A genomewide admixture mapping panel for Hispanic/Latino populations

Genome-wide association analyses identify distinct genetic architectures for age-related macular degeneration across ancestries

To effectively reduce vision loss due to age-related macular generation (AMD) on a global scale, knowledge of its genetic architecture in diverse populations is necessary. A critical element, AMD risk profiles in African and Hispanic/Latino ancestries, remains largely unknown. We combined data in the Million Veteran Program with five other cohorts to conduct the first multi-ancestry genome-wide association study of AMD and discovered 63 loci (30 novel). We observe marked cross-ancestry heterogeneity at major risk loci, especially in African-ancestry populations which demonstrate a primary signal in a major histocompatibility complex class II haplotype and reduced risk at the established CFH and ARMS2/HTRA1 loci. Dissecting local ancestry in admixed individuals, we find significantly smaller marginal effect sizes for CFH risk alleles in African ancestry haplotypes. Broadening efforts to include ancestrally distinct populations helped uncover genes and pathways that boost risk in an ancestry-dependent manner and are potential targets for corrective therapies.

Novel risk loci for COVID-19 hospitalization among admixed American populations

The genetic basis of severe COVID-19 has been thoroughly studied, and many genetic risk factors shared between populations have been identified. However, reduced sample sizes from non-European groups have limited the discovery of population-specific common risk loci. In this second study nested in the SCOURGE consortium, we conducted a genome-wide association study (GWAS) for COVID-19 hospitalization in admixed Americans, comprising a total of 4702 hospitalized cases recruited by SCOURGE and seven other participating studies in the COVID-19 Host Genetic Initiative. We identified four genome-wide significant associations, two of which constitute novel loci and were first discovered in Latin American populations (BAZ2B and DDIAS). A trans-ethnic meta-analysis revealed another novel cross-population risk locus in CREBBP. Finally, we assessed the performance of a cross-ancestry polygenic risk score in the SCOURGE admixed American cohort. This study constitutes the largest GWAS for COVID-19 hospitalization in admixed Latin Americans conducted to date. This allowed to reveal novel risk loci and emphasize the need of considering the diversity of populations in genomic research.

Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations

Asthma has striking disparities across ancestral groups, but the molecular underpinning of these differences is poorly understood and minimally studied. A goal of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to understand multi-omic signatures of asthma focusing on populations of African ancestry. RNASeq and DNA methylation data are generated from nasal epithelium including cases (current asthma, N = 253) and controls (never-asthma, N = 283) from 7 different geographic sites to identify differentially expressed genes (DEGs) and gene networks. We identify 389 DEGs; the top DEG, FN1, was downregulated in cases (q = 3.26 × 10-9) and encodes fibronectin which plays a role in wound healing. The top three gene expression modules implicate networks related to immune response (CEACAM5; p = 9.62 × 10-16 and CPA3; p = 2.39 × 10-14) and wound healing (FN1; p = 7.63 × 10-9). Multi-omic analysis identifies FKBP5, a co-chaperone of glucocorticoid receptor signaling known to be involved in drug response in asthma, where the association between nasal epithelium gene expression is likely regulated by methylation and is associated with increased use of inhaled corticosteroids. This work reveals molecular dysregulation on three axes - increased Th2 inflammation, decreased capacity for wound healing, and impaired drug response - that may play a critical role in asthma within the African Diaspora.

Local Ancestry at the Major Histocompatibility Complex Region is Not a Major Contributor to Disease Heterogeneity in a Multiethnic Lupus Cohort

OBJECTIVE

Systemic lupus erythematosus (SLE) is an autoimmune disease resulting in debilitating clinical manifestations that vary in severity by race and ethnicity with a disproportionate burden in African American, Mestizo, and Asian populations compared with populations of European descent. Differences in global and local genetic ancestry may shed light on the underlying mechanisms contributing to these disparities, including increased prevalence of lupus nephritis, younger age of symptom onset, and presence of autoantibodies.

METHODS

A total of 1,139 European, African American, and Mestizos patients with SLE were genotyped using the Affymetrix LAT1 World array. Global ancestry proportions were estimated using ADMIXTURE, and local ancestry was estimated using RFMIXv2.0. We investigated associations between lupus nephritis, age at onset, and autoantibody status with both global and local ancestry proportions within the Major Histocompatibility Complex region.

RESULTS

Our results showed small effect sizes that did not meet the threshold for statistical significance for global or local ancestry proportions in either African American or Mestizo patients with SLE who presented with the clinical manifestations of interest compared with those who did not.

CONCLUSION

These findings suggest that local genetic ancestry within the Major Histocompatibility Complex region is not a major contributor to these SLE manifestations among patients with SLE from admixed populations.

The first genome-wide association study in the Argentinian and Chilean populations identifies shared genetics with Europeans in Alzheimer's disease

INTRODUCTION

Genome-wide association studies (GWAS) are fundamental for identifying loci associated with diseases. However, they require replication in other ethnicities.

METHODS

We performed GWAS on sporadic Alzheimer's disease (AD) including 539 patients and 854 controls from Argentina and Chile. We combined our results with those from the European Alzheimer and Dementia Biobank (EADB) in a meta-analysis and tested their genetic risk score (GRS) performance in this admixed population.

RESULTS

We detected apolipoprotein E ε4 as the single genome-wide significant signal (odds ratio  = 2.93 [2.37-3.63], P = 2.6 × 10-23 ). The meta-analysis with EADB summary statistics revealed four new loci reaching GWAS significance. Functional annotations of these loci implicated endosome/lysosomal function. Finally, the AD-GRS presented a similar performance in these populations, despite the score diminished when the Native American ancestry rose.

DISCUSSION

We report the first GWAS on AD in a population from South America. It shows shared genetics modulating AD risk between the European and these admixed populations.

HIGHLIGHTS

This is the first genome-wide association study on Alzheimer's disease (AD) in a population sample from Argentina and Chile. Trans-ethnic meta-analysis reveals four new loci involving lysosomal function in AD. This is the first independent replication for TREM2L, IGH-gene-cluster, and ADAM17 loci. A genetic risk score (GRS) developed in Europeans performed well in this population. The higher the Native American ancestry the lower the GRS values.

Novel and replicated clinical and genetic risk factors for toxicity from high-dose methotrexate in pediatric acute lymphoblastic leukemia

STUDY OBJECTIVE

Methotrexate (MTX) is a key component of treatment for high-risk pediatric acute lymphoblastic leukemia (ALL) but may cause acute kidney injury and prolonged hospitalization due to delayed clearance. The purpose of this study is to identify clinical and genetic factors that may predict which children are at risk for creatinine increase and prolonged MTX clearance.

DESIGN

We conducted a single-center, retrospective cohort study of pediatric patients with ALL who received 4000-5000 mg/m2 of MTX. Measurements We performed germline genotyping to determine genetic ancestry and allele status for 49 single nucleotide polymorphisms (SNPs) identified from the literature as related to MTX disposition. Bayesian hierarchical ordinal regression models for creatinine increase and for prolonged MTX clearance were developed.

MAIN RESULTS

Hispanic ethnicity, body mass index (BMI) < 3%, BMI between 85%-95%, and Native American genetic ancestry were found to be associated with an increased risk for creatinine elevation. Older age, Black race, and use of the intensive monitoring protocol were associated with a decreased risk for creatinine elevation. Older age, B- compared to T-ALL, and the minor alleles of rs2838958/SLC19A1 and rs7317112/ABCC4 were associated with an increased risk for delayed clearance. Black race, MTX dose reduction, and the minor allele of rs2306283/SLCO1B1 were found to be associated with a decreased risk for delayed clearance.

CONCLUSIONS

These predictors of MTX toxicities may allow for more precise individualized toxicity risk prediction.

