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

Creation and Characterization of a Breast Cancer Tissue Microarray Including Black and White Patients from Florida and Hispanic Patients from Puerto Rico and Florida

Breast cancer is a leading cause of cancer-related mortality among women worldwide and is known to have higher mortality among women with African ancestry. Herein, we describe the creation and characterization of a multiethnic breast cancer tissue microarray (ME-BrTMA) representing tumors from non-Hispanic White (n = 41), non-Hispanic Black (NHB; n = 45), and Hispanic patients from Puerto Rico (n = 36) and Florida (n = 52). This ME-BrTMA comprises five blocks with a total of 610 cores: 371 breast cancer tumor cores, 93 breast stromal cores, 96 normal breast tissue cores, 30 non-breast cancer tumor cores, and 20 cores representing normal tissues. Initial characterization of the ME-BrTMA includes standard IHC staining of well-characterized clinical biomarkers, including the estrogen hormone receptors and progesterone hormone receptors, HER2, and Ki-67, interpreted by the coauthoring pathologist (Marilin Rosa). The IHC results indicated good but imperfect alignment with clinical diagnoses. Cores from breast cancer tumors from the NHB cohort most frequently scored negative for estrogen receptor (63%, P < 0.005) and progesterone receptor (80%, P < 0.005) and most frequently have high expression of the Ki-67 proliferation marker (38%, P < 0.05). Prediction Analysis of Microarray 50 (PAM50) analysis using RNA from secondary patient blocks showed that the NHB group also most frequently scored in the basal-like category (61%, P < 0.05). Taken together, the initial characterization of the ME-BrTMA suggests that it may serve as a representative resource to understand the underlying biology of breast cancer and its relationship to patient outcomes.

SIGNIFICANCE

The ME-BrTMA described herein provides a resource that may serve as a tool to understand the underlying biology of breast cancer.

The Applicability of Existing Reference Equations for the 6-Minute Walk Test in Healthy Children and Adolescents Living in a City at a High Altitude

OBJECTIVES

This study aimed to evaluate the applicability of existing 6MWT reference equations to healthy children and adolescents living in a high-altitude city.

METHODS

Healthy children aged 5 to 15 years attending two non-randomly selected schools in Bogotá were invited to participate in the study. All participants performed the 6MWT according to the European Respiratory Society/American Thoracic Society technical standards. To identify the model or set of 6MWT equations that best predicted individually measured 6MWT values in our population, we identified the narrowest limits of agreement (LOA) (mean difference between measured and predicted values ± 1.96 SD) after constructing Bland-Altman plots. We performed separate analyzes based on sex and onset of puberty, which was assumed to occur at 12 years of age for girls and 13 years of age for boys.

RESULTS

105 children and adolescents (61 girls, 58.1%) with a mean age of 10.04 years (±2.21), ranging from 6 to 15 years, were evaluated. We determined that equations derived from two different studies conducted in Brazil, de Assis, and Oliveira 6MWT equations provided the narrowest LOA in the Bland-Altman plots for the individually-measured 6MWT values for all study participants, except for the older female participants who obtained narrower LOA with the Ulrich equations.

CONCLUSION

For the mean walked distance of the 6MWT, we have provided information on the 6MWT predictive equations that may be most appropriate for use in healthy children living in Bogota, Colombia, a city at 2640 m altitude.

Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored

There is growing research on the allosteric behaviour of proteins, including studies on allosteric mutations that contribute to human diseases and the development of allosteric drugs. Allostery also plays a key role in drug metabolism, an essential factor in drug development. However, population specific variations, particularly in 3D protein structures, remain understudied. This study focuses on CYP3A4, a key enzyme responsible for metabolizing over 50% of FDA-approved drugs and often linked to adverse drug reactions. Given the vast genetic diversity of Africa, we investigated 13 CYP3A4 alleles from African populations using post-molecular dynamics analyses, with 12 being single variations and one containing a double variation. Except for one, all allele variations were located away from the active site, suggesting allosteric effects. Our comparative analyses of reference and variant structures, through hydrogen bond interactions, dynamic residue network analysis and substrate channel dynamics, revealed notable differences at both global and residue levels. The *32-I335T variant showed the largest changes compared to the reference structure, while *3-M445T (near normal metabolizer) exhibited the least change, with other variants falling in between. The *32-I335T variant showed a distorted conformation in the radius of gyration, a distinct kink in the I helix with specific hydrogen bonds and altered channel patterns. The *12-L373F variant, associated with reduced metabolism of midazolam and quinine, showed increased rigidity in its vicinity, potentially interfering with catalytic activity. Our findings align with clinical and wet lab data, suggesting that our approaches could be applied to analyse variants without clinical evidence.

