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1.
Cell ; 185(23): 4256-4258, 2022 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-36288728

RESUMEN

Genome-wide association studies (GWASs) can require immense sample sizes to identify variants associated with human health across the frequency spectrum. As the Global Biobank Meta-analysis Initiative (GBMI), Zhou et al. describe a collaborative network across 23 biobanks and 2.2 million participants to address challenges of underrepresentation of diversity in genomic research.


Asunto(s)
Estudio de Asociación del Genoma Completo , Genómica , Humanos , Bancos de Muestras Biológicas
2.
Cell ; 184(8): 2068-2083.e11, 2021 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-33861964

RESUMEN

Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations. Here, we propose a framework for repurposing data from electronic health records (EHRs) in concert with genomic data to explore the demographic ties that can impact disease burdens. Using data from a diverse biobank in New York City, we identified 17 communities sharing recent genetic ancestry. We observed 1,177 health outcomes that were statistically associated with a specific group and demonstrated significant differences in the segregation of genetic variants contributing to Mendelian diseases. We also demonstrated that fine-scale population structure can impact the prediction of complex disease risk within groups. This work reinforces the utility of linking genomic data to EHRs and provides a framework toward fine-scale monitoring of population health.


Asunto(s)
Etnicidad/genética , Salud Poblacional , Bases de Datos Genéticas , Registros Electrónicos de Salud , Genómica , Humanos , Autoinforme
3.
Nat Rev Genet ; 25(11): 768-784, 2024 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-38806721

RESUMEN

Gene-environment interactions (G × E), the interplay of genetic variation with environmental factors, have a pivotal impact on human complex traits and diseases. Statistically, G × E can be assessed by determining the deviation from expectation of predictive models based solely on the phenotypic effects of genetics or environmental exposures. Despite the unprecedented, widespread and diverse use of G × E analytical frameworks, heterogeneity in their application and reporting hinders their applicability in public health. In this Review, we discuss study design considerations as well as G × E analytical frameworks to assess polygenic liability dependent on the environment, to identify specific genetic variants exhibiting G × E, and to characterize environmental context for these dynamics. We conclude with recommendations to address the most common challenges and pitfalls in the conceptualization, methodology and reporting of G × E studies, as well as future directions.


Asunto(s)
Interacción Gen-Ambiente , Herencia Multifactorial , Humanos , Herencia Multifactorial/genética , Variación Genética , Predisposición Genética a la Enfermedad , Fenotipo , Modelos Genéticos
4.
Nature ; 632(8023): 122-130, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39020179

RESUMEN

Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity1-5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project6, spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, which mirrored the variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-expression quantitative trait loci (eQTLs) and cis-splicing QTLs (sQTLs), respectively). We identified more than 15,000 putatively causal eQTLs and more than 16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1,310 eQTLs and 1,657 sQTLs that are largely private to underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations. Moreover, the apparent 'population-specific' effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands our understanding of human gene expression diversity and provides an inclusive resource for studying the evolution and function of human genomes.


Asunto(s)
Regulación de la Expresión Génica , Variación Genética , Genoma Humano , Internacionalidad , Sitios de Carácter Cuantitativo , Empalme del ARN , Grupos Raciales , Femenino , Humanos , Masculino , Artefactos , Sesgo , Línea Celular , Estudios de Cohortes , Conjuntos de Datos como Asunto , Epigenómica , Evolución Molecular , Regulación de la Expresión Génica/genética , Genética de Población , Genoma Humano/genética , Linfocitos/citología , Linfocitos/metabolismo , Sitios de Carácter Cuantitativo/genética , Grupos Raciales/genética , Empalme del ARN/genética , Análisis de Secuencia de ARN
5.
Nature ; 622(7984): 775-783, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37821706

RESUMEN

Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories and complex trait architectures remain hidden owing to insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution and inference of identity-by-descent segments, we inferred ancestral population sizes across Mesoamerican regions over time, unravelling Indigenous, colonial and postcolonial demographic dynamics2-6. We observed variation in runs of homozygosity among genomic regions with different ancestries reflecting distinct demographic histories and, in turn, different distributions of rare deleterious variants. We conducted genome-wide association studies (GWAS) for 22 complex traits and found that several traits are better predicted using the Mexican Biobank GWAS compared to the UK Biobank GWAS7,8. We identified genetic and environmental factors associating with trait variation, such as the length of the genome in runs of homozygosity as a predictor for body mass index, triglycerides, glucose and height. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide.