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations

Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.

Asparaginase toxicity in Hispanic adult and pediatric patients with acute lymphoblastic leukemia: current understanding

INTRODUCTION

Asparaginase is essential to chemotherapy regimens for acute lymphoblastic leukemia (ALL). Survival of patients with ALL has improved since incorporating asparaginase into chemotherapy backbones. Hispanic patients have a higher incidence of ALL than other ethnicities and suffer inferior outcomes. The inferior outcome of Hispanics is due to several factors, including the increased incidence of high-risk genetic subtypes and susceptibility to treatment-related toxicity.

AREAS COVERED

We summarize the current knowledge of asparaginase-related toxicity by comparing their incidence between Hispanic and non-Hispanic patients. These toxicities include hypersensitivity, hepatotoxicity, pancreatitis, thrombosis, and hypertriglyceridemia. The PubMed database and Google Scholar were used to search for this review from October 2022 to June 2023.

EXPERT OPINION

Except for hepatotoxicity and hypertriglyceridemia secondary to asparaginase-based treatments, which may develop more frequently among Hispanic patients with ALL, other toxicities were comparable between Hispanic and non-Hispanic patients. Nevertheless, studies with larger cohorts and more accurate capturing of Hispanic ethnicity should be conducted to fill the gaps in the current knowledge.

Ortholog genes from cactophilic Drosophila provide insight into human adaptation to hallucinogenic cacti

Cultural transformations of lifestyles and dietary practices have been key drivers of human evolution. However, while most of the evidence of genomic adaptations is related to the hunter-gatherer transition to agricultural societies, little is known on the influence of other major cultural manifestations. Shamanism is considered the oldest religion that predominated throughout most of human prehistory and still prevails in many indigenous populations. Several lines of evidence from ethno-archeological studies have demonstrated the continuity and importance of psychoactive plants in South American cultures. However, despite the well-known importance of secondary metabolites in human health, little is known about its role in the evolution of ethnic differences. Herein, we identified candidate genes of adaptation to hallucinogenic cactus in Native Andean populations with a long history of shamanic practices. We used genome-wide expression data from the cactophilic fly Drosophila buzzatii exposed to a hallucinogenic columnar cactus, also consumed by humans, to identify ortholog genes exhibiting adaptive footprints of alkaloid tolerance. Genomic analyses in human populations revealed a suite of ortholog genes evolving under recent positive selection in indigenous populations of the Central Andes. Our results provide evidence of selection in genetic variants related to alkaloids toxicity, xenobiotic metabolism, and neuronal plasticity in Aymara and Quechua populations, suggesting a possible process of gene-culture coevolution driven by religious practices.

Demographic history differences between Hispanics and Brazilians imprint haplotype features

Admixture is known to greatly impact the genetic landscape of a population and, while genetic variation underlying human phenotypes has been shown to differ among populations, studies on admixed subjects are still scarce. Latin American populations are the result of complex demographic history, such as 2 or 3-way admixing events, bottlenecks and/or expansions, and adaptive events unique to the American continent. To explore the impact of these events on the genetic structure of Latino populations, we evaluated the following haplotype features: linkage disequilibrium, shared identity by descent segments, runs of homozygosity, and extended haplotype homozygosity (integrated haplotype score) in Latinos represented in the 1000 Genome Project along with array data from 171 Brazilians sampled in the South and Southeast regions of Brazil. We found that linkage disequilibrium decay relates to the amount of American and African ancestry. The extent of identity by descent sharing positively correlates with historical effective population sizes, which we found to be steady or growing, except for Puerto Ricans and Colombians. Long runs of homozygosity, a particular instance of autozygosity, was only enriched in Peruvians and Native Americans. We used simulations to account for random sampling and linkage disequilibrium to filter positive selection indexes and found 244 unique markers under selection, 26 of which are common to 2 or more populations. Some markers exhibiting positive selection signals had estimated time to the most recent common ancestor consistent with human adaptation to the American continent. In conclusion, Latino populations present highly divergent haplotype characteristics that impact genetic architecture and underlie complex phenotypes.

A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects

BACKGROUND

The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestries.

METHODS

We characterized the role of admixture and founder effects on the origination of the mutational landscape that led to neurodegenerative disorders under these historical circumstances. Genomes from 900 Colombian individuals with Alzheimer's disease (AD) [n = 376], frontotemporal lobar degeneration-motor neuron disease continuum (FTLD-MND) [n = 197], early-onset dementia not otherwise specified (EOD) [n = 73], and healthy participants [n = 254] were analyzed. We examined their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes.

RESULTS

We identified 21 pathogenic variants in AD-FTLD related genes, and PSEN1 harbored the majority (11 pathogenic variants). Variants were identified from all three continental ancestries. TREM2 heterozygous and homozygous variants were the most common among AD risk genes (102 carriers), a point of interest because the disease risk conferred by these variants differed according to ancestry. Several gene variants that have a known association with MND in European populations had FTLD phenotypes on a Native American haplotype. Consistent with founder effects, identity by descent among carriers of the same variant was frequent.

CONCLUSIONS

Colombian demography with multiple mini-bottlenecks probably enhanced the detection of founder events and left a proportionally higher frequency of rare variants derived from the ancestral populations. These findings demonstrate the role of genomically defined ancestry in phenotypic disease expression, a phenotypic range of different rare mutations in the same gene, and further emphasize the importance of inclusiveness in genetic studies.

Genome-wide association study of asthma, total IgE, and lung function in a cohort of Peruvian children

BACKGROUND

Genetic ancestry plays a role in asthma health disparities.

OBJECTIVE

Our aim was to evaluate the impact of ancestry on and identify genetic variants associated with asthma, total serum IgE level, and lung function.

METHODS

A total of 436 Peruvian children (aged 9-19 years) with asthma and 291 without asthma were genotyped by using the Illumina Multi-Ethnic Global Array. Genome-wide proportions of indigenous ancestry populations from continental America (NAT) and European ancestry from the Iberian populations in Spain (IBS) were estimated by using ADMIXTURE. We assessed the relationship between ancestry and the phenotypes and performed a genome-wide association study.

RESULTS

The mean ancestry proportions were 84.7% NAT (case patients, 84.2%; controls, 85.4%) and 15.3% IBS (15.8%; 14.6%). With adjustment for asthma, NAT was associated with higher total serum IgE levels (P < .001) and IBS was associated with lower total serum IgE levels (P < .001). NAT was associated with higher FEV1 percent predicted values (P < .001), whereas IBS was associated with lower FEV1 values in the controls but not in the case patients. The HLA-DR/DQ region on chromosome 6 (Chr6) was strongly associated with total serum IgE (rs3135348; P = 3.438 × 10-10) and was independent of an association with the haplotype HLA-DQA1∼HLA-DQB1:04.01∼04.02 (P = 1.55 × 10-05). For lung function, we identified a locus (rs4410198; P = 5.536 × 10-11) mapping to Chr19, near a cluster of zinc finger interacting genes that colocalizes to the long noncoding RNA CTD-2537I9.5. This novel locus was replicated in an independent sample of pediatric case patients with asthma with similar admixture from Brazil (P = .005).

CONCLUSION

This study confirms the role of HLA in atopy, and identifies a novel locus mapping to a long noncoding RNA for lung function that may be specific to children with NAT.

