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1.
Int J Obes (Lond) ; 47(6): 434-442, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36806387

RESUMO

BACKGROUND: Genome-wide association studies have shown that body mass index (BMI), an estimate of obesity, is highly polygenic. Individual variants typically have small effect sizes, making it challenging to identify unique loci in under-represented ethnic groups which lack statistical power due to their small sample size. Yet obesity is a major health disparity and is particularly prevalent in southwestern American Indians. Here, we identify and characterize a new locus for BMI that was detected by analyzing moderate associations with BMI obtained in a population-based sample of southwestern American Indians together with the well-powered GIANT dataset. METHODS: Genotypes for 10.5 million variants were tested for association with BMI in 5870 American Indians and 2600 variants that showed an association P < 10-3 in the American Indian sample were combined in a meta-analysis with the BMI data reported in GIANT (N = 240,608). The newly identified gene, NFIA-AS2 was functionally characterized, and the impact of its lead associated variant rs1777538 was studied both in-silico and in-vitro. RESULTS: Rs1777538 (T/C; C allele frequency = 0.16 in American Indians and 0.04 in GIANT, meta-analysis P = 5.0 × 10-7) exhibited a large effect in American Indians (1 kg/m2 decrease in BMI per copy of C allele). NFIA-AS2 was found to be a nuclear localized long non-coding RNA expressed in tissues pertinent to human obesity. Analysis of this variant in human brown preadipocytes showed that NFIA-AS2 transcripts carrying the C allele had increased RNA degradation compared to the T allele transcripts (half-lives = 9 h, 13 h respectively). During brown adipogenesis, NFIA-AS2 featured a stage-specific regulation of nearby gene expression where rs1777538 demonstrated an allelic difference in regulation in the mature adipocytes (the strongest difference was observed for L1TD1, P = 0.007). CONCLUSION: Our findings support a role for NFIA-AS2 in regulating pathways that impact BMI.


Assuntos
Índice de Massa Corporal , Índios Norte-Americanos , Obesidade , RNA Longo não Codificante , Humanos , Indígena Americano ou Nativo do Alasca , Estudo de Associação Genômica Ampla , Índios Norte-Americanos/genética , Fatores de Transcrição NFI/genética , Obesidade/genética , Polimorfismo de Nucleotídeo Único/genética , RNA Longo não Codificante/genética , Sudoeste dos Estados Unidos
2.
Eur J Hum Genet ; 30(10): 1159-1166, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35688891

RESUMO

Insulin-like growth factor binding protein 4 (IGFBP4) is involved in adipogenesis, and IGFBP4 null mice have decreased body fat through decreased PPAR-γ expression. In the current study, we assessed whether variation in the IGFBP4 coding region influences body mass index (BMI) in American Indians who are disproportionately affected by obesity. Whole exome sequence data from a population-based sample of 6779 American Indians with longitudinal measures of BMI were used to identify variation in IGFBP4 that associated with BMI. A novel variant that predicts a p.Ser76Thr in IGFBP4 (Thr-allele frequency = 0.02) was identified which associated with the maximum BMI measured during adulthood (BMI 39.8 kg/m2 for Thr-allele homozygotes combined with heterozygotes vs. 36.2 kg/m2 for Ser-allele homozygotes, ß = 6.7% per Thr-allele, p = 8.0 × 10-5, adjusted for age, sex, birth-year and the first five genetic principal components) and the maximum age- and sex-adjusted BMI z-score measured during childhood/adolescence (z-score 0.70 SD for Thr-allele heterozygotes vs. 0.32 SD for Ser-allele homozygotes, ß = 0.37 SD per Thr-allele, p = 8.8 × 10-6). In vitro functional studies showed that IGFBP4 with the Thr-allele (BMI-increasing) had a 55% decrease (p = 0.0007) in FOXO-induced transcriptional activity, reflecting increased activation of the PI3K/AKT pathway mediated through increased IGF signaling. Over-expression and knock-down of IGFBP4 in OP9 cells during differentiation showed that IGFBP4 upregulates adipogenesis through PPARγ, CEBPα, AGPAT2 and SREBP1 expression. We propose that this American Indian specific variant in IGFBP4 affects obesity via an increase of IGF signaling.


