Genetic admixture and gallbladder disease in Mexican Americans

Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL

B-Precursor acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Although 80% of B-ALL patients are able to be cured, significant challenges persist. Significant disparities in clinical outcomes and mortality rates exist between racial/ethnic populations. The objective of this study was to determine whether gene expression levels significantly differ between ethnic populations. We compared gene expression levels between four ethnic populations (Whites, Blacks, Hispanics, and Asians) in the United States. Additionally, we performed network and pathway analysis to identify gene networks and pathways. Gene expression data involved 198 samples distributed as follows: 126 Whites, 51 Hispanics, 13 Blacks, and 8 Asians. We identified 300 highly significantly (P < 0.001) differentially expressed genes between the four ethnic populations. Among the identified genes included the genes PHF6, BRD3, CRLF2, and RNF135 which have been implicated in pediatric B-ALL. We identified key pathways implicated in B-ALL including the PDGF, PI3/AKT, ERBB2-ERBB3, and IL-15 signaling pathways.

Relationship between gallbladder surgery and ethnic admixture in African American and Hispanic American women

OBJECTIVES

The objective of this study was to investigate whether differences in admixture in African American and Hispanic American adult women are associated with differences in gallbladder surgery.

METHODS

Gallbladder surgery history on entry to the Women's Health Initiative's (WHI) study was used as a dichotomous outcome measure for this study. The proportion of European, sub-Saharan African, and Amerindian (AMI) admixture was estimated for 10,841 African American and 4,620 Hispanic American women in WHI using 92 ancestry informative markers. Logistic regression analyses assessed the relationship between admixture and gallbladder surgery in WHI women (enrollment at ages >50, mean age 61 years) with or without adjusting for multiple covariates, including measures of adiposity, parity, alcohol use, and education.

RESULTS

There was a significant positive association between AMI admixture and the frequency of gallbladder surgery in Hispanic Americans. The odds ratio (OR) and 95% confidence intervals (CIs) for AMI admixture group was OR=2.97, CI=2.01-4.38, P<10(-4). Although there were strong positive associations with parity and adiposity, and negative associations with alcohol consumption and education, accounting for these covariates did not remove the admixture association (OR=2.46, CI=1.62-3.73). In contrast, the effect of African admixture was nearly indistinguishable from that of the European admixture, both of which were protective in the Hispanic American group, and African admixture had a marginal association with decreased gallbladder surgery in the African American group. Measures of adiposity were associated with increased risk for gallbladder surgery and remained significant after accounting for admixture and each of the other covariates. Education level and alcohol use were associated with decreased risk for gallbladder disease. However, after accounting for the other covariates these variably remained significant.

CONCLUSIONS

AMI admixture is strongly associated with gallbladder surgery in women, even after adjustment for selected risk factors for cholelithiasis. Additional studies to ascertain the specific genetic risk factors underlying these associations are warranted.

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.

Ethnic differences in the effect of asthma on pulmonary function in children

RATIONALE

The impact of asthma on chronic lung function deficits is well known. However, there has been little study of ethnic differences in these asthma-associated deficits.

OBJECTIVES

To examine whether there are ethnic differences in the effects of asthma on children's lung function.

METHODS

We evaluated the impact of asthma on lung function in 3,245 Hispanic and non-Hispanic white school children (age 10-18 yr) in a longitudinal analysis of the Southern California Children's Health Study. Sex-specific mixed-effects regression spline models were fitted separately for each ethnic group.

MEASUREMENTS AND MAIN RESULTS

Large deficits in flows were observed among children with asthma diagnosed before age 4 years regardless of ethnicity. Hispanic girls with asthma had greater deficits in flows than non-Hispanic girls and were largest for maximal midexpiratory flow (-5.13% compared with -0.58%, respectively). A bigger impact of asthma in Hispanic girls was also found for FEV(1), FEF(75), and PEF (P value 0.04, 0.07, and 0.005, respectively). These ethnic differences were limited to girls diagnosed after age 4 years. In boys, asthma was also associated with greater deficits in flows among Hispanic than in non-Hispanic white children (differences that were not statistically significant). Ethnic differences in prevalence of pets and pests in the home, health insurance coverage, parental education, and smoking did not explain the pattern of lung function differences.

CONCLUSIONS

Larger asthma-associated lung function deficits in Hispanics, especially among girls, merit further investigation to determine public health implications and to identify causes amenable to intervention.

