793953), and between GSK3B (rs6438552) and IGF1 (rs35767) polymorphisms, with information gain values of 21.24%, 8.37%, 9.93%, and 5.73%, respectively. Additionally, our model allowed us to identify high- and low-risk genotypes among COL2A1 rs1793953, GSK3B rs6438552, AKT2 rs8100018, and IGF1 rs35767 polymorphisms.

CONCLUSIONS

Knowing the interactions of these polymorphisms involved in HIF-1α signaling pathway could provide a new diagnostic support tool to identify individuals at high risk of developing knee OA.

Common gene variants interactions related to uric acid transport are associated with knee osteoarthritis susceptibility

BACKGROUND

The presence of genetic variants in uric acid (UA) transporters can be associated with hyperuricemia, and therefore with an increased risk of monosodium urate (MSU) crystal precipitation. The inflammatory process triggered by these crystals leads to cartilage damage, which, in turn, could promote knee osteoarthritis (KOA).

OBJECTIVE

To determine whether genetic polymorphisms of the UA transporters and their interactions are associated with KOA.

MATERIALS AND METHODS

Two hundred forty-three unrelated Mexican-mestizo individuals were recruited for this case-control study. Ninety-three of them were KOA patients but without gout, and one hundred and fifty healthy individuals with no symptoms or signs of KOA were recruited as controls. Forty-one single-nucleotide polymorphisms (SNPs) involved in the UA transporters were genotyped with OpenArray technology in a QuantStudio 12K flex-System with both cases and controls.

RESULTS

After adjusting by age, gender, BMI, and ancestry, significant associations were found for eight SNPs: rs1260326 (GCKR), rs780093 (GCKR), rs17050272 (INHBB), rs1471633 (PDZK1), rs12129861 (PDZK1), rs7193778 (IGF1R), rs17786744 (STC1), and rs1106766 (R3HDM2). With respect to gene-gene interactions, the pairwise interactions of rs112129861 (PDZK1) and rs7193778 (IGF1R); rs17050272 (INHBB) and rs1106766 (R3HDM2); rs1106766 (R3HDM2) and rs780093 (GCKR); rs1260326 (GCKR) and rs17786744 (STC1); and rs17786744 (STC1) and rs1106766 (R3HDM2) make it possible to visualize the synergistic or antagonistic effect of their genotypes or alleles on KOA development.

CONCLUSIONS

Our preliminary results show that the common gene variants related to UA transport are associated with KOA in the Mexican population. Further studies must be carried out to corroborate it.

Gene-gene interactions of the Wnt/β-catenin signaling pathway in knee osteoarthritis

This study was designed to investigate whether genetic polymorphisms of the Wnt/β-catenin signaling pathway and its interactions are involved in the development of knee osteoarthritis (KOA). Patients with KOA (n = 131) and healthy individuals (n = 190) with different ancestry from two Mexican populations (Mexico City and Guadalajara City) were analyzed. Twenty-five SNPs from thirteen genes (WISP1, DKK1, SOST, FRZB, LRP1, LRP4, LRP5, LRP6, GSKB, ADAMTS5, GDF5, FMN2 and COL11A1) involved in the Wnt/β-catenin signaling pathway were genotyped. Genetic and allelic frequencies and gene-gene interactions were performed for this study. After adjusting for age, sex, BMI and admixture, significant associations were found for five SNPs in Mexico City: LRP6 rs12314259 (G/G genotype OR 0.22, P = 0.029; and G allele OR 0.48, P = 0.022), SOST rs851054 (C/T genotype OR 0.42, P = 0.027; and T allele OR 0.62, P = 0.026), FMN2 rs986690 (G/A genotype OR 0.42, P = 0.034; and A allele OR 0.50, P = 0.015), FRZB rs409238 (A/G genotype, OR 2.41, P = 0.022), and COL11A1 rs2615977 (A/C genotype OR 2.39, P = 0.024); no associations for Guadalajara City were found. With respect to gene-gene interactions, the pairwise interactions of WISP1-COL11A1, COL11A1-FRZB, FRZB-SOST and WISP1-FMN2 make it possible to visualize the synergistic or antagonistic effect of their genotypes or alleles in both populations. These results suggest that gene-gene interactions in the Wnt/β-catenin signaling pathway play a role in the etiology of KOA.

Associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent

This study examines associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent (NMS). In structured interviews, we asked 507 NMS to select from a list of eight ethnic identity terms identified in previous research. We estimated genomic ancestry for each individual from 291,917 single nucleotide polymorphisms (SNPs) and compared genomic ancestry, age, and birthplace between groups of individuals who identified using each ethnic identity term. Eighty-eight per cent of NMS who identified as "Hispanic," "Nuevomexicano/a," and "Spanish," on average, were born in New Mexico, as were the vast majority of their parents and grandparents. Thirty-three per cent of NMS who identified as "Mexican" and "Mexican American" were born in Mexico, as were 59 per cent of their parents and 67 per cent of their grandparents. Average Native American and African ancestry proportions in "Hispanic" (0.26, 0.02, respectively), "Spanish" (0.25, 0.01), and "Nuevomexicano/a" (0.24, 0.01) NMS were significantly lower than in "Mexican American" (0.37, 0.04) NMS. Significant age differences between older "Spanish" and younger "Nuevomexicano/a" individuals, combined with widespread use of the term "Hispanic," may reflect ongoing nomenclature changes. Patterns of correspondence between ethnic identity, ethnic nomenclatures, and genomic ancestry reflect historical patterns of migration, colonization, and cultural change.

Social-group identity and population substructure in admixed populations in New Mexico and Latin America

We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The “Spanish” group had significantly lower Native American ancestry and higher European ancestry than the “Mexican” group. Positive F_IS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.

Adaptation of human skin color in various populations

BACKGROUND

Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine.