Asunto(s)
Bancos de Muestras Biológicas , Genética Médica , Genoma Humano , Genómica , Hispánicos o Latinos , Humanos , Glucemia/genética , Glucemia/metabolismo , Estatura/genética , Índice de Masa Corporal , Interacción Gen-Ambiente , Marcadores Genéticos/genética , Estudio de Asociación del Genoma Completo , Hispánicos o Latinos/clasificación , Hispánicos o Latinos/genética , Homocigoto , México , Fenotipo , Triglicéridos/sangre , Triglicéridos/genética , Reino Unido , Genoma Humano/genética
6.
Nat Rev Genet ; 23(11): 665-679, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35581355

RESUMEN

Genome-wide association studies using large-scale genome and exome sequencing data have become increasingly valuable in identifying associations between genetic variants and disease, transforming basic research and translational medicine. However, this progress has not been equally shared across all people and conditions, in part due to limited resources. Leveraging publicly available sequencing data as external common controls, rather than sequencing new controls for every study, can better allocate resources by augmenting control sample sizes or providing controls where none existed. However, common control studies must be carefully planned and executed as even small differences in sample ascertainment and processing can result in substantial bias. Here, we discuss challenges and opportunities for the robust use of common controls in high-throughput sequencing studies, including study design, quality control and statistical approaches. Thoughtful generation and use of large and valuable genetic sequencing data sets will enable investigation of a broader and more representative set of conditions, environments and genetic ancestries than otherwise possible.


Asunto(s)
Exoma , Estudio de Asociación del Genoma Completo , Exoma/genética , Predisposición Genética a la Enfermedad , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Secuenciación del Exoma
7.
Nature ; 591(7849): 211-219, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33692554

RESUMEN

Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative benchmarking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.


Asunto(s)
Predisposición Genética a la Enfermedad , Genética Médica/normas , Herencia Multifactorial/genética , Humanos , Reproducibilidad de los Resultados , Medición de Riesgo/normas
8.
Trends Genet ; 39(11): 813-815, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37524625

RESUMEN

Polygenic scores (PGSs) aggregate the effects of variants across the genome to estimate genetic liability, but have lower performance in external study populations. A new study by Ding et al. has applied a novel framework to estimate the individual-level predictive accuracy of PGSs, and demonstrates that performance reduction occurs linearly with genetic distance.

9.
Am J Hum Genet ; 110(2): 336-348, 2023 02 02.
Artículo en Inglés | MEDLINE | ID: mdl-36649706

RESUMEN

Genome-wide association studies (GWASs) have been performed to identify host genetic factors for a range of phenotypes, including for infectious diseases. The use of population-based common control subjects from biobanks and extensive consortia is a valuable resource to increase sample sizes in the identification of associated loci with minimal additional expense. Non-differential misclassification of the outcome has been reported when the control subjects are not well characterized, which often attenuates the true effect size. However, for infectious diseases the comparison of affected subjects to population-based common control subjects regardless of pathogen exposure can also result in selection bias. Through simulated comparisons of pathogen-exposed cases and population-based common control subjects, we demonstrate that not accounting for pathogen exposure can result in biased effect estimates and spurious genome-wide significant signals. Further, the observed association can be distorted depending upon strength of the association between a locus and pathogen exposure and the prevalence of pathogen exposure. We also used a real data example from the hepatitis C virus (HCV) genetic consortium comparing HCV spontaneous clearance to persistent infection with both well-characterized control subjects and population-based common control subjects from the UK Biobank. We find biased effect estimates for known HCV clearance-associated loci and potentially spurious HCV clearance associations. These findings suggest that the choice of control subjects is especially important for infectious diseases or outcomes that are conditional upon environmental exposures.