Assuntos
Índios Norte-Americanos , Proteína 4 de Ligação a Fator de Crescimento Semelhante à Insulina , Animais , Índice de Massa Corporal , Humanos , Índios Norte-Americanos/genética , Proteína 4 de Ligação a Fator de Crescimento Semelhante à Insulina/genética , Camundongos , Obesidade/genética , PPAR gama/genética , Fosfatidilinositol 3-Quinases/genética , Polimorfismo de Nucleotídeo Único , Proteínas Proto-Oncogênicas c-akt/genética , Indígena Americano ou Nativo do Alasca
3.
Nat Commun ; 12(1): 5942, 2021 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-34642312

RESUMO

The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.


Assuntos
Etnicidade/genética , Genoma Humano , Migração Humana/história , Índios Norte-Americanos/genética , Filogenia , Dinâmica Populacional/estatística & dados numéricos , Etnicidade/classificação , Variação Genética , Genômica/métodos , História Antiga , Humanos , Índios Norte-Americanos/classificação , México , Filogeografia
4.
J Physiol Anthropol ; 40(1): 11, 2021 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-34454619

RESUMO

BACKGROUND: Metabolic syndrome (MetS) is a complex cluster of risk factors, considered as a polygenic and multifactorial entity. The objective of this study was to determine the association of rs9939609-FTO polymorphism and MetS components in adult women of Mayan communities of Chiapas. METHODS: In a cross-sectional study, sociodemographic, anthropometric, clinical, and biochemical data were obtained from 291 adult women from three regions of Chiapas, Mexico. The prevalence of MetS and the allele and genotype frequencies of the rs9939609-FTO were estimated. Multivariate logistic regression models were used to assess the association of the single nucleotide polymorphism (SNP) with each of the MetS components. RESULTS: The MetS prevalence was 60%. We found a statistically significant association between rs9939609-FTO and hyperglycemia in the dominant model (OR 2.6; 95% CI 1.3-5.3; p = 0.007). CONCLUSIONS: Women from Mayan communities of Chiapas presented a high prevalence of MetS and a relevant association of the FTO variant with hyperglycemia. This is the first study carried out in these Mayan indigenous communities from Chiapas.


Assuntos
Dioxigenase FTO Dependente de alfa-Cetoglutarato/genética , Índios Norte-Americanos , Síndrome Metabólica , Polimorfismo de Nucleotídeo Único/genética , Adulto , Estudos Transversais , Feminino , Humanos , Índios Norte-Americanos/genética , Índios Norte-Americanos/estatística & dados numéricos , Síndrome Metabólica/epidemiologia , Síndrome Metabólica/genética , México/epidemiologia , Pessoa de Meia-Idade
5.
Mol Biol Rep ; 48(9): 6343-6348, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34383246

RESUMO

BACKGROUND: MATE2-K is an efflux transporter protein of organic cation expressed mainly in the kidney and encoded by the SLC47A2 gene. Different variants of this gene have shown an impact on the pharmacokinetics of various drugs, including metformin, which represents one of the most widely used drugs in treating type 2 diabetes. The SLC47A2 gene variants have been scarcely studied in Mexican populations, especially in Native American groups. For this reason, we analyzed the distribution of the variants rs12943590, rs35263947, and rs9900497 within the SLC47A2 gene in 173 Native Americans (Tarahumara, Huichol, Maya, Puerépecha) and 182 Mestizos (admixed) individuals from Mexico. METHODS AND RESULTS: Genotypes were determined through TaqMan probes (qPCR). The Hardy-Weinberg agreement was confirmed for all three SLC47A2 gene variants in all the Mexican populations analyzed. When worldwide populations were included for comparison purposes, for alleles and genotypes a relative interpopulation homogeneity was observed for rs35263947 (T allele; range 23.3-51.1%) and rs9900497 (T allele; range 18.6-40.9%). Conversely, heterogeneity was evident for rs12943590 (A allele, range 22.1-59.1%), where the most differentiated population was the Huichol, with high frequencies of the risk genotype associated with decreased response to metformin treatment (A/A = 40.9%). CONCLUSIONS: Although the SLC47A2 gene variants allow predicting favorable response to the metformin treatment in Mexican populations, the probable high frequency of ineffectiveness should be discarded in Huichols.