Class II Human Leukocyte Antigen Variants Associate With Risk of Pegaspargase Hypersensitivity

We conducted the first human leukocyte antigen (HLA) allele and genome-wide association study to identify loci associated with hypersensitivity reactions exclusively to the PEGylated preparation of asparaginase (pegaspargase) in racially diverse cohorts of pediatric leukemia patients: St Jude Children's Research Hospital's Total XVI (TXVI, n = 598) and Children's Oncology Group AALL0232 (n = 2,472) and AALL0434 (n = 1,189). Germline DNA was genotyped using arrays. Genetic variants not genotyped directly were imputed. HLA alleles were imputed using SNP2HLA or inferred using BWAkit. Analyses between genetic variants and hypersensitivity were performed in each cohort first using cohort-specific covariates and then combined using meta-analyses. Nongenetic risk factors included fewer intrathecal injections (P = 2.7 × 10-5 in TXVI) and male sex (P = 0.025 in AALL0232). HLA alleles DQB1*02:02, DRB1*07:01, and DQA1*02:01 had the strongest associations with pegaspargase hypersensitivity (P < 5.0 × 10-5 ) in patients with primarily European ancestry (EA), with the three alleles associating in a single haplotype. The top allele HLA-DQB1*02:02 was tagged by HLA-DQB1 rs1694129 in EAs (r2  = 0.96) and less so in non-EAs. All single nucleotide polymorphisms associated with pegaspargase hypersensitivity reaching genome-wide significance in EAs were in class II HLA loci, and were partially replicated in non-EAs, as is true for other HLA associations. The rs9958628 variant, in ARHGAP28 (previously linked to immune response in children) had the strongest genetic association (P = 8.9 × 10-9 ) in non-EAs. The HLA-DQB1*02:02-DRB1*07:01-DQA1*02:01 associated with hypersensitivity reactions to pegaspargase is the same haplotype associated with reactions to non-PEGylated asparaginase, even though the antigens differ between the two preparations.

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.

Novel risk factors for glucarpidase use in pediatric acute lymphoblastic leukemia: Hispanic ethnicity, age, and the ABCC4 gene

BACKGROUND

Carboxypeptidase G₂ (CPDG₂ ; glucarpidase) is a rescue drug for patients at risk for kidney injury from high-dose methotrexate (MTX). As there are no strategies for predicting patients who will require CDPG₂ , we evaluated the role of demographic, clinical, and genetic factors for CPDG₂ use.

PROCEDURE

Cases who received CPDG₂ and controls who did not were identified by chart review of acute lymphoblastic leukemia (ALL) patients who received MTX doses between 1000 and 5000 mg/m² between 2010 and 2017. We used multivariable Bayesian logistic regression to evaluate the association of CPDG₂ use with demographic and clinical variables and, on a subset of patients, with genetic ancestry and 49 single nucleotide variants previously associated with MTX toxicity.

RESULTS

We identified 423 patients who received 1592 doses of MTX. Of the 18 patients who received CPDG₂ , 17 (94%) were Hispanic. No patients who received 1000 or 2000 mg/m² of MTX received CPDG₂ . Hispanic ethnicity (odds ratio: 4.68; 95% compatibility interval: 1.63-15.06) and older age (1.87 [1.17-3.17]) were associated with receiving CPDG₂ . Of the 177 patients in the genomic cohort, 11 received CPDG₂ . Each additional G allele of rs7317112 in ABCC4 increased the odds of requiring CPDG₂ (3.10 [1.12-6.75]). Six other loci (NTRK1/rs10908521, TSG1/rs9345389, STT3B/rs1353327, SCLO1B1/rs4149056, GATA3/rs3824662, ARID5B/rs10821936) demonstrated probabilities of association between 88% and 97%.

CONCLUSION

We demonstrated that demographic characteristics, including Hispanic ethnicity and age, are associated with CPDG₂ use. Additionally, we provide evidence that inherited genetic variation is associated with risk of requiring CPDG₂ . If validated in independent populations, this information could be leveraged to develop targeted toxicity prevention strategies for children with ALL.

Summix: A method for detecting and adjusting for population structure in genetic summary data

Publicly available genetic summary data have high utility in research and the clinic, including prioritizing putative causal variants, polygenic scoring, and leveraging common controls. However, summarizing individual-level data can mask population structure, resulting in confounding, reduced power, and incorrect prioritization of putative causal variants. This limits the utility of publicly available data, especially for understudied or admixed populations where additional research and resources are most needed. Although several methods exist to estimate ancestry in individual-level data, methods to estimate ancestry proportions in summary data are lacking. Here, we present Summix, a method to efficiently deconvolute ancestry and provide ancestry-adjusted allele frequencies (AFs) from summary data. Using continental reference ancestry, African (AFR), non-Finnish European (EUR), East Asian (EAS), Indigenous American (IAM), South Asian (SAS), we obtain accurate and precise estimates (within 0.1%) for all simulation scenarios. We apply Summix to gnomAD v.2.1 exome and genome groups and subgroups, finding heterogeneous continental ancestry for several groups, including African/African American (∼84% AFR, ∼14% EUR) and American/Latinx (∼4% AFR, ∼5% EAS, ∼43% EUR, ∼46% IAM). Compared to the unadjusted gnomAD AFs, Summix's ancestry-adjusted AFs more closely match respective African and Latinx reference samples. Even on modern, dense panels of summary statistics, Summix yields results in seconds, allowing for estimation of confidence intervals via block bootstrap. Given an accompanying R package, Summix increases the utility and equity of public genetic resources, empowering novel research opportunities.

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.

Dementia Research in the Caribbean Hispanic Islands: Present Findings and Future Trends

During the last decade, the Caribbean Hispanic islands experienced accelerated demographic aging, representing the fastest aging region within Latin America. Age-related non-communicable diseases, including dementia, are now reported at high prevalence. The Caribbean islands share similar genetic ancestry, culture, migration patterns, and risk profiles, providing a unique setting to understand dementia in the Caribbean-Hispanics. This perspective article aimed to describe the impact of dementia in the Caribbean, at a local and regional level and reflect on research strategies to address dementia. We report on 10/66 project findings, described research projects and regional plans for the region. According to our results, the prevalence of dementia in the Caribbean is the highest in Latin America, with 11.7% in Dominican Republic, 11.6% in Puerto Rico, and 10.8% in Cuba. Preliminary data from new waves of the 10/66 study shows increasing numbers of dementia cases. Furthermore, dementia is expected to be one of the most serious medical and social issues confronted by Caribbean health systems. However, there is a scarcity of knowledge, awareness, and health services to deal with this public health crisis. In light of the new evidence, local and regional strategies are underway to better understand dementia trends for the region and develop policies aimed to decrease the impact of dementia. Implementation of our national plans is critical to deal with an aging population with high dementia rates. Current recommendations include emphasizing public health prevention campaigns to address modifiable risk factors and expand support to caregiver and family interventions.

Differential admixture in Latin American populations and its impact on the study of colorectal cancer

Genome-wide association studies focused on searching genes responsible for several diseases. Admixture mapping studies proposed a more efficient alternative capable of detecting polymorphisms contributing with a small effect on the disease risk. This method focuses on the higher values of linkage disequilibrium in admixed populations. To test this, we analyzed 10 genomic regions previously defined as related with colorectal cancer among nine populations and studied the variation pattern of haplotypic structures and heterozygosity values on seven categories of SNPs. Both analyses showed differences among chromosomal regions and studied populations. Admixed Latin-American samples generally show intermediate values. Heterozygosity of the SNPs grouped in categories varies more in each gene than in each population. African related populations have more blocks per chromosomal region, coherently with their antiquity. In sum, some similarities were found among Latin American populations, but each chromosomal region showed a particular behavior, despite the fact that the study refers to genes and regions related with one particular complex disease. This study strongly suggests the necessity of developing statistical methods to deal with di- or tri-hybrid populations, as well as to carefully analyze the different historic and demographic scenarios, and the different characteristics of particular chromosomal regions and evolutionary forces.