Genetic variants associated with fasting blood lipids in the U.S. population: Third National Health and Nutrition Examination Survey

BACKGROUND

The identification of genetic variants related to blood lipid levels within a large, population-based and nationally representative study might lead to a better understanding of the genetic contribution to serum lipid levels in the major race/ethnic groups in the U.S. population.

METHODS

Using data from the second phase (1991-1994) of the Third National Health and Nutrition Examination Survey (NHANES III), we examined associations between 22 polymorphisms in 13 candidate genes and four serum lipids: high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TG). Univariate and multivariable linear regression and within-gene haplotype trend regression were used to test for genetic associations assuming an additive mode of inheritance for each of the three major race/ethnic groups in the United States (non-Hispanic white, non-Hispanic black, and Mexican American).

RESULTS

Variants within APOE (rs7412, rs429358), PON1 (rs854560), ITGB3 (rs5918), and NOS3 (rs2070744) were found to be associated with one or more blood lipids in at least one race/ethnic group in crude and adjusted analyses. In non-Hispanic whites, no individual polymorphisms were associated with any lipid trait. However, the PON1 A-G haplotype was significantly associated with LDL-C and TC. In non-Hispanic blacks, APOE variant rs7412 and haplotype T-T were strongly associated with LDL-C and TC; whereas, rs5918 of ITGB3 was significantly associated with TG. Several variants and haplotypes of three genes were significantly related to lipids in Mexican Americans: PON1 in relation to HDL-C; APOE and NOS3 in relation to LDL-C; and APOE in relation to TC.

CONCLUSIONS

We report the significant associations of blood lipids with variants and haplotypes in APOE, ITGB3, NOS3, and PON1 in the three main race/ethnic groups in the U.S. population using a large, nationally representative and population-based sample survey. Results from our study contribute to a growing body of literature identifying key determinants of plasma lipoprotein concentrations and could provide insight into the biological mechanisms underlying serum lipid and cholesterol concentrations.

A genomewide admixture mapping panel for Hispanic/Latino populations

Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is ~1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as "f value") and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas.

The role of self-defined race/ethnicity in population structure control

Population-based association studies are powerful tools for the genetic mapping of complex diseases. However, this method is sensitive to potential confounding by population structure. While statistical methods that use genetic markers to detect and control for population structure have been the focus of current literature, the utility of self-defined race/ethnicity in controlling for population structure has been controversial. In this study of 1334 individuals, who self-identified as either African American, European American or Hispanic, we demonstrated that when the true underlying genetic structure and the self-defined racial/ethnic groups were roughly in agreement with each other, the self-defined race/ethnicity information was useful in the control of population structure.

Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians

Markers with large differences in allele frequencies between ethnicities provide ancestry information that can be applied to genetic studies. We identified over 100 biallelic ancestry informative markers (AIMs) with large allele frequency differences between European Americans (EA) and Pima Amerindians from laboratory and database screens. For 35 of these markers, Mayan, Yavapai and Quechuan Amerindians were genotyped and compared with EA and Pima allele frequencies. Markers with large allele frequency differences between EA and one Amerindian tribe showed only small differences between the Amerindian tribes. Examination of structure in individuals demonstrated a clear separation of subjects of European from those of Amerindian ancestry, and similarity between individuals from disparate Amerindian populations. The AIMs demonstrated the variation in ancestral composition of individual Mexican Americans, providing evidence of applicability in admixture mapping and in controlling for structure in association tests. In addition, a high percentage of single-nucleotide polymorphisms (SNPs) selected on the basis of large frequency differences between EA and Asian populations had large allele frequency differences between EA and Amerindians, suggesting an efficient method for greatly expanding AIMs for use in admixture mapping/structure analysis in Mexican Americans. Together, these data provide additional support for the practical application of admixture mapping in the Mexican American population.

Genetic admixture in three Mexican Mestizo populations based on D1S80 and HLA-DQA1 loci

This study compares genetic polymorphisms at the D1S80 and HLA-DQA1 loci in three Mexican Mestizo populations from three large states (Nuevo León, Jalisco, and the Federal District). Allele frequency distributions are relatively homogenous in the three samples; only the Federal District population shows minor differences of the HLA-DQA1 allele frequencies compared with the other two. In terms of genetic composition, these Mestizo populations show evidence of admixture with predominantly Spanish-European (50-60%) and Amerindian (37-49%) contributions; the African contribution (1-3%) is minor. Together with the observation that in Nuevo León, the admixture estimates based on D1S80 and HLA-DQA1, are virtually the same as those reported earlier from blood group loci, suggests that DNA markers, such as D1S80 and HLA-DQA1 are useful for examining genetic homogeneity/heterogeneity across Mestizo populations of Mexico. The inverse relationship of the proportion of gene diversity due to population differences (Gst) to within population gene diversity (Hs) is also consistent with theoretical predictions, supporting the use of these markers for population genetics studies.