Assuntos
Indígena Americano ou Nativo do Alasca/genética , Genética Populacional/métodos , Índios Norte-Americanos/genética , Proteínas de Transporte de Cátions Orgânicos/genética , Polimorfismo de Nucleotídeo Único , Alelos , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/genética , Frequência do Gene , Haplótipos , Voluntários Saudáveis , Humanos , Hipoglicemiantes/uso terapêutico , Metformina/uso terapêutico , México/etnologia , Plantas Medicinais , Resultado do Tratamento
6.
Biomed Pharmacother ; 142: 112009, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34388523

RESUMO

Genetic factors that affect variability in metformin response have been poorly studied in the Latin American population, despite its being the initial drug therapy for type 2 diabetes, one of the most prevalent diseases in that region. Metformin pharmacokinetics is carried out by members of the membrane transporters superfamily (SLCs), being the multidrug and toxin extrusion protein 1 (MATE1), one of the most studied. Some genetic variants in MATE1 have been associated with reduced in vitro metformin transport. They include rs77474263 p.[L125F], a variant present at a frequency of 13.8% in Latin Americans, but rare worldwide (less than 1%). Using exome sequence data and TaqMan genotyping, we revealed that the Mexican population has the highest frequency of this variant: 16% in Mestizos and 27% in Amerindians, suggesting a possible Amerindian origin. To elucidate the metformin pharmacogenetics, a children cohort was genotyped, allowing us to describe, for the first time, a MATE1 rs77474263 TT homozygous individual. An additive effect of the L125F variant was observed on blood metformin accumulation, revealing the highest metformin and lactate serum levels in the TT homozygote, and intermediate metformin values in the heterozygotes. Moreover, a molecular dynamics analysis suggested that the genetic variant effect on metformin efflux could be due to a decreased protein permeability. We conclude that pharmacogenetics could be useful in enhancing metformin pharmacovigilance in populations having a high frequency of the risk genotype, especially considering that these populations also have a higher susceptibility to the diseases for which metformin is the first-choice drug.


Assuntos
Hipoglicemiantes/farmacocinética , Metformina/farmacocinética , Proteínas de Transporte de Cátions Orgânicos/genética , Farmacogenética , Adolescente , Adulto , Criança , Estudos de Coortes , Feminino , Variação Genética , Genótipo , Humanos , Índios Norte-Americanos/genética , Ácido Láctico/sangue , Masculino , México , Simulação de Dinâmica Molecular
7.
Commun Biol ; 4(1): 918, 2021 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-34321601

RESUMO

Long chain polyunsaturated fatty acids (LC-PUFAs) have critical signaling roles that regulate dyslipidemia and inflammation. Genetic variation in the FADS gene cluster accounts for a large portion of interindividual differences in circulating and tissue levels of LC-PUFAs, with the genotypes most strongly predictive of low LC-PUFA levels at strikingly higher frequencies in Amerind ancestry populations. In this study, we examined relationships between genetic ancestry and FADS variation in 1102 Hispanic American participants from the Multi-Ethnic Study of Atherosclerosis. We demonstrate strong negative associations between Amerind genetic ancestry and LC-PUFA levels. The FADS rs174537 single nucleotide polymorphism (SNP) accounted for much of the AI ancestry effect on LC-PUFAs, especially for low levels of n-3 LC-PUFAs. Rs174537 was also strongly associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides (TGs) and E-selectin in MESA Hispanics. Our study demonstrates that Amerind ancestry provides a useful and readily available tool to identify individuals most likely to have FADS-related n-3 LC-PUFA deficiencies and associated cardiovascular risk.