Asunto(s)
Enfermedades Transmisibles , Hepatitis C , Humanos , Estudio de Asociación del Genoma Completo , Enfermedades Transmisibles/genética , Fenotipo , Hepatitis C/genética , Hepacivirus
10.
Nature ; 583(7817): 572-577, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32641827

RESUMEN

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1-6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around AD 1200) contemporaneous with the settlement of remote Oceania13-15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.


Asunto(s)
Flujo Génico/genética , Genoma Humano/genética , Migración Humana/historia , Indígenas Centroamericanos/genética , Indígenas Sudamericanos/genética , Islas , Nativos de Hawái y Otras Islas del Pacífico/genética , América Central/etnología , Colombia/etnología , Europa (Continente)/etnología , Genética de Población , Historia Medieval , Humanos , Polimorfismo de Nucleótido Simple/genética , Polinesia , América del Sur/etnología , Factores de Tiempo
11.
Am J Hum Genet ; 109(2): 299-310, 2022 02 03.
Artículo en Inglés | MEDLINE | ID: mdl-35090584

RESUMEN

Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQß1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQß1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQß1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQß1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQß1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.


Asunto(s)
Cadenas beta de HLA-DQ/genética , Hepacivirus/patogenicidad , Hepatitis C/genética , Interacciones Huésped-Patógeno/genética , Polimorfismo de Nucleótido Simple , Enfermedad Aguda , Alelos , Sustitución de Aminoácidos , Población Negra , Femenino , Expresión Génica , Estudio de Asociación del Genoma Completo , Genotipo , Cadenas beta de HLA-DQ/inmunología , Hepacivirus/crecimiento & desarrollo , Hepacivirus/inmunología , Hepatitis C/etnología , Hepatitis C/inmunología , Hepatitis C/virología , Interacciones Huésped-Patógeno/inmunología , Humanos , Leucina/inmunología , Leucina/metabolismo , Masculino , Prolina/inmunología , Prolina/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/inmunología , Remisión Espontánea , Población Blanca
12.
Am J Hum Genet ; 109(6): 1117-1139, 2022 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-35588731

RESUMEN

Preeclampsia is a multi-organ complication of pregnancy characterized by sudden hypertension and proteinuria that is among the leading causes of preterm delivery and maternal morbidity and mortality worldwide. The heterogeneity of preeclampsia poses a challenge for understanding its etiology and molecular basis. Intriguingly, risk for the condition increases in high-altitude regions such as the Peruvian Andes. To investigate the genetic basis of preeclampsia in a population living at high altitude, we characterized genome-wide variation in a cohort of preeclamptic and healthy Andean families (n = 883) from Puno, Peru, a city located above 3,800 meters of altitude. Our study collected genomic DNA and medical records from case-control trios and duos in local hospital settings. We generated genotype data for 439,314 SNPs, determined global ancestry patterns, and mapped associations between genetic variants and preeclampsia phenotypes. A transmission disequilibrium test (TDT) revealed variants near genes of biological importance for placental and blood vessel function. The top candidate region was found on chromosome 13 of the fetal genome and contains clotting factor genes PROZ, F7, and F10. These findings provide supporting evidence that common genetic variants within coagulation genes play an important role in preeclampsia. A selection scan revealed a potential adaptive signal around the ADAM12 locus on chromosome 10, implicated in pregnancy disorders. Our discovery of an association in a functional pathway relevant to pregnancy physiology in an understudied population of Native American origin demonstrates the increased power of family-based study design and underscores the importance of conducting genetic research in diverse populations.