Real-World Safety and Effectiveness of Dimethyl Fumarate in Hispanic or Latino Patients with Multiple Sclerosis: 3-Year Results from ESTEEM

INTRODUCTION

Compared with the non-Hispanic/non-Latino population, Hispanic/Latino patients with multiple sclerosis (MS) are reported to exhibit greater disease severity. Geographical location and genetics play a role in differences observed across Hispanic/Latino subpopulations. We evaluated real-world safety and effectiveness of dimethyl fumarate (DMF) on MS disease activity in Hispanic/Latino patients.

METHODS

ESTEEM is an ongoing, 5-year, multinational, prospective study evaluating long-term safety and effectiveness of DMF in patients with MS. This interim analysis included patients newly prescribed DMF in routine practice at 394 sites globally.

RESULTS

Overall, 4986 non-Hispanic/non-Latino and 98 Hispanic/Latino patients were analyzed; median (range) follow-up was 18 (2-37) months. Unadjusted annualized relapse rates (ARRs) for 12 months before DMF initiation versus 36 months post DMF initiation, respectively, were: non-Hispanic/non-Latino patients, 0.82 (95% CI 0.80-0.84) versus 0.10 (95% CI 0.09-0.10), 88% lower ARR (P < 0.0001); Hispanic/Latino patients, 0.80 (95% CI 0.65-1.00) versus 0.09 (95% CI 0.06-0.14), 89% lower ARR (P < 0.0001). In total, 28 (29%) Hispanic/Latino patients reported adverse events leading to treatment discontinuation; gastrointestinal (GI) disorders (n = 10, 10%) were the most common, consistent with the non-Hispanic/non-Latino population (8%). Median lymphocyte counts decreased by approximately 24% in the first year (vs 36% decrease in non-Hispanic/non-Latino patients) then remained stable and above the lower limit of normal in most patients.

CONCLUSIONS

Relapse rates remained low in Hispanic/Latino patients, consistent with non-Hispanic/non-Latino patients. The safety profile of DMF in Hispanic/Latino patients was consistent with safety findings from the non-Hispanic/non-Latino ESTEEM population, demonstrating the real-world treatment benefit of DMF in the Hispanic/Latino patient cohort.

Novel Variants in LRRK2 and GBA Identified in Latino Parkinson Disease Cohort Enriched for Caribbean Origin

Background: The Latino population is greatly understudied in biomedical research, including genetics. Very little information is available on presence of known variants originally identified in non-Hispanic white patients or novel variants in the Latino population. The Latino population is admixed, with contributions of European, African, and Amerindian ancestries. Therefore, the ancestry surrounding a gene (local ancestry, LA) can be any of the three contributing ancestries and thus can determine the presence or risk effect of variants detected. Methods: We sequenced the major exons and exons of reported Latino-specific variants in GBA and LRRK2 and performed genome-wide genotyping for LA assessments in 79 Latino Parkinson disease (PD) patients, of which ~80% identified as Caribbean Latino. Results: We observed five carriers of LRRK2 p.G2019S, one GBA p.T408M, and three GBA p.N409S on European as well as three GBA p.L13R on African LA backgrounds. Previous Latino variant GBA p.K237E was not observed in this dataset. A novel highly conserved and predicted damaging variant LRRK2 p.D734N was identified in two unrelated individuals with African LA. Additionally, we identified rare, functional variants LRRK2 p.P1480L and GBA p.S310G in one individual each heterozygous for European/Amerindian LA. Discussion: Additional functional analysis will be needed to determine the pathogenicity of the novel variants in PD. However, the identification of novel disease variants in the Latino cohort potentially contributing to PD supports to importance of inclusion of Latinos in genetics research to provide insight in PD genetics in Latinos specifically as well as other populations with the same ancestral contributions.

Intermediate hyperglycaemia and 10-year mortality in resource-constrained settings: the PERU MIGRANT Study

AIM

To determine whether intermediate hyperglycaemia, defined by fasting plasma glucose and HbA1c criteria, is associated with mortality in a 10-year cohort of people in a Latin American country.

METHODS

Analysis of the PERU MIGRANT Study was conducted in three different population groups (rural, rural-to-urban migrant, and urban). The baseline assessment was conducted in 2007/2008, with follow-up assessment in 2018. The outcome was all-cause mortality, and the exposure was intermediate hyperglycaemia, using three definitions: (1) impaired fasting glucose, defined according to American Diabetes Association criteria [fasting plasma glucose 5.6-6.9 mmol/l (100-125 mg/dl)]; (2) intermediate hyperglycaemia defined according to American Diabetes Association criteria [HbA1c levels 39-46 mmol/mol (5.7-6.4%)]; and (3) intermediate hyperglycaemia defined according to the International Expert Committee criteria [HbA1c levels 42-46 mmol/mol (6.0-6.4%)]. Crude and adjusted hazard ratios and 95% CIs were estimated using Cox proportional hazard models.

RESULTS

At baseline, the mean (sd) age of the study population was 47.8 (11.9) years and 52.5% of the cohort were women. The study cohort was divided into population groups as follows: 207 people (20.0%) in the rural population group, 583 (59.7%) in the rural-to-urban migrant group and 198 (20.3%) in the urban population group. The prevalence of intermediate hyperglycaemia was: 6%, 12.9% and 38.5% according to the American Diabetes Association impaired fasting glucose definition, the International Expert Committee HbA1c -based definition and the American Diabetes Association HbA1c -based definition, respectively, and the mortality rate after 10 years was 63/976 (7%). Intermediate hyperglycaemia was associated with all-cause mortality using the HbA1c -based definitions in the crude models [hazard ratios 2.82 (95% CI 1.59-4.99) according to the American Diabetes Association and 2.92 (95% CI 1.62-5.28) according to the International Expert Committee], whereas American Diabetes Association-defined impaired fasting glucose was not [hazard ratio 0.84 (95% CI 0.26-2.68)]. In the adjusted model, however, only the American Diabetes Association HbA1c -based definition was associated with all-cause mortality [hazard ratio 1.91 (95% CI 1.03-3.53)], whereas the International Expert Committee HbA1c -based and American Diabetes Association impaired fasting glucose-based definitions were not [hazard ratios 1.42 (95% CI 0.75-2.68) and 1.09 (95% CI 0.33-3.63), respectively].

CONCLUSIONS

Intermediate hyperglycaemia defined using the American Diabetes Association HbA1c criteria was associated with an elevated mortality rate after 10 years in a cohort from Peru. HbA1c appears to be a factor associated with mortality in this Peruvian population.

Ophthalmic genetics in South America

South America comprises of heterogeneous topographies, populations, and health care systems. Therefore, it is not surprising to see differences among the countries regarding expertise, education, and practices of ophthalmic genetics for patients with rare eye diseases. Nevertheless, common challenges such as limited genetics training in medical schools and among ophthalmologists, scarcity of diagnostic tools for phenotyping, and expensive genetic testing not covered by the public healthcare systems, are seen in all of them. Here, we provide a detailed report of the current status of ophthalmic genetics, described by the personal views of local ophthalmologists from Brazil, Colombia, Argentina, and Chile. By reporting our strengths and weaknesses as a region, we intend to highlight the need for guidelines on how to manage these patients aligned with public health policies. Our region contributes to research worldwide, with thousands of well diagnosed patients from a number of unique and genetically diverse populations. The constant expansion of ophthalmic genetics and molecular diagnostics requires us to join forces to collaborate across South America and with other countries to improve access to next-generation diagnostics and ultimately improve patient care.

Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia

BACKGROUND

Type 1 diabetes (T1D) is a complex disease with a higher incidence in Europeans than other populations. The Colombians Living in Medellin (CLM) is admixed with ancestry contributions from Europeans, Native Americans (NAT) and Africans (AFR).

AIM

Our aim was to analyze the genetic admixture component at candidate T1D loci in Colombian individuals with the disease.