Assuntos
Ácidos Graxos Dessaturases/genética , Ácidos Graxos Ômega-3/deficiência , Variação Genética , Hispânico ou Latino/genética , Índios Norte-Americanos/genética , Família Multigênica , Ácidos Graxos Dessaturases/metabolismo , Hereditariedade , Humanos , Estudos Longitudinais , Estados Unidos
8.
Lipids Health Dis ; 20(1): 70, 2021 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-34256778

RESUMO

BACKGROUND: LCAT (lecithin-cholesterol acyltransferase) deficiency is characterized by two distinct phenotypes, familial LCAT deficiency (FLD) and Fish Eye disease (FED). This is the first systematic review evaluating the ethnic distribution of LCAT deficiency, with particular emphasis on Latin America and the discussion of three Mexican-Mestizo probands. METHODS: A systematic review was conducted following the PRISMA (Preferred Reporting Items for Systematic review and Meta-Analysis) Statement in Pubmed and SciELO. Articles which described subjects with LCAT deficiency syndromes and an assessment of the ethnic group to which the subject pertained, were included. RESULTS: The systematic review revealed 215 cases (154 FLD, 41 FED and 20 unclassified) pertaining to 33 ethnic/racial groups. There was no association between genetic alteration and ethnicity. The mean age of diagnosis was 42 ± 16.5 years, with fish eye disease identified later than familial LCAT deficiency (55 ± 13.8 vs. 41 ± 14.7 years respectively). The prevalence of premature coronary heart disease was significantly greater in FED vs. FLD. In Latin America, 48 cases of LCAT deficiency have been published from six countries (Argentina (1 unclassified), Brazil (38 FLD), Chile (1 FLD), Columbia (1 FLD), Ecuador (1 FLD) and Mexico (4 FLD, 1 FED and 1 unclassified). Of the Mexican probands, one showed a novel LCAT mutation. CONCLUSIONS: The systematic review shows that LCAT deficiency syndromes are clinically and genetically heterogeneous. No association was confirmed between ethnicity and LCAT mutation. There was a significantly greater risk of premature coronary artery disease in fish eye disease compared to familial LCAT deficiency. In FLD, the emphasis should be in preventing both cardiovascular disease and the progression of renal disease, while in FED, cardiovascular risk management should be the priority. The LCAT mutations discussed in this article are the only ones reported in the Mexican- Amerindian population.


Assuntos
Etnicidade/genética , Deficiência da Lecitina Colesterol Aciltransferase/etnologia , Etnicidade/estatística & dados numéricos , Predisposição Genética para Doença/etnologia , Predisposição Genética para Doença/genética , Humanos , Índios Norte-Americanos/genética , Índios Norte-Americanos/estatística & dados numéricos , Deficiência da Lecitina Colesterol Aciltransferase/genética , México , Fosfatidilcolina-Esterol O-Aciltransferase/genética , Grupos Raciais/genética , Grupos Raciais/estatística & dados numéricos
9.
J Appl Genet ; 62(3): 445-453, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33880741

RESUMO

The peopling of the Americas by Native Americans occurred in 4 waves of which the last was Nadene language speakers of whom Athabaskans are the largest group. As the Europeans were entering the Southwestern states of the USA, Athabaskan hunting-gathering tribes were migrating South from Canada along the Rocky Mountains and undergoing potential bottlenecks reflected in autosomal recessive diseases shared by Apaches and Navajos. About 300 years ago, the Navajo developing a sedentary culture learned from Pueblo Indians while the Apache remained hunter-gathers. Although most of the tribe was rounded up and forced to relocate to Bosque Redondo, the adult breeding population was large enough to prevent a genetic bottleneck. However, some Navajo underwent further population bottlenecks while hiding from the brutal US Army action (under Kit Carson's guidance). This led to an increased frequency of other autosomal recessive diseases. Recent advances in population genetics, pathophysiology of the diseases, and social/ethical issues concerning their study are reviewed.