DISCUSSION

Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies.

CONCLUSION

Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.

American College of Cardiology/American Heart Association (ACC/AHA) Class I Guidelines for the Treatment of Cholesterol to Reduce Atherosclerotic Cardiovascular Risk: Implications for US Hispanics/Latinos Based on Findings From the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Background

The prevalence estimates of statin eligibility among Hispanic/Latinos living in the United States under the new 2013 American College of Cardiology/American Heart Association (ACC/AHA) cholesterol treatment guidelines are not known.

Methods and Results

We estimated prevalence of statin eligibility under 2013 ACC/AHA and 3rd National Cholesterol Education Program Adult Treatment Panel (NCEP/ATP III) guidelines among Hispanic Community Health Study/Study of Latinos (n=16 415; mean age 41 years, 40% males) by using sampling weights calibrated to the 2010 US census. We examined the characteristics of Hispanic/Latinos treated and not treated with statins under both guidelines. We also redetermined the statin‐therapy eligibility by using black risk estimates for Dominicans, Cubans, Puerto Ricans, and Central Americans. Compared with NCEP/ATP III guidelines, statin eligibility increased from 15.9% (95% CI 15.0–16.7%) to 26.9% (95% CI 25.7–28.0%) under the 2013 ACC/AHA guidelines. This was mainly driven by the ≥7.5% atherosclerotic cardiovascular disease risk criteria (prevalence 13.9% [95% CI 13.0–14.7%]). Of the participants eligible for statin eligibility under NCEP/ATP III and ACC/AHA guidelines, only 28.2% (95% CI 26.3–30.0%) and 20.6% (95% CI 19.4–21.9%) were taking statins, respectively. Statin‐eligible participants who were not taking statins had a higher prevalence of cardiovascular risk factors compared with statin‐eligible participants who were taking statins. There was no significant increase in statin eligibility when atherosclerotic cardiovascular disease risk was calculated by using black estimates instead of recommended white estimates (increase by 1.4%, P=0.12) for Hispanic/Latinos.

Conclusions

The eligibility of statin therapy increased consistently across all Hispanic/Latinos subgroups under the 2013 ACC/AHA guidelines and therefore will potentially increase the number of undertreated Hispanic/Latinos in the United States.

Implementing an Internet-Delivered Skin Cancer Genetic Testing Intervention to Improve Sun Protection Behavior in a Diverse Population: Protocol for a Randomized Controlled Trial

Background

Limited translational genomic research currently exists to guide the availability, comprehension, and appropriate use of personalized genomics in diverse general population subgroups. Melanoma skin cancers are preventable, curable, common in the general population, and disproportionately increasing in Hispanics.

Objective

Variants in the melanocortin-1 receptor (MC1R) gene are present in approximately 50% of the population, are major factors in determining sun sensitivity, and confer a 2-to-3-fold increase in melanoma risk in the general population, even in populations with darker skin. Therefore, feedback regarding MC1R risk status may raise risk awareness and protective behavior in the general population.

Methods

We are conducting a randomized controlled trial examining Internet presentation of the risks and benefits of personalized genomic testing for MC1R gene variants that are associated with increased melanoma risk. We will enroll a total of 885 participants (462 participants are currently enrolled), who will be randomized 6:1 to personalized genomic testing for melanoma risk versus waiting list control. Control participants will be offered testing after outcome assessments. Participants will be balanced across self-reported Hispanic versus non-Hispanic ethnicity (n=750 in personalized genomic testing for melanoma risk arm; n=135 in control arm), and will be recruited from a general population cohort in Albuquerque, New Mexico, which is subject to year-round sun exposure. Baseline surveys will be completed in-person with study staff and follow-up measures will be completed via telephone.

Results

Aim 1 of the trial will examine the personal utility of personalized genomic testing for melanoma risk in terms of short-term (3-month) sun protection and skin screening behaviors, family and physician communication, and melanoma threat and control beliefs (ie, putative mediators of behavior change). We will also examine potential unintended consequences of testing among those who receive average-risk personalized genomic testing for melanoma risk findings, and examine predictors of sun protection at 3 months as the outcome. These findings will be used to develop messages for groups that receive average-risk feedback. Aim 2 will compare rates of test consideration in Hispanics versus non-Hispanics, including consideration of testing pros and cons and registration of a decision to either accept or decline testing. Aim 3 will examine personalized genomic testing for melanoma risk feedback comprehension, recall, satisfaction, and cancer-related distress in those who undergo testing, and whether these outcomes differ by ethnicity (Hispanic vs non-Hispanic), or sociocultural or demographic factors. Final outcome data collection is anticipated to be complete by October 2017, at which point data analysis will commence.

Conclusions

This study has important implications for personalized genomics in the context of melanoma risk, and may be broadly applicable as a model for delivery of personalized genomic feedback for other health conditions.

Perceived Discrimination and Nocturnal Blood Pressure Dipping Among Hispanics: The Influence of Social Support and Race

OBJECTIVE

Little is known about the relationship of perceived racism to ambulatory blood pressure (ABP) in Hispanics. We explored possible associations between ABP nocturnal dipping and perceived racism in a Hispanic cohort.

METHODS

Participants included 180 community-dwelling Hispanics from the Northern Manhattan Study. Measures included perceived racism, socioeconomic status, social support, and ABP monitoring. Nocturnal ABP nondipping was defined as a less than 10% decline in the average asleep systolic blood pressure relative to the awake systolic blood pressure.