METHODS

Seventy-four ancestry informative markers (AIMs), which tagged 41 T1D candidate loci/genes, were tested by studying a cohort of 200 Northwest Colombia diseased individuals. T1D status was classified by testing for glutamic acid decarboxylase (GAD-65 kDa) and protein tyrosine-like antigen-2 auto-antibodies in serum samples. Candidate loci/genes included HLA, INS, PTPN22, CTLA4, IL2RA, SUMO4, CLEC16A, IFIH1, EFR3B, IL7R, NRP1 and RNASEH1, amongst others. The 1,000 genome database was used to analyze data from 94 individuals corresponding to the reference CLM. As the data did not comply with a normal distribution, medians were compared between groups using the Mann-Whitney U-test.

RESULTS

Both T1D patients and individuals from CLM displayed mainly European ancestry (61.58 vs 62.06) followed by Native American (27.34 vs 27.46) and to a lesser extent the AFR ancestry (10.28 vs 10.65) components. However, compared to CLM, ancestry of T1D patients displayed a decrease of NAT ancestry at gene EFR3B (24.30 vs 37.10) and an increase at genes IFIH1 (32.07 vs 14.99) and IL7R (52.18 vs 39.18). Also, for gene NRP1 (36.67 vs 0.003), we observed a non-AFR contribution (attributed to NAT). Autoimmune patients (positive for any of two auto-antibodies) displayed lower NAT ancestry than idiopathic patients at the MHC region (20.36 vs 31.88). Also, late onset patients presented with greater AFR ancestry than early onset patients at gene IL7R (19.96 vs 6.17). An association analysis showed that, even after adjusting for admixture, an association exists for at least seven such AIMs, with the strongest findings on chromosomes 5 and 10 (gene IL7R, P = 5.56 × 10^-6 and gene NRP1, P = 8.70 × 10^-19, respectively).

CONCLUSION

Although Colombian T1D patients have globally presented with higher European admixture, specific T1D loci have displayed varying levels of Native American and AFR ancestries in diseased individuals.

Step-Up Therapy in Black Children and Adults with Poorly Controlled Asthma

BACKGROUND

Morbidity from asthma is disproportionately higher among black patients than among white patients, and black patients constitute the minority of participants in trials informing treatment. Data indicate that patients with inadequately controlled asthma benefit more from addition of a long-acting beta-agonist (LABA) than from increased glucocorticoids; however, these data may not be informative for treatment in black patients.

METHODS

We conducted two prospective, randomized, double-blind trials: one involving children and the other involving adolescents and adults. In both trials, the patients had at least one grandparent who identified as black and had asthma that was inadequately controlled with low-dose inhaled glucocorticoids. We compared combinations of therapy, which included the addition of a LABA (salmeterol) to an inhaled glucocorticoid (fluticasone propionate), a step-up to double to quintuple the dose of fluticasone, or both. The treatments were compared with the use of a composite measure that evaluated asthma exacerbations, asthma-control days, and lung function; data were stratified according to genotypic African ancestry.

RESULTS

When quintupling the dose of fluticasone (to 250 μg twice a day) was compared with adding salmeterol (50 μg twice a day) and doubling the fluticasone (to 100 μg twice a day), a superior response occurred in 46% of the children with quintupling the fluticasone and in 46% of the children with doubling the fluticasone and adding salmeterol (P = 0.99). In contrast, more adolescents and adults had a superior response to added salmeterol than to an increase in fluticasone (salmeterol-low-dose fluticasone vs. medium-dose fluticasone, 49% vs. 28% [P = 0.003]; salmeterol-medium-dose fluticasone vs. high-dose fluticasone, 49% vs. 31% [P = 0.02]). Neither the degree of African ancestry nor baseline biomarkers predicted a superior response to specific treatments. The increased dose of inhaled glucocorticoids was associated with a decrease in the ratio of urinary cortisol to creatinine in children younger than 8 years of age.

CONCLUSIONS

In contrast to black adolescents and adults, almost half the black children with poorly controlled asthma had a superior response to an increase in the dose of an inhaled glucocorticoid and almost half had a superior response to the addition of a LABA. (Funded by the National Heart, Lung, and Blood Institute; BARD ClinicalTrials.gov number, NCT01967173.).

Distribution of local ancestry and evidence of adaptation in admixed populations

Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events.

Exacerbation-prone asthma in the context of race and ancestry in Asthma Clinical Research Network trials

BACKGROUND

Minority groups of African descent experience disproportionately greater asthma morbidity compared with other racial groups, suggesting that genetic variation from a common ancestry could influence exacerbation risk.

OBJECTIVE

We evaluated clinical trial measures in the context of self-reported race and genetic ancestry to identify risk factors for asthma exacerbations.

METHODS

One thousand eight hundred forty multiethnic subjects from 12 Asthma Clinical Research Network and AsthmaNet trials were analyzed for incident asthma exacerbations with Poisson regression models that included clinical measures, self-reported race (black, non-Hispanic white, and other), and estimates of global genetic African ancestry in a subgroup (n = 760).

RESULTS

Twenty-four percent of 1840 subjects self-identified as black. Black and white subjects had common risk factors for exacerbations, including a history of 2 or more exacerbations in the previous year and FEV₁ percent predicted values, whereas chronic sinusitis, allergic rhinitis, and gastroesophageal reflux disease were only associated with increased exacerbation risk in black subjects. In the combined multiethnic cohort, neither race (P = .30) nor percentage of genetic African ancestry as a continuous variable associated with exacerbation risk (adjusted rate ratio [RR], 1.26 [95% CI, 0.94-1.70; P = .13]; RR per 1-SD change [32% ancestry], 0.97 [95% CI, 0.78-1.19; P = .74]). However, in 161 black subjects with genetic data, those with African ancestry greater than the median (≥82%) had a significantly greater risk of exacerbation (RR, 3.06 [95% CI, 1.09-8.6; P = .03]).

CONCLUSION

Black subjects have unique risk factors for asthma exacerbations, of which global African genetic ancestry had the strongest effect.

Analysis of dietary patterns and cross-sectional and longitudinal associations with hypertension, high BMI and type 2 diabetes in Peru

OBJECTIVE

To determine if specific dietary patterns are associated with risk of hypertension, type 2 diabetes mellitus (T2DM) and high BMI in four sites in Peru.

DESIGN

We analysed dietary patterns from a cohort of Peruvian adults in four geographical settings using latent class analysis. Associations with prevalence and incidence of hypertension, T2DM and high BMI were assessed using Poisson regression and generalised linear models, adjusted for potential confounders.

SETTING

Four sites in Peru varying in degree of urbanisation.

PARTICIPANTS

Adults aged ≥35 years (n 3280).

RESULTS

We identified four distinct dietary patterns corresponding to different stages of the Peruvian nutrition transition, reflected by the foods frequently consumed in each pattern. Participants consuming the 'stage 3' diet, characterised by high proportional consumption of processed foods, animal products and low consumption of vegetables, mostly consumed in the semi-urban setting, showed the highest prevalence of all health outcomes (hypertension 32·1 %; T2DM 10·7 %; high BMI 75·1 %). Those with a more traditional 'stage 1' diet characterised by potato and vegetables, mostly consumed in the rural setting, had lower prevalence of hypertension (prevalence ratio; 95 CI: 0·57; 0·43, 0·75), T2DM (0·36; 0·16, 0·86) and high BMI (0·55; 0·48, 0·63) compared with the 'stage 3' diet. Incidence of hypertension was highest among individuals consuming the 'stage 3' diet (63·75 per 1000 person-years; 95 % CI 52·40, 77·55).

CONCLUSIONS

The study found more traditional diets were associated with a lower prevalence of three common chronic diseases, while prevalence of these diseases was higher with a diet high in processed foods and low in vegetables.