Major Histocompatibility Complex Class I and II Allele Frequencies and Disease Associations in Mexicans: A Systematic Review and Meta-Analysis

BACKGROUND

The major histocompatibility complex (MHC) plays a crucial role in immune responses and is associated with disease susceptibility. This study systematically reviews MHC class I and class II allele frequencies and their associations with diseases in the Mexican population from 1979 to 2023.

METHODS

A systematic review following PRISMA guidelines was conducted. Reports were obtained from the Allele Frequency Net Database and PubMed using keywords related to HLA and Mexican populations. A total of 776 reports were screened, and 214 were retained for final analysis. Seventy-six studies comprising allele frequency data from over 20,000 individuals across Mexican states and indigenous communities were analyzed. In addition, over 138 articles were examined to identify alleles associated with various diseases.

RESULTS

The analysis identified 117 alleles whose frequencies varied regionally within Mexico. While DPA1*01, DPB1*04:01, and DQA1*03 were predominant, DRB1*04, DQB1*03, and DQA1*05 were also prominent but variable. Certain alleles, such as A*02, B*35, C*04, and C*07, were relatively common in the population. Numerous disease correlations were uncovered, such as B*27's strong association with spondyloarthropathies. DRB1*15:01 and DRB1*04 conferred an increase in multiple sclerosis, while DRB1*04 may protect against some skin diseases.

CONCLUSION

This review improves the understanding of MHC allele frequencies and disease associations in Mexicans, highlighting genetic diversity. The findings lay the groundwork for future research on genetic predispositions and health outcomes, aiding healthcare strategies in this diverse population. Further studies are needed to address data gaps and refine genetic profiles for targeted medical applications.

Genetic Ancestry and Lung Cancer in Latin American Patients: A Crucial Step for Understanding a Diverse Population

Lung cancer is the second leading cause of cancer-related deaths in Latin America. While incidence and mortality rates are higher in other populations, the ``Hispanic paradox'' observed in US Hispanics reflects a lower mortality rate for mortality from non-small cell lung cancer (NSCLC) despite socioeconomic disparities, which may be related to epigenetic and cultural factors. Genetic studies have identified single nucleotide polymorphisms associated with ancestry as key contributors to lung cancer risk and outcomes, emphasizing the importance of genomic insights for early detection and personalized treatments. This narrative review explores the impact of genetic ancestry on lung cancer in Hispanic/Latino populations. We searched MEDLINE and Google Scholar for "((SNP) OR (germline) OR (variant)) AND (lung cancer) AND ((Hispanic) OR (Latin))," focusing on Latin American studies. We included articles published up to December 2024. Specific variation in genes such as XRCC1, CYP1A1, CYP1A2, SEMA3B, PADPRP, and mEPHX have been associated with increased lung cancer risk. Lung cancer incidence and prognosis vary significantly among Hispanics due to their diverse genetic ancestry. Understanding ancestry-specific genetic variations may help personalize treatment and improve outcomes for this population.

Real-World Incidence of Anaplastic Lymphoma Kinase Alterations in Hispanics with Non-Small Cell Lung Cancer at a Large Academic Institution in Los Angeles

SIGNIFICANCE

This study identified a higher incidence of ALK alterations in Hispanic patients with NSCLC (12.76%) compared with that in non-Hispanic patients (5.36%) treated at a large academic center in Los Angeles, highlighting the impact of race on molecular alteration profiles and emphasizing the need to increase access to molecular analyses for this population. The variability in mutational alterations may be influenced by biological and environmental factors.

Pharmacogenomics Tools for Precision Public Health and Lessons for Low- and Middle-Income Countries: A Scoping Review

Pharmacogenomics is the integration of genomics and pharmacology to optimize drug response and reduce side effects. In terms of personalized or individualized medicine, PGx is defined as the identification and analysis of specific genetic variants associated with particular drug treatments for each patient. Under a precision public health (PPH) approach, population-level data are analyzed to generate public health strategies. The objective of this study was to conduct a scoping review of technological tools, examining their evolution, the predominance of high-income countries in their development, and the gaps and needs for genomic data and advances in low- and middle-income countries (LMICs). This review was conducted in accordance with the ScPRISMA guidelines. A search was conducted in PubMed, Web of Science and Embase until January 2024. A total of 40 documents were selected, which revealed the continuous evolution and progressive development of pharmacogenomic tools. The technological tools developed come from high-income countries, particularly the United States, Canada, China, and several European nations, where international collaboration has been essential to maintain and expand these tools, which have evolved to keep pace with the rapid generation of genomic data. This trend shows a scarce development of technological tools for public health precision in LMICs, which evidences the need to increase investment in genomic research infrastructure in this aspect and in the development of capacities to guarantee global accessibility and boost PPH for all populations.

