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Am J Hum Genet ; 108(10): 1836-1851, 2021 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-34582791


Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.

Asma/epidemiologia , Biomarcadores/metabolismo , Dermatite Atópica/epidemiologia , Leucócitos/patologia , Polimorfismo de Nucleotídeo Único , Doença Pulmonar Obstrutiva Crônica/epidemiologia , Locos de Características Quantitativas , Asma/genética , Asma/metabolismo , Asma/patologia , Dermatite Atópica/genética , Dermatite Atópica/metabolismo , Dermatite Atópica/patologia , Predisposição Genética para Doença , Genoma Humano , Estudo de Associação Genômica Ampla , Humanos , National Heart, Lung, and Blood Institute (U.S.) , Fenótipo , Prognóstico , Proteoma/análise , Proteoma/metabolismo , Doença Pulmonar Obstrutiva Crônica/genética , Doença Pulmonar Obstrutiva Crônica/metabolismo , Doença Pulmonar Obstrutiva Crônica/patologia , Reino Unido/epidemiologia , Estados Unidos/epidemiologia , Sequenciamento Completo do Genoma
Blood Cells Mol Dis ; 86: 102504, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32949984


In a recent clinical trial, the metabolite l-glutamine was shown to reduce painful crises in sickle cell disease (SCD) patients. To support this observation and identify other metabolites implicated in SCD clinical heterogeneity, we profiled 129 metabolites in the plasma of 705 SCD patients. We tested correlations between metabolite levels and six SCD-related complications (painful crises, cholecystectomy, retinopathy, leg ulcer, priapism, aseptic necrosis) or estimated glomerular filtration rate (eGFR), and used Mendelian randomization (MR) to assess causality. We found a potential causal relationship between l-glutamine levels and painful crises (N = 1278, odds ratio (OR) [95% confidence interval] = 0.68 [0.52-0.89], P = 0.0048). In two smaller SCD cohorts (N = 299 and 406), the protective effect of l-glutamine was observed (OR = 0.82 [0.50-1.34]), although the MR result was not significant (P = 0.44). We identified 66 significant correlations between the levels of other metabolites and SCD-related complications or eGFR. We tested these correlations for causality using MR analyses and found no significant causal relationship. The baseline levels of quinolinic acid were associated with prospectively ascertained survival in SCD patients, and this effect was dependent on eGFR. Metabolomics provide a promising approach to prioritize small molecules that may serve as biomarkers or drug targets in SCD.

Anemia Falciforme/sangue , Anemia Falciforme/complicações , Glutamina/sangue , Dor/etiologia , Adolescente , Adulto , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Análise da Randomização Mendeliana , Pessoa de Meia-Idade , Dor/sangue , Adulto Jovem
Blood Cells Mol Dis ; 65: 60-65, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28552477


Deoxy-hemoglobin S polymerization into rigid fibers is the direct cause of the clinical sequelae observed in sickle cell disease (SCD). The rate of polymerization of sickle hemoglobin is determined primarily by intracellular hemoglobin concentration, itself dependent on the amount of sickle hemoglobin and on red blood cell (RBC) volume. Dense, dehydrated RBC (DRBC) are observed in SCD patients, and their number correlates with hemolytic parameters and complications such as renal dysfunction, leg ulcers and priapism. To identify new genes involved in RBC hydration in SCD, we performed the first genome-wide association study for DRBC in 374 sickle cell anemia (HbSS) patients. We did not find genome-wide significant results, indicating that variants that modulate DRBC have modest-to-weak effects. A secondary analysis demonstrated a nominal association (P=0.003) between DRBC in SCD patients and a variant associated with mean corpuscular hemoglobin concentration (MCHC) in non-anemic individuals. This intronic variant controls the expression of ATP2B4, the main calcium pump in erythrocytes. Our study highlights ATP2B4 as a promising target for modulation of RBC hydration in SCD patients.

Anemia Falciforme/sangue , Anemia Falciforme/genética , Eritrócitos/metabolismo , Estudo de Associação Genômica Ampla , Hemoglobina Falciforme/genética , Hemoglobina Falciforme/metabolismo , Adulto , Alelos , Índices de Eritrócitos , Feminino , Variação Genética , Genótipo , Humanos , Masculino , ATPases Transportadoras de Cálcio da Membrana Plasmática/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Adulto Jovem
Nat Genet ; 49(4): 625-634, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28218758


Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

Variação Genética/genética , Mutagênese/genética , Locos de Características Quantitativas/genética , Elementos Reguladores de Transcrição/genética , Células Cultivadas , DNA Intergênico/genética , Dosagem de Genes/genética , Estudo de Associação Genômica Ampla/métodos , Células HEK293 , Humanos