Asunto(s)
Preeclampsia , Altitud , Factores de Coagulación Sanguínea , Proteínas Sanguíneas/genética , Estudios de Casos y Controles , Factor VII/genética , Factor X/genética , Femenino , Humanos , Perú/epidemiología , Placenta , Preeclampsia/epidemiología , Preeclampsia/genética , Embarazo
13.
Am J Hum Genet ; 109(4): 669-679, 2022 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-35263625

RESUMEN

One mechanism by which genetic factors influence complex traits and diseases is altering gene expression. Direct measurement of gene expression in relevant tissues is rarely tenable; however, genetically regulated gene expression (GReX) can be estimated using prediction models derived from large multi-omic datasets. These approaches have led to the discovery of many gene-trait associations, but whether models derived from predominantly European ancestry (EA) reference panels can map novel associations in ancestrally diverse populations remains unclear. We applied PrediXcan to impute GReX in 51,520 ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) participants (35% African American, 45% Hispanic/Latino, 10% Asian, and 7% Hawaiian) across 25 key cardiometabolic traits and relevant tissues to identify 102 novel associations. We then compared associations in PAGE to those in a random subset of 50,000 White British participants from UK Biobank (UKBB50k) for height and body mass index (BMI). We identified 517 associations across 47 tissues in PAGE but not UKBB50k, demonstrating the importance of diverse samples in identifying trait-associated GReX. We observed that variants used in PrediXcan models were either more or less differentiated across continental-level populations than matched-control variants depending on the specific population reflecting sampling bias. Additionally, variants from identified genes specific to either PAGE or UKBB50k analyses were more ancestrally differentiated than those in genes detected in both analyses, underlining the value of population-specific discoveries. This suggests that while EA-derived transcriptome imputation models can identify new associations in non-EA populations, models derived from closely matched reference panels may yield further insights. Our findings call for more diversity in reference datasets of tissue-specific gene expression.


Asunto(s)
Enfermedades Cardiovasculares , Estudio de Asociación del Genoma Completo , Predisposición Genética a la Enfermedad , Humanos , Estilo de Vida , Polimorfismo de Nucleótido Simple , Transcriptoma
14.
Nature ; 570(7762): 514-518, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-31217584

RESUMEN

Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.


Asunto(s)
Pueblo Asiatico/genética , Población Negra/genética , Estudio de Asociación del Genoma Completo/métodos , Hispánicos o Latinos/genética , Grupos Minoritarios , Herencia Multifactorial/genética , Salud de la Mujer , Estatura/genética , Estudios de Cohortes , Femenino , Genética Médica/métodos , Equidad en Salud/tendencias , Disparidades en el Estado de Salud , Humanos , Masculino , Estados Unidos
15.
J Infect Dis ; 228(8): 979-989, 2023 10 18.
Artículo en Inglés | MEDLINE | ID: mdl-36967705

RESUMEN

BACKGROUND: Diarrhea is the second leading cause of death in children under 5 years old worldwide. Known diarrhea risk factors include sanitation, water sources, and pathogens but do not fully explain the heterogeneity in frequency and duration of diarrhea in young children. We evaluated the role of host genetics in diarrhea. METHODS: Using 3 well-characterized birth cohorts from an impoverished area of Dhaka, Bangladesh, we compared infants with no diarrhea in the first year of life to those with an abundance, measured by either frequency or duration. We performed a genome-wide association analysis for each cohort under an additive model and then meta-analyzed across the studies. RESULTS: For diarrhea frequency, we identified 2 genome-wide significant loci associated with not having any diarrhea, on chromosome 21 within the noncoding RNA AP000959 (C allele odds ratio [OR] = 0.31, P = 4.01 × 10-8), and on chromosome 8 within SAMD12 (T allele OR = 0.35, P = 4.74 × 10-7). For duration of diarrhea, we identified 2 loci associated with no diarrhea, including the same locus on chromosome 21 (C allele OR = 0.31, P = 1.59 × 10-8) and another locus on chromosome 17 near WSCD1 (C allele OR = 0.35, P = 1.09 × 10-7). CONCLUSIONS: These loci are in or near genes involved in enteric nervous system development and intestinal inflammation and may be potential targets for diarrhea therapeutics.


Asunto(s)
Diarrea , Estudio de Asociación del Genoma Completo , Niño , Humanos , Lactante , Preescolar , Bangladesh/epidemiología , Factores de Riesgo , Diarrea/epidemiología , Diarrea/genética , Alelos
16.
Mol Biol Evol ; 39(4)2022 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-35460423

RESUMEN

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.