Categorization of humans in biomedical research: genes, race and disease

A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.

Individual estimates of European genetic admixture associated with lower body-mass index, plasma glucose, and prevalence of type 2 diabetes in Pima Indians

Individual genetic admixture estimates (IA) from European Americans (EAs) were computed in 7,996 members of the Gila River Indian Community (Arizona). Parental populations for the analysis were European Americans and full-heritage Pima Indians. A logistic regression was performed on 7,796 persons, to assess association of IA with type 2 diabetes. The odds ratio, comparing diabetes risk in full-heritage EAs with full-heritage Pima Indians, was 0.329 (95% confidence interval [CI] 0.225-0.482). Proportional-hazards analysis was performed on 5,482 persons who were nondiabetic at their first examination and 1,215 subjects who developed diabetes during the study. The hazard risk ratio for IA was 0.455 (95% CI 0.301-0.688). Nondiabetic persons had significantly more European IA. In nondiabetic Pimans, multivariate linear regressions of quantitative predictors of type 2 diabetes mellitus, including fasting plasma glucose, 2-h post-load plasma glucose, and body-mass index, showed significant inverse relations with IA when controlled for sex and age. These results illustrate the ongoing evolution of populations by the mechanism of gene flow and its effect on disease risk in the groups with admixture. When the two parental populations differ in disease prevalence, higher or lower risk is associated with admixture, depending on the origin of the admixed alleles and the relative magnitude of the disease prevalence in the parental populations. These data also illustrate the strong genetic components in type 2 diabetes and are consistent with one susceptibility locus common to obesity and diabetes.

Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations

Single-nucleotide polymorphisms (SNPs) may be extremely important for deciphering the impact of genetic variation on complex human diseases. The ultimate value of SNPs for linkage and association mapping studies depends in part on the distribution of SNP allele frequencies and intermarker linkage disequilibrium (LD) across populations. Limited information is available about these distributions on a genomewide scale, particularly for LD. Using 114 SNPs from 33 genes, we compared these distributions in five American populations (727 individuals) of African, European, Chinese, Hispanic, and Japanese descent. The allele frequencies were highly correlated across populations but differed by >20% for at least one pair of populations in 35% of SNPs. The correlation in LD was high for some pairs of populations but not for others (e.g., Chinese American or Japanese American vs. any other population). Regardless of population, average minor-allele frequencies were significantly higher for SNPs in noncoding regions (20%-25%) than for SNPs in coding regions (12%-16%). Interestingly, we found that intermarker LD may be strongest with pairs of SNPs in which both markers are nonconservative substitutions, compared to pairs of SNPs where at least one marker is a conservative substitution. These results suggest that population differences and marker location within the gene may be important factors in the selection of SNPs for use in the study of complex disease with linkage or association mapping methods.

Prevalence and ethnic differences in gallbladder disease in the United States

BACKGROUND & AIMS

Gallbladder disease is one of the most common conditions in the United States, but its true prevalence is unknown. A national population-based survey was performed to determine the age, sex, and ethnic distribution of gallbladder disease in the United States.

METHODS

The third National Health and Nutrition Examination Survey (NHANES III) conducted gallbladder ultrasonography among a representative U.S. sample of more than 14, 000 persons. The diagnosis of gallbladder disease by detection of gallstones or cholecystectomy was made with excellent reproducibility.

RESULTS

An estimated 6.3 million men and 14.2 million women aged 20-74 years had gallbladder disease. Age-standardized prevalence was similar for non-Hispanic white (8. 6%) and Mexican American (8.9%) men, and both were higher than non-Hispanic black men (5.3%). These relationships persisted with multivariate adjustment. Among women, age-adjusted prevalence was highest for Mexican Americans (26.7%) followed by non-Hispanic whites (16.6%) and non-Hispanic blacks (13.9%). Among women, multivariate adjustment reduced the risk of gallbladder disease for both Mexican Americans and non-Hispanic blacks compared with non-Hispanic whites.

CONCLUSIONS

More than 20 million persons have gallbladder disease in the United States. Ethnic differences in gallbladder disease prevalence differed according to sex and were only partly explained by known risk factors.