Ancestry and Risk of Hepatic Fibrosis and Inflammation in Patients With HCV Infection

Worldwide, ∼184 million people have chronic hepatitis C virus (HCV) infection.¹ Persistent racial disparities in outcomes are observed among HCV-infected patients. Hispanic patients with chronic HCV are more likely than non-Hispanic white (NHW) patients to develop advanced hepatic fibrosis and inflammation.^2,3 Conversely, black patients with HCV infection are at lowest risk. The factors that contribute to this racial disparity are multifactorial, including lifestyle, genetics, and medical care. Limited data in other diseases suggest that genetic ancestry determined using ancestry-informative markers (AIMs) may help explain racial and ethnic differences in disease risk or severity.⁴ AIMs are sets of single-nucleotide polymorphisms (SNPs) that determine a person's ancestral continent of origin and the genetic ancestry proportions assigned to each individual serves as a proxy for his or her genetic ancestral background. We examined the risk of hepatic fibrosis and inflammation in HCV-infected patients according to both genetic ancestry and self-reported race/ethnicity.

Motivations for Participation in Parkinson Disease Genetic Research Among Hispanics versus Non-Hispanics

Involvement of participants from different racial and ethnic groups in genomic research is vital to reducing health disparities in the precision medicine era. Racial and ethnically diverse populations are underrepresented in current genomic research, creating bias in result interpretation. Limited information is available to support motivations or barriers of these groups to participate in genomic research for late-onset, neurodegenerative disorders. To evaluate willingness for research participation, we compared motivations for participation in genetic studies among 113 Parkinson disease (PD) patients and 49 caregivers visiting the Movement Disorders clinic at the University of Miami. Hispanics and non-Hispanics were equally motivated to participate in genetic research for PD. However, Hispanic patients were less likely to be influenced by the promise of scientific advancements (N = 0.01). This lack of scientific interest, but not other motivations, was found to be likely confounded by lower levels of obtained education (N = 0.001). Overall, these results suggest that underrepresentation of Hispanics in genetic research may be partly due to reduced invitations to these studies.

Inconsistency in race and ethnic classification in pharmacogenetics studies and its potential clinical implications

Introduction

Racial and ethnic categories are frequently used in pharmacogenetics literature to stratify patients; however, these categories can be inconsistent across different studies. To address the ongoing debate on the applicability of traditional concepts of race and ethnicity in the context of precision medicine, we aimed to review the application of current racial and ethnic categories in pharmacogenetics and its potential impact on clinical care.

Methods

One hundred and three total pharmacogenetics papers involving the CYP2C9, CYP2C19, and CYP2D6 genes were analyzed for their country of origin, racial, and ethnic categories used, and allele frequency data. Correspondence between the major continental racial categories promulgated by National Institutes of Health (NIH) and those reported by the pharmacogenetics papers was evaluated.

Results

The racial and ethnic categories used in the papers we analyzed were highly heterogeneous. In total, we found 66 different racial and ethnic categories used which fall under the NIH race category “White”, 47 different racial and ethnic categories for “Asian”, and 62 different categories for “Black”. The number of categories used varied widely based on country of origin: Japan used the highest number of different categories for “White” with 17, Malaysia used the highest number for “Asian” with 24, and the US used the highest number for “Black” with 28. Significant variation in allele frequency between different ethnic subgroups was identified within 3 major continental racial categories.

Conclusion

Our analysis showed that racial and ethnic classification is highly inconsistent across different papers as well as between different countries. Evidence-based consensus is necessary for optimal use of self-identified race as well as geographical ancestry in pharmacogenetics. Common taxonomy of geographical ancestry which reflects specifics of particular countries and is accepted by the entire scientific community can facilitate reproducible pharmacogenetic research and clinical implementation of its results.

Delimitation of the upstream region of NFKBIA gene associated with HTLV-1-associated myelopathy/tropical spastic paraparesis using candidate Tag-SNPs in Peruvian HTLV-1 infected individuals

In Peru, it is estimated that about 150 000-400 000 people carry the Human T-lymphotropic virus 1 (HTLV-1). Only 10% of HTLV-1 carries develop complications related to HTLV-1. HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic disabling inflammatory disease affecting the spinal cord. HAM/TSP produces principally weakness in the lower limbs and bladder disturbances, among other complications. In a previous study, our group identified three SNPs (rs3138053, rs2233406, and rs3138045) located in the promoter region of the NFKBIA gene associated with HAM/TSP. This study aimed to analyze the association between four Tag-SNPs (rs10148482, rs17103274, rs17103282, and rs762009) located in the upstream region of the NFKBIA gene and HAM/TSP, and to delimit the linkage disequilibrium zone in the upstream region of the NFBKIA gene associated with HAM/TSP. The tetra-primers ARMS-PCR technique was used to genotype 4 Tag-SNPs on 140 HAM/TSP patients and 258 asymptomatic carriers. The SNP rs17103282 showed a deviation from Hardy-Weinberg equilibrium (p < .0001). Neither of three Tag-SNPs showed an association with HAM/TSP (P > .05). No linkage disequilibrium between four Tag-SNPs evaluated in this study and previous ones was observed. Here we show the region located in the upstream region of the NFKBIA gene highly associated with HAM/TSP disease in patients infected with HTLV-1 from Lima, Peru.

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Asthma is a complex disease with striking disparities across racial and ethnic groups. Despite its relatively high burden, representation of individuals of African ancestry in asthma genome-wide association studies (GWAS) has been inadequate, and true associations in these underrepresented minority groups have been inconclusive. We report the results of a genome-wide meta-analysis from the Consortium on Asthma among African Ancestry Populations (CAAPA; 7009 asthma cases, 7645 controls). We find strong evidence for association at four previously reported asthma loci whose discovery was driven largely by non-African populations, including the chromosome 17q12-q21 locus and the chr12q13 region, a novel (and not previously replicated) asthma locus recently identified by the Trans-National Asthma Genetic Consortium (TAGC). An additional seven loci reported by TAGC show marginal evidence for association in CAAPA. We also identify two novel loci (8p23 and 8q24) that may be specific to asthma risk in African ancestry populations.

Investigating mitonuclear interactions in human admixed populations

To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in admixed populations. Here, we explored potential mitonuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians and Puerto Ricans. By comparing nuclear versus mitochondrial ancestry in these populations, we first show that mitochondrial DNA (mtDNA) copy number decreases with increasing discordance between nuclear and mtDNA ancestry. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation indicates suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analysed exhibit no such trend, in African Americans and Puerto Ricans, we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (African and Native American, respectively). This possibly reflects compensatory effects of selection in recovering mitonuclear interactions optimized in the source populations. Our results provide evidence of mitonuclear interactions in human admixed populations and we discuss their implications for human health and disease.

Patient Characteristics at Prostate Cancer Diagnosis in Different Races at an Academic Center Serving a Diverse Population

BACKGROUND

In the United States, the prostate cancer (PCa) incidence and death rate has been greater in non-Hispanic black (NHB) men than in non-Hispanic white (NHW) men and slightly lower in Hispanic men than in NHW men. We compared the sociodemographic and baseline prognostic factors at the diagnosis of PCa in different races/ethnicities at a large, academic center serving an ethnically diverse population.

METHODS

The Montefiore Medical Center Cancer Registry was used to generate a comprehensive list of all patients with PCa diagnosed from 2004 to 2014. The clinical Looking Glass (a proprietary searchable database of patient information) and individual patient medical record review were used to obtain data, including age at diagnosis, socioeconomic status (SES), clinical Gleason score, clinical stage, and prostate-specific antigen level at diagnosis. The patients were classified by self-identified race/ethnicity as Hispanic, NHB, NHW, or other. The χ² test was used for categorical variables, and analysis of variance or the Kruskal-Wallis test was used for continuous variables.