RESULTS

Overall, 77.8% of participants reported some form of perceived racism (Perceived Ethnic Discrimination Questionnaire scores >1.0). Greater social support was associated with less perceived discrimination (Spearman r = -0.54, p < .001). Those with higher perceived discrimination scores reported more depressive symptoms (r = 0.25, p < .001). Those with higher Perceived Ethnic Discrimination Questionnaire scores were less likely to show nocturnal ABP nondipping in multivariate models (odds ratio = 0.40, confidence interval = 0.17-0.98, p = .045). Among those with low perceived racism, black Hispanic participants were more likely to have nocturnal ABP nondipping (82.6%) compared with white Hispanics (53.9%; p = .02). Among those with high perceived racism, no associations between race and the prevalence of ABP nondipping was found (black Hispanic = 61.5% versus white Hispanic = 51.4%, p = .39; p interaction = .89).

CONCLUSIONS

Perceived racism is relatively common among US Hispanics and is associated with ABP. Nondipping of ABP, a potential cardiovascular risk factor, was more common in black Hispanic participants with low perceived racism. This finding may reflect different coping mechanisms between black versus white Hispanics and related blood pressure levels during daytime exposures to discrimination.

Mapping asthma-associated variants in admixed populations

Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies.

Association of serum lipids with outcomes in Hispanic hemodialysis patients of the West versus East Coasts of the United States

BACKGROUND

Paradoxical associations exist between serum lipid levels and mortality in patients on maintenance hemodialysis (MHD) including those of Hispanic origin. However, there are significant racial and ethnic variations in patients of 'Hispanic' background. We hypothesized that clinically meaningful differences existed in the association between lipids and survival in Hispanic MHD patients on the West versus East Coast.

METHODS

We examined the survival impact of serum lipids in a 2-year cohort of 15,109 MHD patients of Hispanic origin being treated in California, Texas, representing the West versus New York, New Jersey and Florida representing the East Coast, using Cox models with various degrees of adjustments.

RESULTS

The association of serum total and HDL cholesterol with mortality follows a U-shaped pattern in Hispanic patients residing in the West. This is in contrast to Hispanic patients in the East Coast whose survival seems to improve with increasing total and HDL cholesterol levels. Elevated serum LDL levels in Hispanic patients on the West Coast are associated with a significant increase in mortality, while this association is not observed in patients residing on the East Coast.

CONCLUSIONS

Substantial differences exist in the association of serum lipids with mortality in MHD patients of Hispanic background depending on whether they reside on the West or East Coast of the United States. These geographical variances most likely reflect ethnic, racial and genetic distinctions, which are usually ignored. Future studies should take into account these critical variations in a population of patients who make up a significant portion of our society.

Psychosocial Predictors of Metabolic Syndrome among Latino Groups in the Multi-Ethnic Study of Atherosclerosis (MESA)

OBJECTIVE

We sought to determine the contribution of psychological variables to risk for metabolic syndrome (MetS) among Latinos enrolled in the Multi-Ethnic Study of Atherosclerosis (MESA), and to investigate whether social support moderates these associations, and whether inflammatory markers mediate the association between psychological variables and MetS.

RESEARCH DESIGN AND METHODS

Cross-sectional analyses at study baseline were conducted with a national Latino cohort (n = 1,388) that included Mexican Americans, Dominican Americans, Puerto Rican Americans and Central/South Americans. Hierarchical logistic regression analyses were conducted to test the effects of psychosocial variables (chronic stress, depressive symptoms, and social support) on MetS. In addition, separate subgroup-specific models, controlling for nationality, age, gender, socioeconomic position, language spoken at home, exercise, smoking and drinking status, and testing for the effects of chronic stress, depressive symptoms and inflammation (IL-6, CRP, fibrinogen) in predicting risk for MetS were conducted.

RESULTS

In the overall sample, high chronic stress independently predicted risk for MetS, however this association was found to be significant only in Mexican Americans and Puerto Rican Americans. Social support did not moderate the associations between chronic stress and MetS for any group. Chronic stress was not associated with inflammatory markers in either the overall sample or in each group.

CONCLUSIONS

Our results suggest a differential contribution of chronic stress to the prevalence of MetS by national groups.

Racial/ethnic and socioeconomic differences in bone loss among men

As men age, they lose bone and are susceptible to fracture. Despite having lower fracture rates than women, men have worse fractures than women do. Racial/ethnic and socioeconomic status (SES) disparities in fracture rates exist, yet data on rates of bone loss by race/ethnicity and SES among men are limited. We examined annualized percentage change in bone mineral density (%ΔBMD) at the hip (N = 681), spine (N = 663), and forearm (N = 636) during 7 years of follow-up among men aged 30-79 years at baseline. Multivariable models tested whether race/ethnicity, income, or genetic ancestry predicted annualized %ΔBMD after controlling for an extensive set of covariates. Annualized %ΔBMD ranged from -0.65(0.04)% (femoral neck) to +0.26(0.03)% (1/3 distal radius), and changes were consistent across age groups with the exception of the ultradistal radius, where annualized declines increased with age. Neither self-identified race/ethnicity nor genetic ancestry were associated with annualized %ΔBMD. In contrast, income was strongly associated (dose-response) with annualized %ΔBMD at total hip (independent of confounders, self-identified race/ethnicity, and genetic ancestry). Fully adjusted least-square mean change in annualized %ΔBMD at the total hip were -0.24(0.12)% and -0.16(0.06)% steeper among men with low and moderate incomes, respectively, than among men with higher incomes (overall p = 0.0293). Results show a linear decline in bone that begins relatively early in life among men, that rates of bone loss do not vary with race/ethnicity (self-identified or "objectively" measured), and that income plays an important role in relation to bone loss at the hip. These data suggest that fracture risk in men may be driven in part by income-related differences in bone loss, but also, that the known higher fracture risk among white men is not the result of racial/ethnic differences in bone loss, but rather, early life exposures that lead to attainment of higher peak bone mass among minorities.

