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1.
Arterioscler Thromb Vasc Biol ; 44(4): 969-975, 2024 04.
Artículo en Inglés | MEDLINE | ID: mdl-38385288

RESUMEN

BACKGROUND: Preeclampsia is a hypertensive disorder of pregnancy characterized by widespread vascular inflammation. It occurs frequently in pregnancy, often without known risk factors, and has high rates of maternal and fetal morbidity and mortality. Identification of biomarkers that predict preeclampsia and its cardiovascular sequelae before clinical onset, or even before pregnancy, is a critical unmet need for the prevention of adverse pregnancy outcomes. METHODS: We explored differences in cardiovascular proteomics (Olink Explore 384) in 256 diverse pregnant persons across 2 centers (26% Hispanic, 21% Black). RESULTS: We identified significant differences in plasma abundance of markers associated with angiogenesis, blood pressure, cell adhesion, inflammation, and metabolism between individuals delivering with preeclampsia and controls, some of which have not been widely described previously and are not represented in the preeclampsia placental transcriptome. While we observed a broadly similar pattern in early (<34 weeks) versus late (≥34 weeks) preeclampsia, several proteins related to hemodynamic stress, hemostasis, and immune response appeared to be more highly dysregulated in early preeclampsia relative to late preeclampsia. CONCLUSIONS: These results demonstrate the value of performing targeted proteomics using a panel of cardiovascular biomarkers to identify biomarkers relevant to preeclampsia pathophysiology and highlight the need for larger multiomic studies to define modifiable pathways of surveillance and intervention upstream to preeclampsia diagnosis.


Asunto(s)
Enfermedades Cardiovasculares , Preeclampsia , Embarazo , Femenino , Humanos , Preeclampsia/diagnóstico , Placenta , Resultado del Embarazo , Biomarcadores , Inflamación/complicaciones , Enfermedades Cardiovasculares/diagnóstico , Enfermedades Cardiovasculares/complicaciones , Factor de Crecimiento Placentario
2.
Nat Med ; 30(2): 480-487, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38374346

RESUMEN

Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.


Asunto(s)
Enfermedad Crónica , Puntuación de Riesgo Genético , Salud Poblacional , Adulto , Niño , Humanos , Comunicación , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Factores de Riesgo , Estados Unidos
3.
medRxiv ; 2024 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-38352394

RESUMEN

Metabolic dysfunction-associated steatotic liver disease (MASLD) prevalence is increasing in parallel with an obesity pandemic, calling for novel strategies for prevention and treatment. We defined a circulating proteome of human MASLD across ≈7000 proteins in ≈5000 individuals from diverse, at-risk populations across the metabolic health spectrum, demonstrating reproducible diagnostic performance and specifying both known and novel metabolic pathways relevant to MASLD (central carbon and amino acid metabolism, hepatocyte regeneration, inflammation, fibrosis, insulin sensitivity). A parsimonious proteomic signature of MASLD was associated with a protection from MASLD and its related multi-system metabolic consequences in >26000 free-living individuals, with an additive effect to polygenic risk. The MASLD proteome was encoded by genes that demonstrated transcriptional enrichment in liver, with spatial transcriptional activity in areas of steatosis in human liver biopsy and dynamicity for select targets in human liver across stages of steatosis. We replicated several top relations from proteomics and spatial tissue transcriptomics in a humanized "liver-on-a-chip" model of MASLD, highlighting the power of a full translational approach to discovery in MASLD. Collectively, these results underscore utility of blood-based proteomics as a dynamic "liquid biopsy" of human liver relevant to clinical biomarker and mechanistic applications.

4.
J Clin Transl Sci ; 7(1): e154, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37528943

RESUMEN

Minority populations are largely absent from clinical research trials. The neglect of these populations has become increasingly apparent, with escalating cancer burdens and chronic disease. The challenges to recruitment of minorities in the United States are multiple including trust or lack thereof. Keys to successful recruitment are responding to community issues, its history, beliefs, and its social and economic pressures. The strategy we have used in many low-income, sometimes remote, communities is to recruit staff from the same community and train them in the required basic research methods. They are the first line of communication. After our arrival in the Texas Rio Grande Valley in 2001, we applied these principles learned over years of global research, to studies of chronic diseases. Beginning in 2004, we recruited and trained a team of local women who enrolled in a cohort of over five thousand Mexican Americans from randomly selected households. This cohort is being followed, and the team has remained, acquiring not only advanced skills (ultrasound, FibroScan, retinal photos, measures of cognition, etc.) but capacity to derive key health information. Currently, we are participating in multiple funded studies, including an NIH clinical trial, liver disease, obesity, and diabetes using multiomics aimed at developing precision medicine approaches to chronic disease prevention and treatment.