Population molecular genetics in Brazil: From genomic databases and research to the implementation of precision medicine

Precision medicine (PM) stands on the brink of revolutionizing medical practice throughout the world, holding significant potential for enhancing patient outcomes. However, its practical implementation, particularly in resource-limited countries, is not without challenges. The success of PM largely hinges on the availability of extensive datasets, including genetic and genomic information. This paper delves into the PM landscape and the current state of genetic and genomic testing in Brazil. We also shed light on the unique challenges posed by the country's diverse population and discuss ongoing initiatives to tackle these obstacles.

Cancer genetic counseling in Chile: Addressing barriers, confronting challenges, and seizing opportunities in an underserved Latin American Community

Purpose

Despite the rapid advancements in genomics and the enactment of a new cancer law in Chile, the implementation of cancer genetic counseling continues to face significant challenges because of limited resources and infrastructure.

Methods

We conducted a survey targeting health care providers who offer genetic counseling to patients with cancer and possess training in genetics and counseling. Additionally, we distributed a separate survey to high-risk patients associated with an advocacy group to gather insights on their perceptions of and experiences with cancer genetic counseling.

Results

Among the surveyed providers, 21% were nonmedical professionals who developed their skills through postgraduate continuing education programs. Germline testing was not performed in 47% of cases. Among the participants, 37% considered genetic counseling important for understanding the cause of their cancer, 25% valued knowing their risk of developing future tumors, and 33% believed it would benefit their current cancer treatment. Just over half of the patients (54%) had access to genetic counseling. Among those that received genetic counseling, 85% found it beneficial.

Conclusion

In Chile, barriers to genetic counseling persist, particularly in rural areas and because of a shortage of trained professionals. Public policies recognizing genetic counseling's importance are crucial, along with expanding training and infrastructure. Understanding patient perceptions and increasing the number of trained genetic counseling into cancer care, educating clinicians, and advocating for increased access are key steps for enhancing cancer treatment effectiveness in Chile.

Racial/ethnic differences in the clinical presentation and survival of breast cancer by subtype

Background

Breast cancer (BC) affects racial and ethnic groups differently, leading to disparities in clinical presentation and outcomes. It is unclear how Hispanic ethnicity affects BC outcomes based on geographic location and proximity to the United States (U.S.)/Mexico border. We hypothesized that the impact of race/ethnicity on BC outcomes depends on geographic location and country of origin within each BC subtype.

Methods

We analyzed BC data from the Texas Cancer Registry by race/ethnicity/birthplace according to BC subtype (luminal A/luminal B/human epidermal growth factor receptor 2 [HER2]/triple-negative breast cancer[TNBC]). Other covariates included age, geographic location (U.S., Mexico), residency (border, non-border), treatments, and comorbidities. Crude and adjusted effects of race/ethnicity and birthplace on overall survival (OS) were analyzed using Cox regression methods.

Results

Our analysis of 76,310 patient records with specific BC subtypes revealed that Hispanic and non-Hispanic Black (NHB) patients were diagnosed at a younger age compared with non-Hispanic White (NHW) patients for all BC subtypes. For the 19,748 BC patients with complete data on race/ethnicity/birthplace/residency, Hispanic patients had a higher mortality risk in the Luminal A subtype, regardless of birthplace, whereas U.S.-born Hispanics had a higher risk of death in the TNBC subtype. In contrast, NHB patients had a higher mortality risk in the Luminal A and HER2 subtypes. Residence along the U.S./Mexico border had little impact on OS, with better outcomes in Luminal A patients and worse outcomes in Luminal B patients aged 60-74 years.

Conclusion

Race/ethnicity, geographic birth location, and residency were significant predictors of survival in BC. Migration, acculturation, and reduced healthcare access may contribute to outcome differences.

Genomic ancestry and cancer among Latin Americans

Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.

Genetic Ancestry and Self-Reported "Skin Color/Race" in the Urban Admixed Population of São Paulo City, Brazil

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual's genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations.