RESULTS

We identified 2352 patients with newly diagnosed PCa during the study period, including 778 Hispanic, 1046 NHB, 486 NHW, and 42 other. The NHW men were significantly older at diagnosis (Hispanic, 63.2 years; NHB, 63.4 years; NHW, 67 years; other, 63.0 years; P < .0001). The mean SES for the Hispanic and NHB men was significantly lower (SES below average: Hispanic, 92.8%; NHB, 91.3%; NHW, 56.6%; other, 75%; P < .0001). The Gleason score at diagnosis differed among these race groups (Gleason score ≤6 PCa: Hispanic, 42.8%; NHB, 39.1%; NHW, 52.2%; other, 50%; Gleason score 8-10: Hispanic, 15.8%; NHB, 17.6%; NHW, 14.3%; other, 16.7%; P = .0005). The proportion of men with metastatic disease at diagnosis also differed significantly among the groups (Hispanic, 7.5%; NHB, 9.0%; NHW, 4.3%; other, 9.5%; P = .0139). Using pairwise comparisons, the odds ratio for a higher Gleason score at presentation between NHB and NHW was 1.592 (P < .001) and was 1.378 for Hispanic versus NHW (P = .0200). The pairwise comparison for metastatic disease at diagnosis showed an odds ratio of 2.186 for NHB versus NHW (P = .0087). After adjusting for SES, the odds ratio for a higher Gleason score comparing NHB and NHW was 1.55 (P = .001). Although the odds of metastatic disease were greater in Hispanic men than in NHW men (odds ratio, 1.784), the differences were not statistically significant (P = .1197).

CONCLUSIONS

At our center, the clinical features of men from different racial groups differed significantly at the time of newly diagnosed PCa. Differences included age at diagnosis, SES, Gleason score, and proportion with metastatic disease. Our pairwise comparisons between different ethnic groups suggested that PCa in Hispanic men might be more similar to that in NHB than to that in NHW patients and are generally more aggressive at diagnosis.

Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

BACKGROUND

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.

METHODS

We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.

RESULTS

We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).

CONCLUSION

Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.

Dating admixture events is unsolved problem in multi-way admixed populations

Advances in human sequencing technologies, coupled with statistical and computational tools, have fostered the development of methods for dating admixture events. These methods have merits and drawbacks in estimating admixture events in multi-way admixed populations. Here, we first provide a comprehensive review and comparison of current methods pertinent to dating admixture events. Second, we assess various admixture dating tools. We do so by performing various simulations. Third, we apply the top two assessed methods to real data of a uniquely admixed population from South Africa. Results reveal that current dating admixture models are not sufficiently equipped to estimate ancient admixtures events and to identify multi-faceted admixture events in complex multi-way admixed populations. We conclude with a discussion of research areas where further work on dating admixture-based methods is needed.

Genome-wide association study identifies WNT7B as a novel locus for central corneal thickness in Latinos

The cornea is the outermost layer of the eye and is a vital component of focusing incoming light on the retina. Central corneal thickness (CCT) is now recognized to have a significant role in ocular health and is a risk factor for various ocular diseases, such as keratoconus and primary open angle glaucoma. Most previous genetic studies utilized European and Asian subjects to identify genetic loci associated with CCT. Minority populations, such as Latinos, may aid in identifying additional loci and improve our understanding of the genetic architecture of CCT. In this study, we conducted a genome-wide association study (GWAS) in Latinos, a traditionally understudied population in genetic research, to further identify loci contributing to CCT. Study participants were genotyped using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). All study participants were 40 years of age and older. We assessed the association between individual single nucleotide polymorphisms (SNPs) and CCT using linear regression, adjusting for age, gender and principal components of genetic ancestry. To expand genomic coverage and to interrogate additional SNPs, we imputed SNPs from the 1000 Genomes Project reference panels. We identified a novel SNP, rs10453441 (P = 6.01E-09), in an intron of WNT7B that is associated with CCT. Furthermore, WNT7B is expressed in the human cornea. We also replicated 11 previously reported loci, including IBTK, RXRA-COL5A1, COL5A1, FOXO1, LRRK1 and ZNF469 (P < 1.25E-3). These findings provide further insight into the genetic architecture of CCT and illustrate that the use of minority groups in GWAS will help identify additional loci.

The 22Rv1 prostate cancer cell line carries mixed genetic ancestry: Implications for prostate cancer health disparities research using pre-clinical models

BACKGROUND

Understanding how biological factors contribute to prostate cancer (PCa) health disparities requires mechanistic functional analysis of specific genes or pathways in pre-clinical cellular and animal models of this malignancy. The 22Rv1 human prostatic carcinoma cell line was originally derived from the parental CWR22R cell line. Although 22Rv1 has been well characterized and used in numerous mechanistic studies, no racial identifier has ever been disclosed for this cell line. In accordance with the need for racial diversity in cancer biospecimens and recent guidelines by the NIH on authentication of key biological resources, we sought to determine the ancestry of 22RV1 and authenticate previously reported racial identifications for four other PCa cell lines.

METHODS

We used 29 established Ancestry Informative Marker (AIM) single nucleotide polymorphisms (SNPs) to conduct DNA ancestry analysis and assign ancestral proportions to a panel of five PCa cell lines that included 22Rv1, PC3, DU145, MDA-PCa-2b, and RC-77T/E.

RESULTS

We found that 22Rv1 carries mixed genetic ancestry. The main ancestry proportions for this cell line were 0.41 West African (AFR) and 0.42 European (EUR). In addition, we verified the previously reported racial identifications for PC3 (0.73 EUR), DU145 (0.63 EUR), MDA-PCa-2b (0.73 AFR), and RC-77T/E (0.74 AFR) cell lines.

CONCLUSIONS

Considering the mortality disparities associated with PCa, which disproportionately affect African American men, there remains a burden on the scientific community to diversify the availability of biospecimens, including cell lines, for mechanistic studies on potential biological mediators of these disparities. This study is beneficial by identifying another PCa cell line that carries substantial AFR ancestry. This finding may also open the door to new perspectives on previously published studies using this cell line.

Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system

Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature. We link the gene, COL27A1, with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease.

Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations. Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor. This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor.

Belbin et al. used this computational technique to identify a mutation that may cause unusually short stature or bone and joint problems in up to 2% of people of Puerto Rican descent. In the experiments, the genomes of about 32,000 New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature. The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and joint problems. People who inherited one copy had an increased likelihood of joint or bone problems.

This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth. The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had previously been linked to a disorder called Steel syndrome that was thought to be rare. Belbin et al. showed this condition is actually fairly common in people whose ancestors recently came from Puerto Rico, but may often go undiagnosed by their physicians. The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation.

Family-based exome-wide association study of childhood acute lymphoblastic leukemia among Hispanics confirms role of ARID5B in susceptibility

We conducted an exome-wide association study of childhood acute lymphoblastic leukemia (ALL) among Hispanics to confirm and identify novel variants associated with disease risk in this population. We used a case-parent trio study design; unlike more commonly used case-control studies, this study design is ideal for avoiding issues with population stratification bias among this at-risk ethnic group. Using 710 individuals from 323 Guatemalan and US Hispanic families, two inherited SNPs in ARID5B reached genome-wide level significance: rs10821936, RR = 2.31, 95% CI = 1.70–3.14, p = 1.7×10⁻⁸ and rs7089424, RR = 2.22, 95% CI = 1.64–3.01, p = 5.2×10⁻⁸. Similar results were observed when restricting our analyses to those with the B-ALL subtype: ARID5B rs10821936 RR = 2.22, 95% CI = 1.63–3.02, p = 9.63×10⁻⁸ and ARID5B rs7089424 RR = 2.13, 95% CI = 1.57–2.88, p = 2.81×10⁻⁷. Notably, effect sizes observed for rs7089424 and rs10821936 in our study were >20% higher than those reported among non-Hispanic white populations in previous genetic association studies. Our results confirmed the role of ARID5B in childhood ALL susceptibility among Hispanics; however, our assessment did not reveal any strong novel inherited genetic risks for acute lymphoblastic leukemia among this ethnic group.