5.
Cardiovasc Diabetol ; 22(1): 231, 2023 08 31.
Artículo en Inglés | MEDLINE | ID: mdl-37653519

RESUMEN

BACKGROUND: Adipokines are hormones secreted from adipose tissue and are associated with cardiometabolic diseases (CMD). Functional differences between adipokines (leptin, adiponectin, and resistin) are known, but inconsistently reported associations with CMD and lack of studies in Hispanic populations are research gaps. We investigated the relationship between subclinical atherosclerosis and multiple adipokine measures. METHODS: Cross-sectional data from the Cameron County Hispanic Cohort (N = 624; mean age = 50; Female = 70.8%) were utilized to assess associations between adipokines [continuous measures of adiponectin, leptin, resistin, leptin-to-adiponectin ratio (LAR), and adiponectin-resistin index (ARI)] and early atherosclerosis [carotid-intima media thickness (cIMT)]. We adjusted for sex, age, body mass index (BMI), smoking status, cytokines, fasting blood glucose levels, blood pressure, lipid levels, and medication usage in the fully adjusted linear regression model. We conducted sexes-combined and sex-stratified analyses to account for sex-specificity and additionally tested whether stratification of participants by their metabolic status (metabolically elevated risk for CMD as defined by having two or more of the following conditions: hypertension, dyslipidemia, insulin resistance, and inflammation vs. not) influenced the relationship between adipokines and cIMT. RESULTS: In the fully adjusted analyses, adiponectin, leptin, and LAR displayed significant interaction by sex (p < 0.1). Male-specific associations were between cIMT and LAR [ß(SE) = 0.060 (0.016), p = 2.52 × 10-4], and female-specific associations were between cIMT and adiponectin [ß(SE) = 0.010 (0.005), p = 0.043] and ARI [ß(SE) = - 0.011 (0.005), p = 0.036]. When stratified by metabolic health status, the male-specific positive association between LAR and cIMT was more evident among the metabolically healthy group [ß(SE) = 0.127 (0.015), p = 4.70 × 10-10] (p for interaction by metabolic health < 0.1). However, the female-specific associations between adiponectin and cIMT and ARI and cIMT were observed only among the metabolically elevated risk group [ß(SE) = 0.014 (0.005), p = 0.012 for adiponectin; ß(SE) = - 0.015 (0.006), p = 0.013 for ARI; p for interaction by metabolic health < 0.1]. CONCLUSION: Associations between adipokines and cIMT were sex-specific, and metabolic health status influenced the relationships between adipokines and cIMT. These heterogeneities by sex and metabolic health affirm the complex relationships between adipokines and atherosclerosis.


Asunto(s)
Adipoquinas , Aterosclerosis , Femenino , Masculino , Humanos , Persona de Mediana Edad , Leptina , Resistina , Adiponectina , Grosor Intima-Media Carotídeo , Estudios Transversales , Hispánicos o Latinos
6.
medRxiv ; 2023 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-37333246

RESUMEN

Polygenic risk scores (PRS) have improved in predictive performance supporting their use in clinical practice. Reduced predictive performance of PRS in diverse populations can exacerbate existing health disparities. The NHGRI-funded eMERGE Network is returning a PRS-based genome-informed risk assessment to 25,000 diverse adults and children. We assessed PRS performance, medical actionability, and potential clinical utility for 23 conditions. Standardized metrics were considered in the selection process with additional consideration given to strength of evidence in African and Hispanic populations. Ten conditions were selected with a range of high-risk thresholds: atrial fibrillation, breast cancer, chronic kidney disease, coronary heart disease, hypercholesterolemia, prostate cancer, asthma, type 1 diabetes, obesity, and type 2 diabetes. We developed a pipeline for clinical PRS implementation, used genetic ancestry to calibrate PRS mean and variance, created a framework for regulatory compliance, and developed a PRS clinical report. eMERGE's experience informs the infrastructure needed to implement PRS-based implementation in diverse clinical settings.