Assuntos
Doenças Genéticas Inatas/etnologia , Índios Norte-Americanos , Adulto , Genes Recessivos , Genética Populacional , Humanos , Índios Norte-Americanos/genética , Idioma , Sudoeste dos Estados Unidos
10.
Clin Transl Sci ; 14(5): 1713-1718, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-33650294

RESUMO

To compare etonogestrel pharmacokinetic and pharmacodynamic outcomes by both self-reported race/ethnicity and genetically determined ancestry among contraceptive implant users. We conducted a secondary analysis of our parent pharmacogenomic study of 350 implant users. We genotyped these reproductive-aged (18-45 years) women for 88 ancestry-informative single nucleotide polymorphisms. We then assigned each participant a proportion value for African (AFR), European (EUR), and Indigenous American (AMR) ancestry based on reference population data. We correlated genetic ancestry with self-reported race/ethnicity and utilized genetic ancestry proportion values as variables for previously performed association analyses with serum etonogestrel concentrations and progestin-related side effects (e.g., bothersome bleeding and subjective weight gain). We successfully estimated genetically determined ancestry for 332 participants. EUR, AFR, and AMR ancestry were each highly correlated with self-reported White/non-Hispanic race (r = 0.64, p = 4.14 × 10-40 ), Black/African American race (r = 0.88, p = 1.36 × 10-107 ), and Hispanic/Latina ethnicity (r = 0.68, p = 4.03 × 10-47 ), respectively. Neither genetically determined ancestry nor self-reported race/ethnicity were significantly associated with serum etonogestrel concentrations. AFR ancestry and self-reported Black race had similar associations with reporting monthly periods (odds ratio [OR] 2.18, p = 0.09 vs. OR 2.22, p = 0.02) and having received treatment for bothersome bleeding (OR 5.19, p = 0.005 vs. OR 4.73, p = 2.0 × 10-4 ). In multivariable logistic regression for subjective weight gain, AMR ancestry dropped out of the model in preference for self-reported Hispanic/Latina ethnicity. We found no new associations between genetically determined ancestry and contraceptive implant pharmacodynamics/pharmacokinetics. Self-reported race/ethnicity were strong surrogates for genetically determined ancestry among this population of contraceptive implant users. Our data suggest that self-reported race/ethnicity, capturing societal and cultural aspects, remain important to the investigation of progestin-related side effects.


Assuntos
Contraceptivos Hormonais/farmacocinética , Desogestrel/efeitos adversos , Farmacogenética/métodos , Adolescente , Adulto , População Negra/genética , Contraceptivos Hormonais/administração & dosagem , Contraceptivos Hormonais/efeitos adversos , Desogestrel/administração & dosagem , Desogestrel/farmacocinética , Implantes de Medicamento , Estudos de Viabilidade , Feminino , Humanos , Índios Norte-Americanos/genética , Variantes Farmacogenômicos , Polimorfismo de Nucleotídeo Único , Autorrelato/estatística & dados numéricos , Hemorragia Uterina/induzido quimicamente , Hemorragia Uterina/genética , Aumento de Peso/efeitos dos fármacos , Aumento de Peso/genética , População Branca/genética , Adulto Jovem
11.
Am J Phys Anthropol ; 175(1): 238-250, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33522608