Prevalence of chronic pelvic pain and associated factors among indigenous women of reproductive age in Ecuador

BACKGROUND

Chronic pelvic pain is a common disease that affects approximately 4% of women of reproductive age in developed countries. This number is estimated to be higher in developing countries, with a significant negative personal and socioeconomic impact on women. The lack of data on this condition in several countries, particularly those in development and in socially and biologically vulnerable populations such as the indigenous, makes it difficult to guide public policies.

OBJECTIVES

To evaluate the prevalence of chronic pelvic pain (dysmenorrhea, dyspareunia, non-cyclical pain) and identify which variables are independently associated with the presence of the condition in indigenous women from Otavalo-Ecuador.

DESIGN

A cross-sectional study was carried out including a sample of 2429 women of reproductive age between 14 and 49 years old, obtained from April 2022 to March 2023. A directed questionnaire was used, collected by bilingual interviewers (Kichwa and Spanish) belonging to the community itself; the number of patients was selected by random sampling proportional to the number of women estimated by sample calculation. Data are presented as case prevalence, odds ratio, and 95% confidence interval, with p < 0.05.

RESULTS

The prevalence of primary dysmenorrhea, non-cyclic pelvic pain, and dyspareunia was, respectively, 26.6%, 8.9%, and 3.9%.all forms of chronic pain were independently associated with each other. Additionally, dysmenorrhoea was independently associated with hypertension, intestinal symptoms, miscegenation, long cycles, previous pregnancy, use of contraceptives and pear body shape. Pain in other sites, late menarche, exercise, and pear body shape were associated with non-cyclic pelvic pain. And, urinary symptoms, previous pregnancy loss, miscegenation, and pear body shape were associated with dyspareunia.

CONCLUSION

The prevalence of primary dysmenorrhea and non-cyclical chronic pelvic pain was notably high, in contrast with the frequency of reported dyspareunia. Briefly, our results suggest an association between dysmenorrhoea and conditions related to inflammatory and/or systemic metabolic disorders, including a potential causal relationship with other manifestations of pelvic pain, and between non-cyclical pelvic pain and signs/symptoms suggesting central sensitization. The report of dyspareunia may be influenced by local cultural values and beliefs.

TwinsMX: Exploring the Genetic and Environmental Influences on Health Traits in the Mexican Population

TwinsMX registry is a national research initiative in Mexico that aims to understand the complex interplay between genetics and environment in shaping physical and mental health traits among the country's population. With a multidisciplinary approach, TwinsMX aims to advance our knowledge of the genetic and environmental mechanisms underlying ethnic variations in complex traits and diseases, including behavioral, psychometric, anthropometric, metabolic, cardiovascular and mental disorders. With information gathered from over 2800 twins, this article updates the prevalence of several complex traits; and describes the advances and novel ideas we have implemented such as magnetic resonance imaging. The future expansion of the TwinsMX registry will enhance our comprehension of the intricate interplay between genetics and environment in shaping health and disease in the Mexican population. Overall, this report describes the progress in the building of a solid database that will allow the study of complex traits in the Mexican population, valuable not only for our consortium, but also for the worldwide scientific community, by providing new insights of understudied genetically admixed populations.

Prevalence of oncogenic driver mutations in Hispanics/Latin patients with lung cancer. A systematic review and meta-analysis

INTRODUCTION

The frequency of actionable mutations varies between races, and Hispanic/Latino (H/L) people are a population with different proportions of ancestry. Our purpose was to establish prevalence of actionable mutations in the H/L population with NSCLC.

METHODS

EMBASE, LILACS, MEDLINE, and Virtual Health Library were searched for studies published up to April 2023 that evaluated the prevalence of ALK, BRAF, EGFR, HER-2, KRAS, MET, NTRK, RET, ROS1 in H/L patients. Meta-analyses were done to determine prevalence using a random effects model.

RESULTS

Fifty-five articles were included. EGFR and KRAS were the most prevalent genes with high heterogeneity across the countries. The overall mutation frequency for EGFR was 22%. The most frequent mutations in the EGFR gene were del19 (10%) and L858R (7%). The mean of KRAS mutation was a 14% prevalence. KRASG12C was the most frequent mutation with a 7% prevalence in an entire population. The overall frequency of ALK rearrangement was 5%. The mean frequency of ROS-1 rearrangement was 2%, and the frequencies of HER-2, MET, BRAF, RET, NTRK molecular alterations were 4%, 3%, 2%, 2%, and 1% respectively. Almost half of the cases were male, and 65.8% had a history of tobacco exposure. The most common clinical stage was IV.

