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PubMed2022

Uric Acid Levels Are Associated with Bone Mineral Density in Mexican Populations: A Longitudinal Study.

Background: Inconsistent epidemiological evidence between uric acid (UA) and bone mineral density (BMD) has been observed. Therefore, we evaluated the association between UA and BMD in Mexican adults. Methods: This analysis was conducted on 1423 participants from the Health Workers Cohort Study. We explored cross-sectional associations using linear regression and longitudinal associations using fixed-effects linear regression by sex and age groups (<45 and ≥45 years). Results: In females <45 years old, the cross-sectional analysis showed that UA levels were positively associated with total hip BMD. However, in the longitudinal analysis, we observed a negative association with the femoral neck and lumbar spine BMD. In contrast, in males <45 years old, we found an increase in total hip and femoral neck BMD in the groups with high levels of UA in the longitudinal association. On the other hand, in females ≥45 years old, we observed a longitudinal association between UA and loss of BMD at different sites. We did not observe an association between UA levels and BMD in males ≥45 years old. Conclusions: Our results suggest higher serum UA levels are associated with low BMD at different skeletal sites in Mexican females. Further studies are needed to delineate the underlying mechanisms behind this observation.

Male↗

PubMed2026

Association of TCF7L2 and LEPR gene variants (rs7903146 and rs1137101) with primary knee osteoarthritis in a northern Mexican Mestizo population.

INTRODUCTION: There is a growing interest in the study of Obesity, Diabetes, and their genetic polymorphisms for the risk of developing osteoarthritis. This study analyzed the associations among the rs1137101 LEPR gene and rs7903146 polymorphisms TCF7L2 gene with primary knee osteoarthritis in a population from northern Mexico. METHODS: We conducted a case-control study with 438 Mexican Mestizo participants, selected non-randomly by convenience. We included age, diabetes, and body mass index for analysis. The presence of the TCF7L2 (n = 236) and LEPR (n = 405) gene genotypes was determined using real-time PCR with the rhAmpTM SNP Assay methodology. We performed comparisons between groups using the chi-square test, Fisher´s exact test, the Mann-Whitney U test, and adjusted regression model analysis. RESULTS: The CC genotype of the rs7903146 polymorphism was significantly associated as risk factor with obesity (p = 0.043; OR 2.021, CI 1.023 - 3.989) and CT genotype as a protective factor (p = 0.016, p = 0.013, and p = 0.008); the CC genotype was significantly associated with primary KOA as a risk factor (p = 0.040; OR 2.061, CI 1.034 - 4.107) and the CT genotype as a protective factor (p = 0.039, and p = 0.041; OR 0.480, CI 0.237 - 0.970). No association was found between the genotypes for LEPR rs1137101 and KOA. CONCLUSION: This study suggests a possible role for the rs7903146 polymorphism of the TCF7L2 gene, in the risk of primary KOA and obesity. We suggest conducting additional studies with a larger population sample, including other polymorphisms of the same genes in different ethnic groups, to corroborate the findings shown in this study. Key Points • We observed significant associations for obesity and primary knee osteoarthritis in the presence of the rs7903146 CC and CT genotypes.

LEPR↗

PubMed2025

Cancer spectrum in Mexican patients with the CHEK2 p.(Leu236Pro) variant: a retrospective study.

This study aimed to characterize, for the first time, the cancer spectrum associated with the most frequent pathogenic CHEK2 variant-NM_007194.4(CHEK2):c.707T > C p.(Leu236Pro)-in Mexican individuals. Although this variant is frequently detected through multi-gene panel testing, limited data on its associated cancer risks complicates genetic counseling and surveillance strategies. We retrospectively analyzed 5,759 patients who underwent multi-gene panel testing between August 2015 and August 2024 due to suspected hereditary cancer syndromes. Among them, 58 CHEK2 p.(Leu236Pro) carriers with confirmed cancer diagnoses were identified. Geographical clustering was observed, with 81% of patients originating from central Mexico, suggesting a possible founder effect. Ten distinct clinical indications for genetic testing were identified, with hereditary breast and ovarian cancer (HBOC) syndrome being the most common (74.1%). The mean age at first diagnosis among carriers was 43.8 ± 12 years, and 61.1% of them reported a family history of cancer in first- or second-degree relatives. A second or third primary cancer occurred in 20.7% of cases. Tumors were identified in 12 anatomical sites. Breast cancer predominated (67.6%, including one male case), followed by ovarian (8.1%), prostate (6.7%), gastric (4.1%), thyroid (2.7%), and endometrial (2.7%) cancers. Lymphoma, lung, sacrococcygeal bone, colorectal, and non-melanoma skin cancers each occurred in a single patient. Significant risk association was identified only for breast, ovarian, and gastric cancers. These results highlight the need for personalized surveillance, especially for breast cancer. Incorporating CHEK2 p.(Leu236Pro) into clinical decision-making tools may enhance risk assessment in the Mexican population, but larger studies are needed to refine risk estimates and to clarify the possible founder effect.