Biogeographical ancestry and race

The use of racial and ethnic categories in biological and biomedical research is controversial-for example, in the comparison of disease risk in different groups or as a means of making use of or controlling for population structure in the mapping of genes to chromosomes. Biogeographical ancestry (BGA) has been recommended as a more accurate and appropriate category. BGA is a product of the collaboration between biological anthropologist Mark Shriver from Pennsylvania State University and molecular biologist Tony Frudakis from the now-defunct biotechnology start-up company DNAPrint genomics, Inc. Shriver and Frudakis portray BGA as a measure of the 'biological', 'genetic', 'natural', and 'objective' components of race and ethnicity, what philosophers of science would call a natural kind. This paper argues that BGA is not a natural kind that escapes social and political connotations of race and ethnicity, as Shriver and Frudakis and other proponents believe, but a construction that is built upon race-as race has been socially constructed in the European scientific and philosophical traditions. More specifically, BGA is not a global category of biological and anthropological classification but a local category shaped by the U.S. context of its production, especially the forensic aim of being able to predict the race or ethnicity of an unknown suspect based on DNA found at the crime scene. Therefore, caution needs to be exercised in the embrace of BGA as an alternative to the use of racial and ethnic categories in biological and biomedical research.

Status of cardiovascular disease and stroke in Hispanics/Latinos in the United States: a science advisory from the American Heart Association

BACKGROUND AND PURPOSE

This American Heart Association (AHA) scientific statement provides a comprehensive overview of current evidence on the burden cardiovascular disease (CVD) among Hispanics in the United States. Hispanics are the largest minority ethnic group in the United States, and their health is vital to the public health of the nation and to achieving the AHA's 2020 goals. This statement describes the CVD epidemiology and related personal beliefs and the social and health issues of US Hispanics, and it identifies potential prevention and treatment opportunities. The intended audience for this statement includes healthcare professionals, researchers, and policy makers.

METHODS

Writing group members were nominated by the AHA's Manuscript Oversight Committee and represent a broad range of expertise in relation to Hispanic individuals and CVD. The writers used a general framework outlined by the committee chair to produce a comprehensive literature review that summarizes existing evidence, indicate gaps in current knowledge, and formulate recommendations. Only English-language studies were reviewed, with PubMed/MEDLINE as our primary resource, as well as the Cochrane Library Reviews, Centers for Disease Control and Prevention, and the US Census data as secondary resources. Inductive methods and descriptive studies that focused on CVD outcomes incidence, prevalence, treatment response, and risks were included. Because of the wide scope of these topics, members of the writing committee were responsible for drafting individual sections selected by the chair of the writing committee, and the group chair assembled the complete statement. The conclusions of this statement are the views of the authors and do not necessarily represent the official view of the AHA. All members of the writing group had the opportunity to comment on the initial drafts and approved the final version of this document. The manuscript underwent extensive AHA internal peer review before consideration and approval by the AHA Science Advisory and Coordinating Committee.

RESULTS

This statement documents the status of knowledge regarding CVD among Hispanics and the sociocultural issues that impact all subgroups of Hispanics with regard to cardiovascular health. In this review, whenever possible, we identify the specific Hispanic subgroups examined to avoid generalizations. We identify specific areas for which current evidence was less robust, as well as inconsistencies and evidence gaps that inform the need for further rigorous and interdisciplinary approaches to increase our understanding of the US Hispanic population and its potential impact on the public health and cardiovascular health of the total US population. We provide recommendations specific to the 9 domains outlined by the chair to support the development of these culturally tailored and targeted approaches.

CONCLUSIONS

Healthcare professionals and researchers need to consider the impact of culture and ethnicity on health behavior and ultimately health outcomes. There is a need to tailor and develop culturally relevant strategies to engage Hispanics in cardiovascular health promotion and cultivate a larger workforce of healthcare providers, researchers, and allies with the focused goal of improving cardiovascular health and reducing CVD among the US Hispanic population.

Associations of adiponectin with individual European ancestry in African Americans: the Jackson Heart Study

BACKGROUND

Compared with European Americans, African Americans (AAs) exhibit lower levels of the cardio-metabolically protective adiponectin even after accounting for adiposity measures. Because few studies have examined in AA the association between adiponectin and genetic admixture, a dense panel of ancestry informative markers (AIMs) was used to estimate the individual proportions of European ancestry (PEA) for the AAs enrolled in a large community-based cohort, the Jackson Heart Study (JHS). We tested the hypothesis that plasma adiponectin and PEA are directly associated and assessed the interaction with a series of cardio-metabolic risk factors.

METHODS

Plasma specimens from 1439 JHS participants were analyzed by ELISA for adiponectin levels. Using pseudo-ancestral population genotype data from the HapMap Consortium, PEA was estimated with a panel of up to 1447 genome-wide preselected AIMs by a maximum likelihood approach. Interaction assessment, stepwise linear and cubic multivariable-adjusted regression models were used to analyze the cross-sectional association between adiponectin and PEA.

RESULTS

Among the study participants (62% women; mean age 48 ± 12 years), the median (interquartile range) of PEA was 15.8 (9.3)%. Body mass index (BMI) (p = 0.04) and insulin resistance (p = 0.0001) modified the association between adiponectin and PEA. Adiponectin was directly and linearly associated with PEA (β = 0.62 ± 0.28, p = 0.03) among non-obese (n = 673) and insulin sensitive participants (n = 1141; β = 0.74 ± 0.23, p = 0.001), but not among those obese or with insulin resistance. No threshold point effect was detected for non-obese participants.

CONCLUSIONS

In a large AA population, the individual proportion of European ancestry was linearly and directly associated with plasma adiponectin among non-obese and non insulin-resistant participants, pointing to the interaction of genetic and metabolic factors influencing adiponectin levels.