RESUMO

OBJECTIVE: To analyze the genetic origin, relationships, structure, and admixture in Mayan Native American groups from Guatemala and Mexico based on 15 autosomal short tandem repeats (STRs) loci commonly used in human identification (HID). METHODS: We genotyped 513 unrelated Mayan samples from Guatemala based on 15 STR loci (AmpFlSTR® Identifiler kit). Moreover, we included 4408 genotypes previously reported, as following: Mayas from Guatemala and Mexico (n = 1666) and from Latin American, European, and African (n = 2742) populations. Forensic parameters, genetic distances, admixture, and population structure were assessed. RESULTS: Forensic parameters of the 15 STRs in different Mayan groups from Guatemala were reported. Low (Fst = 0.78%; p = 0.000) and non-significant differentiation (Fst = 1.8%; p = 0.108) were observed in Mayas from Guatemala and Mexico, respectively. The relative homogeneity observed among Mayan groups supported theories of extensive pre-Columbian gene flow and trade throughout the Mayan Empire. The distribution of the three Native American ancestries among these Mayan groups did not support the presumable Guatemalan origin of Tojolabal and Lacandon people (South, Mexico). The nonsignificant differentiation between Ladinos and Mayas suggests a relative panmixia in Guatemala. Mestizos from southeastern Mexico and Guatemala constitute a core of Native American ancestry in Latin America related to the Mayan Empire in Central America. CONCLUSIONS: The higher European admixture and homogeneity in Mexican Mayas of the Yucatan Peninsula suggest more intensive post-Columbian gene flow in this region than in Guatemalan Mayas.


Assuntos
Variação Genética/genética , Índios Centro-Americanos/genética , Índios Norte-Americanos/genética , Repetições de Microssatélites/genética , Antropologia Física , Genética Forense , Fluxo Gênico/genética , Genética Populacional , Guatemala , Humanos , México , População Branca/genética
12.
Clin Transl Sci ; 14(4): 1292-1302, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33503331

RESUMO

The frequencies of genetic variants in the CYP3A4 and CYP3A5 genes differ greatly across global populations, leading to profound differences in the metabolic activity of these enzymes and resulting drug metabolism rates, with important consequences for therapeutic safety and efficacy. Yet, the impact of genetic variants on enzyme activity are incompletely described, particularly in American Indian and Alaska Native (AIAN) populations. To characterize genetic variation in CYP3A4 and CYP3A5 and its effect on enzyme activity, we partnered with AIAN people living in two regions of Alaska: Yup'ik Alaska Native people living in the Yukon-Kuskokwim Delta region of rural southwest Alaska and AIAN people receiving care at the Southcentral Foundation in Anchorage, Alaska. We identified low frequencies of novel and known variation in CYP3A4 and CYP3A5, including low frequencies of the CYP3A4*1G and CYP3A5*1 variants, and linkage disequilibrium patterns that differed from those we previously identified in an American Indian population in western Montana. We also identified increased activity of the CYP3A4*1G allele in vitro and in vivo. We demonstrated that the CYP3A4*1G allele confers increased protein content in human lymphoblastoid cells and both increased protein content and increased activity in human liver microsomes. We confirmed enhanced CYP3A4-mediated 4ß-vitamin D hydroxylation activity in Yup'ik people with the CYP3A4*1G allele. AIAN people in Alaska and Montana who carry the CYP3A4*1G allele-coupled with low frequency of the functional CYP3A5*1 variant-may metabolize CYP3A substrates more rapidly than people with the reference CYP3A4 allele.


Assuntos
Nativos do Alasca/genética , Citocromo P-450 CYP3A/metabolismo , Índios Norte-Americanos/genética , Xenobióticos/metabolismo , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Linhagem Celular Tumoral , Criança , Pré-Escolar , Citocromo P-450 CYP3A/genética , Ensaios Enzimáticos , Feminino , Humanos , Lactente , Recém-Nascido , Desequilíbrio de Ligação , Masculino , Microssomos Hepáticos , Pessoa de Meia-Idade , Testes Farmacogenômicos , Variantes Farmacogenômicos , Polimorfismo de Nucleotídeo Único , Adulto Jovem
13.
Addict Biol ; 26(1): e12877, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32027075