Humans↗

PubMed2026

Type 2 diabetes genetics in 125,000 admixed adults from Mexico City.

Type 2 diabetes (T2D) is a highly heritable, polygenic disease with over 600 loci identified through genome-wide association studies (GWAS). However, despite possessing unique genetic variation shaped by demographic history and admixture, Latin American populations remain markedly underrepresented in global genomic research. To address this gap, we conducted genome- and exome-wide analyses of 19,431 T2D cases and 105,611 controls from the Mexico City Prospective Study (MCPS). We identified 86 independent GWAS associations, including 21 novel signals, 15 of which replicated in external cohorts. Risk alleles at novel loci were enriched in individuals with Indigenous American ancestry. Exome analyses revealed rare and ultra-rare missense variants with substantial risk effects at HNF1A and GCK, as well as a protein-damaging variant in SLC30A8 that reduced T2D risk by 45% in carriers. Integrative analyses indicate that T2D genetic architecture in Mexico is predominantly driven by common regulatory variation acting in the endocrine pancreas. Polygenic risk scores strongly stratified T2D risk and transferred to Indigenous Mexican populations. These findings demonstrate the power of large-scale genetic discovery in diverse populations to refine disease architecture and identify loci with potential therapeutic relevance.

Journal Article↗

PubMed2026

Forensic applicability of genetic profile generation from hair roots and shafts: Integration of retrotransposon polymorphisms and morphological predictors.

Genetic profiles were successfully obtained from hair samples both directly plucked from the scalp and indirectly from personal items such as combs and hairbrushes. Additionally, 100 genetic profiles were generated from buccal swabs from all donors, allowing the calculation of population allele and genotype frequencies. Complete genetic profiles were recovered from samples containing less than 0.012 ng of total nuclear DNA. Nuclear DNA yield per hair root was highly variable, whereas hair shafts yielded up to 2 ng of total nuDNA and in some cases less than 0.1 ng. Multiple correspondence analysis (MCA) revealed that hair growth phase and the presence of a root were not significantly associated with successful profile recovery; instead, greater hair thickness and direct sampling correlated with higher success rates. In certain cases, the Insertion/Null (INNUL) markers system, InnoTyper 21, outperformed the Power Plex Fusion 6 C STR kit. For forensic purposes, using the entire hair shaft provided better profiling outcomes than using the root alone. All Insertion/Null (INNUL) markers were in Hardy-Weinberg equilibrium, except for a few loci showing minor linkage disequilibrium. These results highlight the analytical potential of INNUL markers for obtaining nuclear DNA profiles from hair, even in challenging forensic contexts.

Humans↗

PubMed2026

The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize.

Defining the genetic basis of local adaptation is a key goal of evolutionary biology and crop improvement. Theory predicts that when selective pressures follow differences in the environment, a cline will be established. Clines can be exploited to uncover adaptive variation by association of alleles with the environment. However, monotonic phenotypic change over a cline is not necessarily mirrored in the behavior of genetic variants and population structure can further complicate analysis. To study genetic and phenotypic variation across the environment, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize (Zea mays L. ssp. mays) varieties sourced from distinct agroecological zones. We evaluated the population in a common garden in Mexico and mapped tassel branching and flowering time, two traits that exhibit clinal variation. Variation in tassel branching was dominated by a single QTL with allele effects aligning to a negative elevational cline. By contrast, allele effects associated with 11 identified flowering time QTL were not consistently correlated with any one source environmental factor. Our observations support the prediction that genotype-environment association will be strongest under simple genetic architecture, although, even then, analysis in native populations may be confounded by population structure.