Asunto(s)
Genética de Población , Genoma Humano , Genómica/métodos , Hispánicos o Latinos/genética , Humanos , Polimorfismo de Nucleótido Simple/genética , Población Blanca/genética
17.
Diabetologia ; 65(3): 477-489, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-34951656

RESUMEN

AIMS/HYPOTHESIS: Type 2 diabetes is a growing global public health challenge. Investigating quantitative traits, including fasting glucose, fasting insulin and HbA1c, that serve as early markers of type 2 diabetes progression may lead to a deeper understanding of the genetic aetiology of type 2 diabetes development. Previous genome-wide association studies (GWAS) have identified over 500 loci associated with type 2 diabetes, glycaemic traits and insulin-related traits. However, most of these findings were based only on populations of European ancestry. To address this research gap, we examined the genetic basis of fasting glucose, fasting insulin and HbA1c in participants of the diverse Population Architecture using Genomics and Epidemiology (PAGE) Study. METHODS: We conducted a GWAS of fasting glucose (n = 52,267), fasting insulin (n = 48,395) and HbA1c (n = 23,357) in participants without diabetes from the diverse PAGE Study (23% self-reported African American, 46% Hispanic/Latino, 40% European, 4% Asian, 3% Native Hawaiian, 0.8% Native American), performing transethnic and population-specific GWAS meta-analyses, followed by fine-mapping to identify and characterise novel loci and independent secondary signals in known loci. RESULTS: Four novel associations were identified (p < 5 × 10-9), including three loci associated with fasting insulin, and a novel, low-frequency African American-specific locus associated with fasting glucose. Additionally, seven secondary signals were identified, including novel independent secondary signals for fasting glucose at the known GCK locus and for fasting insulin at the known PPP1R3B locus in transethnic meta-analysis. CONCLUSIONS/INTERPRETATION: Our findings provide new insights into the genetic architecture of glycaemic traits and highlight the continued importance of conducting genetic studies in diverse populations. DATA AVAILABILITY: Full summary statistics from each of the population-specific and transethnic results are available at NHGRI-EBI GWAS catalog ( https://www.ebi.ac.uk/gwas/downloads/summary-statistics ).


Asunto(s)
Diabetes Mellitus Tipo 2 , Estudio de Asociación del Genoma Completo , Glucemia/genética , Diabetes Mellitus Tipo 2/genética , Estudio de Asociación del Genoma Completo/métodos , Genómica , Humanos , Polimorfismo de Nucleótido Simple/genética
18.
Annu Rev Genomics Hum Genet ; 20: 181-200, 2019 08 31.
Artículo en Inglés | MEDLINE | ID: mdl-30978304

RESUMEN

The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.


Asunto(s)
Etnicidad/genética , Variación Genética , Genética Humana/tendencias , Metagenómica/tendencias , Epidemiología Molecular/tendencias , Grupos Raciales/genética , Sesgo , Bases de Datos Factuales , Genoma Humano , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Fenotipo
19.
Circ Res ; 126(12): 1816-1840, 2020 06 05.
Artículo en Inglés | MEDLINE | ID: mdl-32496918

RESUMEN

Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.


Asunto(s)
Estudio de Asociación del Genoma Completo/métodos , Síndrome Metabólico/genética , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo/normas , Humanos , Síndrome Metabólico/epidemiología , Polimorfismo Genético
20.
J Infect Dis ; 223(12): 2090-2098, 2021 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-33119750

RESUMEN

BACKGROUND: Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. METHODS: To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group. RESULTS: A male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor. CONCLUSIONS: These novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.


Asunto(s)
Hepatitis C , Factores Sexuales , Femenino , Estudio de Asociación del Genoma Completo , Hepacivirus/genética , Hepatitis C/genética , Humanos , Masculino , Polimorfismo de Nucleótido Simple , Proteínas Ribosómicas/genética , Septinas/genética , Carga Viral
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