RESUMO

Alcohol and other substance use disorders (AUD and SUD) are complex diseases that are postulated to have a polygenic inheritance and are often comorbid with other disorders. The comorbidities may arise partially through genetic pleiotropy. Identification of specific gene variants accounting for large parts of the variance in these disorders has yet to be accomplished. We describe a flexible strategy that takes a variant-trait association database and determines if a subset of disease/straits are potentially pleiotropic with the disorder under study. We demonstrate its usage in a study of use disorders in two independent cohorts: alcohol, stimulants, cannabis (CUD), and multi-substance use disorders (MSUD) in American Indians (AI) and AUD and CUD in Mexican Americans (MA). Using a machine learning method with variants in GWAS catalog, we identified 229 to 246 pleiotropic variants for AI and 153 to 160 for MA for each SUD. Inflammation was the most enriched for MSUD and AUD in AIs. Neurological disorder was the most significantly enriched for CUD in both cohorts, and for AUD and stimulants in AIs. Of the select pleiotropic genes shared among substances-cohorts, multiple biological pathways implicated in SUD and other psychiatric disorders were enriched, including neurotrophic factors, immune responses, extracellular matrix, and circadian regulation. Shared pleiotropic genes were significantly up-regulated in brain regions playing important roles in SUD, down-regulated in esophagus mucosa, and differentially regulated in adrenal gland. This study fills a gap for pleiotropy detection in understudied admixed populations and identifies pleiotropic variants that may be potential targets of interest for SUD.


Assuntos
Índios Norte-Americanos/genética , Americanos Mexicanos/genética , Transtornos Relacionados ao Uso de Substâncias/genética , Adulto , Alcoolismo/genética , Feminino , Pleiotropia Genética , Estudo de Associação Genômica Ampla , Humanos , Aprendizado de Máquina , Masculino
14.
J Hum Genet ; 66(3): 327-332, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32920600

RESUMO

The Mexican-Mestizo population arose following European contact with the Americas due to the admixture of principally Spaniards, Native Americans, and Africans around 500 years ago. Because the paternal lineage distribution of the Mexican population has been poorly investigated, this study inferred the haplogroups of ten populations based on 1859 haplotypes (Y-STR data) using two haplogroup predictor programs. In the Mexican population sample, we found predominantly European ancestry (50.1%), followed by Native American (32.5%), Eurasian (13.4%), African (2.1%), East African-South Eurasian (1.3%), and Asian (0.6%) ancestries. In general, our results support a contrary north-to-south gradient throughout the Mexican territory of European and Native-American ancestries, respectively. Moreover, the presence of West-European R1b and Sub-Saharan African E1b1a haplogroups agrees with historical and genetic data of gene flow during the European conquest. This study represents the effort to analyze these paternal lineages on a large scale by taking advantage of Y-STR haplotype data to determine the distribution and ancestry proportions in this country.


Assuntos
Cromossomos Humanos Y/genética , Haplótipos/genética , África/etnologia , Ásia/etnologia , População Negra/genética , Simulação por Computador , Europa (Continente)/etnologia , Fluxo Gênico , Frequência do Gene , Genética Populacional , Geografia Médica , Humanos , Índios Norte-Americanos/genética , Masculino , Casamento , México , Herança Paterna/genética , Projetos Piloto , Polimorfismo de Nucleotídeo Único , Espanha/etnologia , População Branca/genética
15.
Cancer ; 126(24): 5222-5229, 2020 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-32926435