Myxovirus resistance, osteopontin and suppressor of cytokine signaling 3 polymorphisms predict hepatitis C virus therapy response in an admixed patient population: comparison with IL28B

OBJECTIVES

Suppressor of cytokine signaling 3, myxovirus resistance protein and osteopontin gene polymorphisms may influence the therapeutic response in patients with chronic hepatitis C, and an association with IL28 might increase the power to predict sustained virologic response. Our aims were to evaluate the association between myxovirus resistance protein, osteopontin and suppressor of cytokine signaling 3 gene polymorphisms in combination with IL28B and to assess the therapy response in hepatitis C patients treated with pegylated-interferon plus ribavirin.

METHOD

Myxovirus resistance protein, osteopontin, suppressor of cytokine signaling 3 and IL28B polymorphisms were analyzed by PCR-restriction fragment length polymorphism, direct sequencing and real-time PCR. Ancestry was determined using genetic markers.

RESULTS

We analyzed 181 individuals, including 52 who were sustained virologic responders. The protective genotype frequencies among the sustained virologic response group were as follows: the G/G suppressor of cytokine signaling 3 (rs4969170) (62.2%); T/T osteopontin (rs2853744) (60%); T/T osteopontin (rs11730582) (64.3%); and the G/T myxovirus resistance protein (rs2071430) genotype (54%). The patients who had ≥3 of the protective genotypes from the myxovirus resistance protein, the suppressor of cytokine signaling 3 and osteopontin had a greater than 90% probability of achieving a sustained response (p<0.0001). The C/C IL28B genotype was present in 58.8% of the subjects in this group. The sustained virological response rates increased to 85.7% and 91.7% by analyzing C/C IL28B with the T/T osteopontin genotype at rs11730582 and the G/G suppressor of cytokine signaling 3 genotype, respectively. Genetic ancestry analysis revealed an admixed population.

CONCLUSION

Hepatitis C genotype 1 patients who were responders to interferon-based therapy had a high frequency of multiple protective polymorphisms in the myxovirus resistance protein, osteopontin and suppressor of cytokine signaling 3 genes. The combined analysis of the suppressor of cytokine signaling 3 and IL28B genotypes more effectively predicted sustained virologic response than IL28B analysis alone.

Socioeconomic status, psychosocial factors, race and nocturnal blood pressure dipping in a Hispanic cohort

BACKGROUND

Little information is available about the relationship of socioeconomic status (SES) to blunted nocturnal ambulatory blood pressure (ABP) dipping among Hispanics and whether this relationship differs by race. We sought to characterize ABP nondipping and its determinants in a sample of Hispanics.

METHODS

We enrolled 180 Hispanic participants not on antihypertensive medications. SES was defined by years of educational attainment. All participants underwent 24-hour ABP monitoring. A decrease of <10% in the ratio between average awake and average asleep systolic BP was considered nondipping.

RESULTS

The mean age of the cohort was 67.1 ± 8.7, mean educational level was 9.4 ± 4.4 years, and 58.9% of the cohort was female. The cohort was comprised of 78.3% Caribbean Hispanics with the rest from Mexico and Central/South America; 41.4% self-identified as white Hispanic, 34.4% self-identified as black Hispanic, and 24.4% did not racially self- identify. The percentage of nondippers was 57.8%. Educational attainment (10.5 years vs. 8.6 years; P <0.01) was significantly higher among dippers than nondippers. In multivariable analyses, each 1-year increase in education was associated with a 9% reduction in the likelihood of being a nondipper (odds ratio [OR], 0.91; 95% confidence interval [CI], 0.84-0.98; P = 0.01). There were significantly greater odds of being a nondipper for black Hispanics than for white Hispanics (OR, 2.83, 95% CI, 1.29-6.23; P = 0.005). Higher SES was significantly protective of nondipping in white Hispanics but not black Hispanics.

CONCLUSIONS

These results document a substantial prevalence of nondipping in a cohort of predominantly normotensive Hispanics. Dipping status varied significantly by race. Lower SES is significantly associated with nondipping status, and race potentially impacts on this relation.

Genetic and structure-function studies of missense mutations in human endothelial lipase

Endothelial lipase (EL) plays a pivotal role in HDL metabolism. We sought to characterize EL and its interaction with HDL as well as its natural variants genetically, functionally and structurally. We screened our biethnic population sample (n = 802) for selected missense mutations (n = 5) and identified T111I as the only common variant. Multiple linear regression analyses in Hispanic subjects revealed an unexpected association between T111I and elevated LDL-C (p-value = 0.012) and total cholesterol (p-value = 0.004). We examined lipase activity of selected missense mutants (n = 10) and found different impacts on EL function, ranging from normal to complete loss of activity. EL-HDL lipidomic analyses indicated that EL has a defined remodeling of HDL without exhaustion of the substrate and a distinct and preference for several fatty acids that are lipid mediators and known for their potent pro- and anti-inflammatory properties. Structural studies using homology modeling revealed a novel α/β motif in the C-domain, unique to EL. The EL dimer was found to have the flexibility to expand and to bind various sizes of HDL particles. The likely impact of the all known missense mutations (n = 18) on the structure of EL was examined using molecular modeling and the impact they may have on EL lipase activity using a novel structure-function slope based on their structural free energy differences. The results of this multidisciplinary approach delineated the impact of EL and its variants on HDL. Moreover, the results suggested EL to have the capacity to modulate vascular health through its role in fatty acid-based signaling pathways.