MAGIC↗

PubMed2026

HLA-DRB1*14 is associated with lower odds of symptomatic SARS-CoV-2 infection in Mexican individuals.

Mexico has been one of the countries most affected by the COVID-19 pandemic. Several factors can influence the susceptibility to SARS-CoV-2 infection, particularly highly polymorphic genes in the HLA system. Therefore, this pilot study analyzed the association between HLA-DRB1 genetic polymorphisms and the susceptibility and/or resistance to symptomatic SARS-CoV-2 infection in a population from the Metropolitan Area of the Valley of Mexico. Individuals with a confirmed SARS-CoV-2 infection were recruited (n = 90), as well as a seronegative control group without reported symptomatic infection (n = 60). The HLA-DRB1 locus was typed using NGS. We found a significant increase in the frequency of the HLA-DRB1*14 allele in the control group (OR = 0.37; 95% CI: 0.18-0.72; p = 0.003; pc = 0.03). These data suggest that HLA-DRB1*14, a prevalent allele in the Mexican population, is associated with a reduced risk of symptomatic SARS-CoV-2 infection in this cohort.

Humans↗

PubMed2025

Ancestry and somatic profile predict acral melanoma origin and prognosis.

Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

Journal Article↗

PubMed2026

Characterization of DPYD pharmacogenetic variation in Mexican patients with gastrointestinal malignancies.

PURPOSE: Fluoropyrimidines are among the most widely used chemotherapeutic agents for gastrointestinal malignancies, but interindividual variability in dihydropyrimidine dehydrogenase (DPD) activity, encoded by DPYD, can lead to severe or lethal toxicities. Most pharmacogenetic data on DPYD originates from European populations, limiting the applicability of current guidelines in admixed groups. METHODS: We evaluated DPYD pharmacogenetic variation and its association with fluoropyrimidine-related adverse events in Mexican patients with gastrointestinal cancers. Adverse events were prospectively assessed using CTCAE v5.0. Genotyping was performed with the Illumina Global Screening Array and analyzed using PLINK and R. RESULTS: A total of 208 patients were enrolled, and 192 samples passed genotyping quality control; 156 patients received fluoropyrimidines. Only three patients (1.5%) carried actionable DPYD variants (rs3918290, rs67376798 and rs75017182), yielding allele frequencies of 0.26%, approximately ten-fold lower than those reported in European cohorts. Genome-wide analyses did not reveal significant genotype-phenotype associations, though suggestive variants in SDK1, ZPBP, and FGF12 were observed. Pharmacodynamic analyses identified frequent variation in TYMS rs2847153 and MTHFR rs1801133, both previously associated with fluoropyrimidine toxicity. Overall, patients exhibited a predominantly Native Mexican ancestry (56.5%), which may explain the markedly low frequency of actionable DPYD alleles commonly found in European populations. CONCLUSIONS: These findings highlight the limited representation of admixed populations in pharmacogenetic research and underscore the need for population-specific data to inform safe and equitable fluoropyrimidine dosing.

Humans↗

PubMed2026

Genomic early growth mechanisms of two endangered Mexican spruces.

This study elucidated the genomic basis of family-level growth variance in the critically endangered endemic Mexican spruces Picea martinezii and P. mexicana by: (i) analyzing family- and population-level variations in seedling basal diameter and height after 12 months of growth under common garden conditions and seed weight as maternal provisioning trait; and (ii) identifying genomic loci (SNPs) associated with these traits. Despite limited sample sizes (77 and 74 families representing all known populations of both species), 32 and 10 outlier SNPs were identified yielding 17 and six annotated candidate genes in P. martinezii and P. mexicana, respectively. These genes showed contrasting multivariate associations suggesting species-specific hypothesized growth strategies at the family level: defense-oriented framework in P. martinezii and plasticity-driven response in P. mexicana. Notably, several candidate genes encode key components of growth hormone pathways, including a gibberellin-regulated protein, a cytokinin hydroxylase and the AP2-like transcription factor ANT, providing valuable insights into how maternal genetic variation corresponds to the hormonal pathways that govern cell proliferation and organ size in the progeny. Integration of these findings with the contrasting demographic histories of both species revealed that population bottlenecks enhance the detectability of growth-associated variants by reducing background genetic variation. These genomic resources provide actionable information for prioritizing conservation measures, implementing assisted gene flow to maintain adaptive potential under climate change and designing future breeding programs. With 80.9-99.6% sequence identity to conserved Picea abies homologs, these findings may extend across the genus.