CONCLUSIONS

The prevalence of driver mutations such as EGFR and KRAS in LA populations differs from what is reported in Asians and Europeans. In the present article, countries with a high proportion of Amerindian ancestry show a greater prevalence of EGFR in contrast to countries with a high proportion of Caucasians. Lack of information on some countries or studies with a small sample size affects the real prevalence data for the region.

Putative role of HLA polymorphism among a Brazilian HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) population

Around ten million people are infected with HTLV-1 worldwide, and 1-4% develop HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), characterized by an important degeneration of the spinal cord, which can lead to death. Distinct HLA alleles have been associated with either HAM/TSP susceptibility or protection. However, these HLA alleles set may change according to the population studied. Brazil is the second country in the number of HTLV-1-infected people and there are few reports addressing the HLA influence on HTLV-1 infection as well as on disease outcome. The objective of this study was to evaluate the influence of HLA alleles as a risk factor for HAM/TSP and the proviral load (PVL) levels, clinical progression, and death outcomes in an admixed Brazilian population. The HLA-A, -B, -C, and -DRB1 were genotyped in 375 unrelated HTLV-1-infected individuals divided into asymptomatic carriers (AC) (n = 165) and HAM/TSP (n = 210) in a longitudinal cohort from 8 to 22 years of follow-up. Because locus B deviated from Hardy-Weinberg Equilibrium for the study groups, the results represented for HLA-B alleles were inconclusive. The alleles HLA-A*68 and -C*07 were related to HAM/TSP risk in multivariate analysis. The alleles HLA-A*33, and -A*36 were associated with protection against disease progression in HAM/TSP patients, while -C*12, -C*14, and -DRB1*08 were associated with increased risk of death. In the AC group, the presence of, -C*06 and -DRB1*15 alleles influenced an increased PVL, in an adjusted linear regression model, while -A*30, -A*34, -C*06, -C*17 and -DRB1*09 alleles were associated with increased PVL in HAM/TSP group compared to HAM/TSP individuals not carrying these alleles. All these alleles were also related to increased PVL associated with clinical progression outcome. Increased PVL associated with the death outcome was linked to the presence of HLA-A*30. PVL has been associated with HLA, and several alleles were related in AC and HAM/TSP patients with or without interacting with clinical progression outcomes. Understanding the prognostic value of HLA in HAM/TSP pathogenesis can provide important biomarkers tools to improve clinical management and contribute to the discovery of new therapeutic interventions.

An updated examination of the perception of barriers for pharmacogenomics implementation and the usefulness of drug/gene pairs in Latin America and the Caribbean

Pharmacogenomics (PGx) is considered an emergent field in developing countries. Research on PGx in the Latin American and the Caribbean (LAC) region remains scarce, with limited information in some populations. Thus, extrapolations are complicated, especially in mixed populations. In this paper, we reviewed and analyzed pharmacogenomic knowledge among the LAC scientific and clinical community and examined barriers to clinical application. We performed a search for publications and clinical trials in the field worldwide and evaluated the contribution of LAC. Next, we conducted a regional structured survey that evaluated a list of 14 potential barriers to the clinical implementation of biomarkers based on their importance. In addition, a paired list of 54 genes/drugs was analyzed to determine an association between biomarkers and response to genomic medicine. This survey was compared to a previous survey performed in 2014 to assess progress in the region. The search results indicated that Latin American and Caribbean countries have contributed 3.44% of the total publications and 2.45% of the PGx-related clinical trials worldwide thus far. A total of 106 professionals from 17 countries answered the survey. Six major groups of barriers were identified. Despite the region's continuous efforts in the last decade, the primary barrier to PGx implementation in LAC remains the same, the "need for guidelines, processes, and protocols for the clinical application of pharmacogenetics/pharmacogenomics". Cost-effectiveness issues are considered critical factors in the region. Items related to the reluctance of clinicians are currently less relevant. Based on the survey results, the highest ranked (96%-99%) gene/drug pairs perceived as important were CYP2D6/tamoxifen, CYP3A5/tacrolimus, CYP2D6/opioids, DPYD/fluoropyrimidines, TMPT/thiopurines, CYP2D6/tricyclic antidepressants, CYP2C19/tricyclic antidepressants, NUDT15/thiopurines, CYP2B6/efavirenz, and CYP2C19/clopidogrel. In conclusion, although the global contribution of LAC countries remains low in the PGx field, a relevant improvement has been observed in the region. The perception of the usefulness of PGx tests in biomedical community has drastically changed, raising awareness among physicians, which suggests a promising future in the clinical applications of PGx in LAC.