Confounding and heterogeneity in genetic association studies with admixed populations

Association studies among admixed populations pose many challenges including confounding of genetic effects due to population substructure and heterogeneity due to different patterns of linkage disequilibrium (LD). We use simulations to investigate controlling for confounding by indicators of global ancestry and the impact of including a covariate for local ancestry. In addition, we investigate the use of an interaction term between a single-nucleotide polymorphism (SNP) and local ancestry to capture heterogeneity in SNP effects. Although adjustment for global ancestry can control for confounding, additional adjustment for local ancestry may increase power when the induced admixture LD is in the opposite direction as the LD in the ancestral population. However, if the induced LD is in the same direction, there is the potential for reduced power because of overadjustment. Furthermore, the inclusion of a SNP by local ancestry interaction term can increase power when there is substantial differential LD between ancestry populations. We examine these approaches in genome-wide data using the University of Southern California's Children's Health Study investigating asthma risk. The analysis highlights rs10519951 (P = 8.5 × 10(-7)), a SNP lacking any evidence of association from a conventional analysis (P = 0.5).

A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations

The determination of the ancestry and genetic backgrounds of the subjects in genetic and general epidemiology studies is a crucial component in the analysis of relevant outcomes or associations. Although there are many methods for differentiating ancestral subgroups among individuals based on genetic markers only a few of these methods provide actual estimates of the fraction of an individual’s genome that is likely to be associated with different ancestral populations. We propose a method for assigning ancestry that works in stages to refine estimates of ancestral population contributions to individual genomes. The method leverages genotype data in the public domain obtained from individuals with known ancestries. Although we showcase the method in the assessment of ancestral genome proportions leveraging largely continental populations, the strategy can be used for assessing within-continent or more subtle ancestral origins with the appropriate data.

VNN1 gene expression levels and the G-137T polymorphism are associated with HDL-C levels in Mexican prepubertal children

BACKGROUND

VNN1 gene expression levels and the G-137T polymorphism have been associated with high density lipoprotein cholesterol (HDL-C) levels in Mexican American adults. We aim to evaluate the contribution of VNN1 gene expression and the G-137T variant to HDL-C levels and other metabolic traits in Mexican prepubertal children.

METHODOLOGY/PRINCIPAL FINDINGS

VNN1 mRNA expression levels were quantified in peripheral blood leukocytes from 224 unrelated Mexican-Mestizo children aged 6-8 years (107 boys and 117 girls) and were genotyped for the G-137T variant (rs4897612). To account for population stratification, a panel of 10 ancestry informative markers was analyzed. After adjustment for admixture, the TT genotype was significantly associated with lower VNN1 mRNA expression levels (P = 2.9 × 10(-5)), decreased HDL-C levels (β = -6.19, P = 0.028) and with higher body mass index (BMI) z-score (β = 0.48, P = 0.024) in the total sample. In addition, VNN1 expression showed a positive correlation with HDL-C levels (r = 0.220; P = 0.017) and a negative correlation with BMI z-score (r = -0.225; P = 0.015) only in girls.

CONCLUSION/SIGNIFICANCE

Our data suggest that VNN1 gene expression and the G-137T variant are associated with HDL-C levels in Mexican children, particularly in prepubertal girls.

Juvenile rheumatoid arthritis and asthma, but not childhood-onset systemic lupus erythematosus are associated with FCRL3 polymorphisms in Mexicans

A regulatory single nucleotide polymorphism located in the 5' region (-169T/C) of the Fc receptor-like 3 (FCRL3_3) gene has been associated with both susceptibility and protection in immune diseases. This case-control study aimed to evaluate the association between FCRL3 polymorphisms and juvenile rheumatoid arthritis (JRA), asthma, and childhood-onset systemic lupus erythematosus (SLE) in a Mexican population. We performed PCR-based genotyping to identify four FCRL3 single nucleotide polymorphisms (FCRL3_3 to FCRL3_6) in patients with JRA (n=202), asthma (n=239), or childhood-onset SLE (n=377), and healthy controls (n=400). The case-control analysis showed a male-gender dependent association between the FCRL3_3C, FCRL3_5C, and FCRL3_6A alleles and either JRA (OR=0.57, p=0.003; OR=0.55, p=0.002; OR=0.53, p=0.0007, respectively) or asthma (OR=0.72, p=0.04; OR=0.74, p=0.05; OR=0.70, p=0.02, respectively). As expected, minor alleles of these SNPs with the CGCA haplotype were also significantly associated with JRA (OR=0.35, p=0.00005) and asthma (OR=0.61, p=0.007). We found no association between FCRL3 SNPs or haplotypes and childhood-onset SLE. These results supported the notion that FCRL3 is involved in the etiology of several immune diseases. Our results also suggested that SNPs located in the FCRL3 gene were protective against JRA and asthma in male Mexican patients.

Association of serum lipid components and obesity with genetic ancestry in an admixed population of elderly women

The prevalence of metabolic disorders varies among ethnic populations and these disorders represent a critical health care issue for elderly women. This study investigated the correlation between genetic ancestry and body composition, metabolic traits and clinical status in a sample of elderly women. Clinical, nutritional and anthropometric data were collected from 176 volunteers. Genetic ancestry was estimated using 23 ancestry-informative markers. Pearsons correlation test was used to examine the relationship between continuous variables and an independent samples t-test was used to compare the means of continuous traits within categorical variables. Overall ancestry was a combination of European (57.49%), Native American (25.78%) and African (16.73%). Significant correlations were found for European ancestry with body mass index (r = 0.165; p = 0.037) and obesity (mean difference (MD) = 5.3%; p = 0.042). African ancestry showed a significant correlation with LDL (r = 0.159, p = 0.035), VLDL (r = -0.185; p = 0.014), hypertriglyceridemia (MD = 6.4%; p = 0.003) and hyperlipidemia (MD = 4.8%; p = 0.026). Amerindian ancestry showed a significant correlation with triglyceride levels (r = 0.150; p = 0.047) and hypertriglyceridemia (MD = 4.5%; p = 0.039). These findings suggest that genetic admixture may influence the etiology of lipid metabolism-related diseases and obesity in elderly women.