RESUMO

BACKGROUND: Breast cancer is one of the most common causes of cancer mortality for all women, including American Indian and Alaska Native (AI/AN) women. The use of the 21-gene recurrence score (RS) appears to be predictive of the benefit of chemotherapy for women with estrogen receptor (ER)-positive breast cancer. The objective of the current study was to compare RS testing between AI/AN and non-Hispanic White (NHW) women with breast cancer. METHODS: The Surveillance, Epidemiology, and End Results program was used to identify women with ER-positive breast cancer from 2004 through 2015. Multivariable logistic regression was used to evaluate factors associated with RS use, with high-risk RS, and with chemotherapy use among those with a high-risk RS. RESULTS: A total of 363,387 NHW patients and 1951 AI/AN patients with ER-positive breast cancer were identified. AI/AN women were found to be less likely to undergo RS testing and, when tested, were more likely to have a high-risk RS. In the multivariable logistic regression analysis, AI/AN women were found to be significantly more likely to have a high-risk RS (odds ratio,1.28; 95% confidence interval, 1.01-1.66). Among untested women, chemotherapy use was higher for AI/AN women; however, the use of chemotherapy was not found to be significantly different between the groups with a high-risk RS. Using Cox proportional hazards models, AI/AN race was found to be significantly associated with worse overall survival. CONCLUSIONS: AI/AN women were less likely to undergo RS testing compared with NHW women and were more likely to have a high-risk RS. Reversing the disparity in genomic expression assay testing is critical to ensure guideline-based breast cancer treatment and improve survival rates for AI/AN women with breast cancer.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama/tratamento farmacológico , Quimioterapia Adjuvante/métodos , Perfilação da Expressão Gênica/métodos , Índios Norte-Americanos/genética , Adulto , Idoso , Nativos do Alasca/genética , Neoplasias da Mama/genética , Feminino , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Modelos Logísticos , Pessoa de Meia-Idade , Guias de Prática Clínica como Assunto , Programa de SEER , Análise de Sobrevida , Resultado do Tratamento , Adulto Jovem
18.
Am J Hum Genet ; 107(2): 251-264, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32640185

RESUMO

Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.


Assuntos
Exoma/genética , Predisposição Genética para Doença/genética , Índios Norte-Americanos/genética , Polimorfismo de Nucleotídeo Único/genética , Alelos , Índice de Massa Corporal , Feminino , Genética Populacional/métodos , Estudo de Associação Genômica Ampla/métodos , Humanos , Masculino , Fenótipo , Sudoeste dos Estados Unidos
20.
Pharmacogenomics J ; 20(6): 845-856, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32483200

RESUMO

Genetic and nongenetic factors may contribute to lamotrigine (LTG) plasma concentration variability among patients. We simultaneously investigated the association of UGT1A1, UGT1A4, UGT2B7, ABCB1, ABCG2, and SLC22A1 variants, as well as antiepileptic drug co-treatment, on LTG plasma concentration in 97 Mexican Mestizo (MM) patients with epilepsy. UGT1A4*1b was associated with lower LTG dose-corrected concentrations. Patients with the UGT2B7-161T allele were treated with 21.22% higher LTG daily dose than those with CC genotype. Two novel UGT1A4 variants (c.526A>T; p.Thr185= and c.496T>C; p.Ser166Leu) were identified in one patient. Patients treated with LTG + valproic acid (VPA) showed higher LTG plasma concentration than patients did on LTG monotherapy or LTG + inducer. Despite the numerous drug-metabolizing enzymes and transporter genetic variants analyzed, our results revealed that co-treatment with VPA was the most significant factor influencing LTG plasma concentration, followed by UGT1A4*1b, and that patients carrying UGT2B7 c.-161T required higher LTG daily doses. These data provide valuable information for the clinical use of LTG in MM patients with epilepsy.


Assuntos
Anticonvulsivantes/sangue , Epilepsia/sangue , Epilepsia/genética , Índios Norte-Americanos/genética , Lamotrigina/sangue , Variantes Farmacogenômicos/genética , Adolescente , Adulto , Idoso , Anticonvulsivantes/administração & dosagem , Quimioterapia Combinada , Epilepsia/tratamento farmacológico , Epilepsia/epidemiologia , Feminino , Humanos , Lamotrigina/administração & dosagem , Masculino , México/epidemiologia , Pessoa de Meia-Idade , Adulto Jovem
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