Picea↗

PubMed2026

A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.

Structural variants (SVs) are increasingly recognized as key contributors to adaptive evolution, yet they remain underexplored compared with single-nucleotide variation. To understand how large-scale genomic changes shape repeated evolution, we leveraged multiple levels of sequence data across the powerful evolutionary model system of the Mexican tetra fish (Astyanax mexicanus). We constructed one of the first pangenome graphs from a naturally evolving vertebrate, enabling comprehensive discovery of SVs among 120 fish from 11 populations. We discover substantial amounts of structural variation and explore the roles of genomic biases and selection in shaping the distribution of these variants. More than 2400 high-confidence cave-specific deletions are enriched in biological pathways involved in vision, metabolism, and behavior and cluster nonrandomly in quantitative trait loci linked to cavefish traits. Additionally, 67 genes harbor unique deletions between independent cavefish lineages. These reused genes show evidence of population-specific selection (99% contain selective sweeps compared with 8%-15% in genes lacking SVs), indicating that deletions likely rose in frequency through repeated positive selection rather than drift. Together, these results reveal that recurrent deletion events have repeatedly contributed to the evolution of cave-adapted phenotypes and highlight deletions as underexplored contributors of adaptive evolution in extreme environments.

Animals↗

PubMed2024

Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle.

The Sardo Negro cattle (SN) is the only zebu cattle breed developed in Mexico. Since its development, the selection could have led to an increase in the homozygosity level in some regions of the genome and made differentiation with other cattle populations. We aimed to identify and characterize selection signatures in SN using medium-density SNP data using four approaches: 1) Runs of homozygosity (ROH) 2) Nucleotide Diversity 3) Tajima's D and 4) the Wright's fixation index (FST). A sample of 555 SN animals genotyped for 65k SNPs was used to obtain ROH segments considered regions under selection. The FST values were estimated by comparing the sample of genotyped SN animals with samples of genotyped animals from the Gir, Brahman, and Ongole breeds. Only one region mapped to 35.78-42.51 Mb on BTA6 was considered a selection signature by the ROH method. This selection signature overlapped with the lowest diversity, negative values of Tajima's D and a diversification region between SN and the other Zebu breeds by FST. We found several candidate genes (LCORL, NCAPG, and SLIT2) related to growth and other economically important productive traits in this common region. Using the FST method, different regions, such as regions on BTA8 (8:93.4-93.9 Mb), BTA11 (11:99.2-99.7), and BTA14 (14: 26.1-26.8) related to growth and milk traits also were defined as candidate selection signatures. The selective signals identified in this study reflected the direction of the selection pressure that primarily involves the increase of live weight traits in the Sardo Negro cattle breeding program.

Animals↗

PubMed2026

Evidence of genome-wide relaxed selection on mildly deleterious mutations in an ancient subterranean catfish.

About one hundred subterranean catfish species have been described, resulting from repeated colonization of cave environments by multiple surface lineages. Most cave-dwelling species are found in the Americas, in particular in South America, but a few species also live in Central and North America. Despite the availability of high-quality genome assemblies for two cave species, the Mexican blind catfish Prietella phreatophila and the Colombian blind catfish Trichomycterus rosablanca, genomic approaches to investigate genetic changes associated with subterranean life or to estimate cave colonization times remain largely unexplored. To fill this gap, we additionally sequenced the genomes of four blind and depigmented subterranean catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Two independent molecular dating methods gave congruent ages, indicating that these catfishes colonized subterranean habitats at different times, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes repeatedly and rapidly adapted to subterranean habitats. The oldest cave species, P. phreatophila, appears to have been thriving in the dark for over 3.5 million years. Moreover, a genome-wide analysis of protein-coding genes suggests weaker purifying selection on mildly deleterious mutations in this cavefish than in other catfish lineages, likely reflecting a long-term small effective population size.

cavefishes↗