Population-Based Resequencing of LIPG and ZNF202 Genes in Subjects with Extreme HDL Levels

Endothelial lipase (LIPG) and zinc finger protein 202 (ZNF202) are two pivotal genes in high density lipoprotein (HDL metabolism). We sought to determine their genetic contribution to variation in HDL-cholesterol levels by comprehensive resequencing of both genes in 235 individuals with high or low HDL-C levels. The selected subjects were 141 Whites (High HDL Group: n = 68, [Formula: see text] Low HDL Group: n = 73, [Formula: see text]) and 94 Hispanics (High HDL Group: n = 46, [Formula: see text] Low HDL Group: n = 48, [Formula: see text]). We identified a total of 185 and 122 sequence variants in LIPG and ZNF202, respectively. We found only two missense variants in LIPG (T111I and N396S) and two in ZNF202 (A154V and K259E). In both genes, there were several variants unique to either the low or high HDL group. For LIPG, the proportion of unique variants differed between the high and low HDL groups in both Whites (p = 0.022) and Hispanics (p = 0.017), but for ZNF202 this difference was observed only in Hispanics (p = 0.021). We also identified a common haplotype in ZNF202 among Whites that was significantly associated with the high HDL group (p = 0.013). These findings provide insights into the genetics of LIPG and ZNF202, and suggest that sequence variants occurring with high frequency in non-exonic regions may play a prominent role in modulating HDL-C levels in the general population.

Genetic ancestry, serum interferon-α activity, and autoantibodies in systemic lupus erythematosus

OBJECTIVE

To investigate and refine the relationships among systemic lupus erythematosus (SLE) and related autoantibodies, interferon-α (IFN-α), and various ancestral backgrounds.

METHODS

We investigated quantitatively defined genetic ancestry through principal component analysis in place of self-reported ancestry.

RESULTS

African ancestry was found to be associated with presence of anti-RNP antibody (p = 0.0026), and anti-RNP was correlated with high levels of IFN-α (p = 2.8 × 10(-5)).

CONCLUSION

Our data support a model in which African ancestry increases the likelihood of SLE-associated autoantibody formation, which subsequently results in higher levels of serum IFN-α.

Developmental and genetic components explain enhanced pulmonary volumes of female Peruvian Quechua

High altitude natives have enlarged vital capacities and residual volumes (RV). Because pulmonary volumes are an indication of functionally relevant traits, such as diffusion capacity, the understanding of the factors (genetic/developmental) that influence lung volumes provides insight into the adaptive responses of highlanders. In order to test for the effect of growth and development at high altitude on lung volumes, we obtained forced vital capacities (FVC), RV, and total lung capacities (TLC) for a sample of 65 Peruvian females of mostly Quechua origins (18-34 years) who were sub-divided into two well-matched groups: 1) sea-level born and raised females (BSL, n = 34) from Lima, Peru (150 m), and 2) high-altitude born and raised females (BHA, n = 31) from Cerro de Pasco, Peru (4,338 m). To determine Quechua origins, Native American ancestry proportion (NAAP) for each individual was assessed using a panel of 70 ancestry informative markers. NAAP was similar between groups (BSL = 91.71%; BHA = 89.93%; P = 0.240), and the analysis confirmed predominantly Quechua origins. After adjusting for body size and NAAP, BHA females had significantly higher FVC (3.79 ± 0.06 l; P < 0.001), RV (0.98 ± 0.03 l; P < 0.001) and TLC (4.80 ± 0.07 l; P < 0.001) compared to BSL females (FVC = 3.33 ± 0.05 l; RV = 0.69 ± 0.03 l; TLC = 4.02 ± 0.06 l). NAAP was not associated with FVC (P = 0.352) or TLC (P = 0.506). However, NAAP was positively associated with RV (P = 0.004). In summary, results indicate that developmental exposure to high altitude in females constitutes an important factor for all lung volumes, whereas both genetic and developmental factors seem to be important for RV.

Relationship between diabetes risk and admixture in postmenopausal African-American and Hispanic-American women

AIMS/HYPOTHESIS

Type 2 diabetes is more prevalent in African-Americans (AFAs) and Hispanic-Americans (HAs) than in European-Americans. We assessed whether continental admixture was correlated with diabetes risk in these high-risk groups.

METHODS

We estimated the proportion of sub-Saharan African (AFR), Amerindian (AMI) and European admixture using 92 ancestry-informative marker genotypes in 16,476 AFA and HA women from the Women's Health Initiative. Cox regression models were used to examine the association between admixture and diabetes risk, with and without accounting for socioeconomic status (SES) and adiposity measurements.

RESULTS

AFR admixture was significantly associated with diabetes risk in AFA women when adjusting for entry age, neighbourhood SES and BMI or waist/hip ratio (WHR) (all p < 0.0001). In HA women, AMI admixture had significant associations with diabetes risk that remained significant after adjustment for SES and BMI (all p < 0.0005). In both AFAs and HAs, SES showed significant negative associations while BMI or WHR had significant positive associations with diabetes risk, with and without adjustment for genetic admixture.

CONCLUSIONS/INTERPRETATION

In AFAs, admixture, SES and BMI/WHR each independently contribute to diabetes risk after accounting for each of the other factors; in HAs, admixture, SES and BMI each independently contribute to diabetes risk after accounting for each of the other factors, whereas admixture is not significantly associated with diabetes risk after accounting for SES and WHR. The findings emphasise the importance of considering both genetic and environmental causes in the aetiology of type 2 diabetes.