Distribution of KIR genes and KIR2DS4 gene variants in two Mexican Mestizo populations

Killer immunoglobulin-like receptors (KIR) are transmembrane proteins that regulate NK and T cell subsets by recognizing HLA-I molecules as ligands. The KIR gene family consists of 16 genes, located at chromosome 19q13.4. KIR gene frequencies vary among populations. In Mexico, HLA and genetic ancestry studies show that Mestizo populations have different genetic backgrounds based on admixture with European, African, and Asian ancestry. This study aimed to evaluate the frequencies of KIR genes and genotypes in Guerrero and Jalisco, two Mexican Mestizo populations located in the south and the west of the country, respectively, and to compare these frequencies with those of other populations. KIR genotyping was performed by SSP-PCR. We observed that KIR gene frequencies were similar in both populations. There were 24 genotypes observed in Guerrero, 38 genotypes observed in Jalisco, 15 genotypes shared in both populations and 32 genotypes unique to one population or the other. In 10 individuals, nine novel genotypes were identified. KIR2DS4 gene variants showed significant differences: The KIR2DS4full gene was more common in Guerrero (p<0.0001), and the KIR2DS4del variant was more common in Jalisco (p<0.05). Differences in KIR2DS4 gene variants and genotypic profiles could be influenced by the genetic admixture in both regions.

Urbanization, mainly rurality, but not altitude is associated with dyslipidemia profiles

Background

Geographical and environmental features such as urbanization and altitude may influence individual's lipid profiles because of the diversity of human-environment interactions including lifestyles.

Objective

To characterize the association between altitude and urbanization and lipid profile among Peruvian adults aged ≥35 years.

Methods

Cross-sectional analysis of the CRONICAS Cohort Study. The outcomes of interest were 6 dyslipidemia traits: hypertriglyceridemia, high low-density lipoprotein cholesterol, low high-density lipoprotein cholesterol (HDL-c), nonisolated low HDL-c, isolated low HDL-c, and high non-HDL-c. The exposures of interest were urbanization level (highly urban, urban, semi-urban, and rural) and altitude (high altitude vs sea level). Prevalence ratios (PRs) and 95% confidence intervals (95% CIs) were calculated using Poisson regression models with robust variance adjusting for potential confounders.

Results

Data from 3037 individuals, 48.5% males, mean age of 55.6 (standard deviation ±12.7) years, were analyzed. The most common dyslipidemia pattern was high non-HDL-c with a prevalence of 88.0% (95% CI: 84.9%–90.7%) in the rural area and 96.0% (95% CI: 94.5%–97.1%) in the semi-urban area. Relative to the highly urban area, living in rural areas was associated with a lower prevalence of hypertriglyceridemia (PR = 0.75; 95% CI: 0.56–0.99) and high non-HDL-c (PR = 0.96; 95% CI: 0.93–0.99), whereas living in semi-urban areas was associated with higher prevalence high low-density lipoprotein cholesterol (PR = 1.37; 95% CI: 1.11–1.67). Compared with sea level areas, high-altitude areas had lower prevalence of high non-HDL-c (PR = 0.97; 95% CI: 0.95–0.99).

Conclusion

Urbanization but not altitude was associated to several dyslipidemia traits, with the exception of high non-HDL-c in high altitude settings.

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Levels of urbanization but not altitude were associated with dyslipidemia traits.

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People in rural in comparison to urban areas had lower prevalence of dyslipidemia.

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Population from semi-urban areas showed high prevalence of some dyslipidemia traits.

Analysis of admixture proportions in seven geographical regions of the state of Guerrero, Mexico

OBJECTIVE

Mexico's current population structure has been defined by admixture between European, Native American, and to some extent African, groups that started in the sixteenth century. The aim of this research was to analyze the relative contributions of these continental population groups to the seven regions of the state of Guerrero, Mexico.

METHODS

A total of 104 ancestry informative markers were analyzed in 480 unrelated women from the seven regions of the state of Guerrero. The individual ancestry proportions were estimated using the software ADMIXMAP v3.2.

RESULTS

The relative Native American, European and African ancestral contributions to the whole sample were estimated to be 69%, 27%, and 1.9%, respectively. We observed significant differences in admixture proportions across the regions. The highest average Native American ancestry was found in the Montaña region and the lowest in Costa Grande. Conversely, the highest European contribution was observed in Costa Grande. The highest African contributions were observed in the regions of Costa Chica and Costa Grande.

CONCLUSIONS

The genetic structure of the population of Guerrero reflects quite well the historical processes that have occurred in this state. Native American population settlements were mainly in the regions of Montaña, Norte, and Centro, where the highest indigenous genetic contribution is observed today. European settlers came from the center of the state to regions with significant agricultural and mining activities. The highest African contributions are observed in coastal regions, in agreement with historical evidence about slave trade routes in the Americas.

MS in self-identified Hispanic/Latino individuals living in the US

Self-identified Hispanic/Latino individuals living with multiple sclerosis (MS) in the continental United States (US) are a diverse group that represents different cultural and ancestral backgrounds. A marked variability in the way MS affects various subgroups of Hispanics in the US has been observed. We reviewed and synthesized available data about MS in Hispanics in the US. There are likely a host of multifactorial elements contributing to these observations that could be explained by genetic, environmental, and social underpinnings. Barriers to adequate MS care in Hispanics are likely to include delivery of culturally competent care and social and economic disadvantages. Considerable efforts, including the formation of a national consortium known as the Alliance for Research in Hispanic Multiple Sclerosis (ARHMS), are underway to help further explore these various factors.

A Genome-Wide Association Study of Vertical Cup-Disc Ratio in a Latino Population

Purpose

Vertical cup-disc ratio (VCDR) is used as a clinical assessment measure to identify and monitor glaucomatous damage to the optic nerve. Previous genetic studies conducted in European and Asian populations have identified many loci associated with VCDR. The genetic factors in other ethnic populations, such as Latino, influencing VCDR remain to be determined. Here, we describe the first genome-wide association study (GWAS) on VCDR in Latino individuals.

Methods

We conducted this GWAS on VCDR using 4537 Latino individuals who were genotyped by using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). Study subjects were 40 years of age and older. Linear regression, adjusting for age, sex, and principal components of genetic ancestry, was conducted to assess the associations between single nucleotide polymorphisms (SNPs) and VCDR. We imputed SNPs from the 1000 Genomes Project to integrate additional SNPs not directly genotyped.

Results

We replicated two previously reported SNPs that reached GWAS significance, rs1900005 and rs7916697, in the ATOH7-PBLD region, as well as identified two suggestive associations in the CDC7-TGFBR3 region on chromosome 1p22.1 and in the ZNF770-DPH6 region on chromosome 15q14. We discovered a novel SNP, rs56238729 (P = 1.22 × 10⁻¹³), in the ATOH7-PBLD region that is significantly associated with VCDR in Latino individuals. We replicated eight previously reported regions, including COL8A1, CDKN2B-CDKN2BAS, BMP2, and CHEK2 (P < 2.17 × 10⁻³).

Conclusions

Our results discovered a novel SNP that is significantly associated with VCDR in Latino individuals and confirmed previously reported loci, providing further insight into the genetic architecture of VCDR.