Ancestry markers from the human chromosome 6: Alu repeats from the MHC in autochthonous Basques

Polymorphic Alu insertions from the MHC class I region were analyzed in 215 autochthonous Basques from Guipuzcoa and Navarre provinces, with the aim of contributing new MHC Alu data in European ancestry populations. We also seek to assess both the genetic position of native Basques among worldwide samples and the efficiency of the MHC Alu elements as ancestry informative markers (AIMs). According to the MDS and AMOVA results, worldwide populations included in the comparative analyses were grouped in three major clusters defined by genetic ancestry (Africans, Asians and Europeans). The δ values (differences in weighted allele frequencies) among ancestry groups indicated that Alu elements within the alpha-block (AluHF, AluHJ and AluHG) showed an adequate resolving power to discriminate appropriately between some of the major ancestry groups. Alpha block Alu were also revealing of the exceptionality of Basques, as they allowed for the detection of genetic heterogeneity even between Basques and the other Iberian collection considered in the analysis (Valencia). Thus, analysis of the Alu loci within the alpha-block may represent a reliable, informative and cost-effective method to explore the ancestry, geographic origins and demographic history of human populations, which can be very helpful for studies into epidemiological, forensic or evolutionary perspectives.

Migration in Afro-Brazilian rural communities: crossing demographic and genetic data

Many studies have used genetic markers to understand global migration patterns of our species. However, there are only few studies of human migration on a local scale. We, therefore, researched migration dynamics in three Afro-Brazilian rural communities, using demographic data and ten Ancestry Informative Markers. In addition to the description of migration and marriage structures, we carried out genetic comparisons between the three populations, as well as between locals and migrants from each community. Genetic admixture analyses were conducted according to the gene-identity method, with Sub-Saharan Africans, Amerindians, and Europeans as parental populations. The three analyzed Afro-Brazilian rural communities consisted of 16% to 30% of migrants, most of them women. The age pyramid revealed a gap in the segment of men aged between 20 to 30 yrs. While endogamous marriages predominated, exogamous marriages were mainly patrilocal. Migration dynamics are apparently associated with matrimonial customs and other social practices of such communities. The impact of migration upon the populations' genetic composition was low but showed an increase in European alleles with a concomitant decrease in the Amerindian contribution. Admixture analysis evidenced a higher African contribution to the gene pool of the studied populations, followed by the contribution of Europeans and Amerindians, respectively.

Ancestral components of admixed genomes in a Mexican cohort

For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study “virtual genomes” of admixed individuals. We apply this approach to a cohort of 492 parent–offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations—Africa, Europe, and America—vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10–15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.

Admixed individuals, such as African Americans and Latinos, arise from mating between individuals from different continents. Detailed knowledge about the ancestral origin of an admixed population not only provides insight regarding the history of the population itself, but also affords opportunities to study the evolutionary biology of the ancestral populations. Applying novel statistical methods, we analyzed the high-density genotype data of nearly 1,500 Mexican individuals from Mexico City, who are admixed among Indigenous Americans, Europeans, and Africans. The relative contributions from the three continental-level ancestral populations vary substantially between individuals. The European ancestors of these Mexican individuals genetically resemble Southern Europeans, such as the Spaniard and the Portuguese. The Indigenous American ancestry of the Mexicans in our study is largely attributed to the indigenous groups residing in the southwestern region of Mexico, although some individuals have inherited varying degrees of ancestry from the Mayans of the Yucatan Peninsula and other indigenous American populations. A search for signatures of selection, focusing on the parts of the genomes derived from an ancestral population (e.g. Indigenous American), identifies regions in which a genetic variant may have been favored by natural selection in that ancestral population.

Ancestral heterogeneity in a biethnic stroke population

To test for and characterize heterogeneity in ancestral contributions to individuals among a population of Mexican American (MA) and non-Hispanic white (NHW) stroke/transient ischemic attack (TIA) cases, data from a community-based stroke surveillance study in south Texas were used. Strokes/TIA cases were identified (2004-2006) with a random sample asked to provide blood. Race-ethnicity was self-reported. Thirty-three ancestry informative markers were genotyped and individual genetic admixture estimated using maximum likelihood methods. Three hypotheses were tested for each MA using likelihood ratio tests: (1) H(0) : μi = 0 (100% Native American), (2) H(0) : μi = 1.00 (100% European), (3) H(0) : μi = 0.59 (average European). Among 154 self-identified MAs, estimated European ancestry varied from 0.26 to 0.98, with an average of 0.59 (SE = 0.014). We rejected hypothesis 1 for every MA and rejected hypothesis 2 for all but two MAs. We rejected hypothesis 3 for 40 MAs (20 < 59%, 20 > 59%). Among 84 self-identified NHWs, the estimated fraction of European ancestry ranged from 0.83 to 1.0, with an average of 0.97 (SE = 0.014). Self-identified MAs, and to a lesser extent NHWs, from an established bi-ethnic community were heterogeneous with respect to genetic admixture. Researchers should not use simple race-ethnic categories as proxies for homogeneous genetic populations when conducting gene mapping and disease association studies in multi-ethnic populations.

Population analysis of vitamin D receptor polymorphisms and the role of genetic ancestry in an admixed population

The vitamin D receptor (VDR) is an essential protein related to bone metabolism. Some VDR alleles are differentially distributed among ethnic populations and display variable patterns of linkage disequilibrium (LD). In this study, 200 unrelated Brazilians were genotyped using 21 VDR single nucleotide polymorphisms (SNPs) and 28 ancestry informative markers. The patterns of LD and haplotype distribution were compared among Brazilian and the HapMap populations of African (YRI), European (CEU) and Asian (JPT+CHB) origins. Conditional regression and haplotype-specific analysis were performed using estimates of individual genetic ancestry in Brazilians as a quantitative trait. Similar patterns of LD were observed in the 5′ and 3′ gene regions. However, the frequency distribution of haplotype blocks varied among populations. Conditional regression analysis identified haplotypes associated with European and Amerindian ancestry, but not with the proportion of African ancestry. Individual ancestry estimates were associated with VDR haplotypes. These findings reinforce the need to correct for population stratification when performing genetic association studies in admixed populations.