7.
Front Genet ; 13: 995488, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36386790

RESUMEN

Objective: Mexican Americans are disproportionally affected by non-alcoholic fatty liver disease (NAFLD), liver fibrosis and hepatocellular carcinoma. Noninvasive means to identify those in this population at high risk for these diseases are urgently needed. Approach: The Cameron County Hispanic Cohort (CCHC) is a population-based cohort with high rates of obesity (51%), type 2 diabetes (28%) and NAFLD (49%). In a subgroup of 564 CCHC subjects, we evaluated 339 genetic variants previously reported to be associated with liver injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in United Kingdom and Japanese cohorts. Results: Association was confirmed for 86 variants. Among them, 27 had higher effect allele frequency in the CCHC than in the United Kingdom and Japanese cohorts, and 16 had stronger associations with AST and ALT than rs738409 (PNPLA3). These included rs17710008 (MYCT1), rs2519093 (ABO), rs1801690 (APOH), rs10409243 (S1PR2), rs1800759 (LOC100507053) and rs2491441 (RGL1), which were also associated with steatosis and/or liver fibrosis measured by vibration-controlled transient elastography. Main contributors to advanced fibrosis risk were rs11240351 (CNTN2), rs1800759 (LOC100507053), rs738409 (PNPLA3) and rs1801690 (APOH), with advanced fibrosis detected in 37.5% of subjects with 3 of these 4 variants [AOR = 11.6 (95% CI) = 3.8-35.3]. AST- and ALT-associated variants implicated distinct pathways (ethanol and galactose degradation versus antigen presentation and B cell development). Finally, 8 variants, including rs62292950 (DNAJC13), were associated with gut microbiome changes. Conclusion: These genotype-phenotype findings may have utility in risk modeling and disease prevention in this high-risk population.

8.
Nat Genet ; 54(4): 412-436, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35379992

RESUMEN

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele.


Asunto(s)
Enfermedad de Alzheimer , Disfunción Cognitiva , Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/patología , Disfunción Cognitiva/psicología , Estudio de Asociación del Genoma Completo , Humanos , Proteínas tau/genética
9.
Hepatology ; 75(4): 955-967, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-34633706

RESUMEN

BACKGROUND AND AIMS: Hispanics are disproportionately affected by NAFLD, liver fibrosis, cirrhosis, and HCC. Preventive strategies and noninvasive means to identify those in this population at high risk for liver fibrosis, are urgently needed. We aimed to characterize the gut microbiome signatures and related biological functions associated with liver fibrosis in Hispanics and identify environmental and genetic factors affecting them. APPROACH AND RESULTS: Subjects of the population-based Cameron County Hispanic Cohort (CCHC; n = 217) were screened by vibration-controlled transient elastography (FibroScan). Among them, 144 (66.7%) had steatosis and 28 (13.0%) had liver fibrosis. The gut microbiome of subjects with liver fibrosis was enriched with immunogenic commensals (e.g., Prevotella copri, Holdemanella, Clostridiaceae 1) and depleted of Bacteroides caccae, Parabacteroides distasonis, Enterobacter, and Marinifilaceae. The liver fibrosis-associated metagenome was characterized by changes in the urea cycle, L-citrulline biosynthesis and creatinine degradation pathways, and altered synthesis of B vitamins and lipoic acid. These metagenomic changes strongly correlated with the depletion of Parabacteroides distasonis and enrichment of Prevotella and Holdemanella. Liver fibrosis was also associated with depletion of bacterial pathways related to L-fucose biosynthesis. Alcohol consumption, even moderate, was associated with high Prevotella abundance. The single-nucleotide polymorphisms rs3769502 and rs7573751 in the NCK adaptor protein 2 (NCK2) gene positively associated with high Prevotella abundance. CONCLUSION: Hispanics with liver fibrosis display microbiome profiles and associated functional changes that may promote oxidative stress and a proinflammatory environment. These microbiome signatures, together with NCK2 polymorphisms, may have utility in risk modeling and disease prevention in this high-risk population.


Asunto(s)
Carcinoma Hepatocelular , Microbioma Gastrointestinal , Neoplasias Hepáticas , Enfermedad del Hígado Graso no Alcohólico , Bacteroidetes , Carcinoma Hepatocelular/complicaciones , Microbioma Gastrointestinal/genética , Hispánicos o Latinos/genética , Humanos , Cirrosis Hepática/complicaciones , Neoplasias Hepáticas/complicaciones , Enfermedad del Hígado Graso no Alcohólico/complicaciones
10.
Am J Hum Genet ; 108(1): 194-201, 2021 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-33357513

RESUMEN

Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.


Asunto(s)
COVID-19/complicaciones , COVID-19/genética , Interacciones Huésped-Patógeno/genética , Neumonía Viral/complicaciones , Neumonía Viral/genética , Bronquitis/genética , COVID-19/patología , COVID-19/fisiopatología , Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Bases de Datos Genéticas , Registros Electrónicos de Salud , Femenino , Estudio de Asociación del Genoma Completo , Genotipo , Hemoglobinas/genética , Humanos , Pacientes Internos , Desequilibrio de Ligamiento , Masculino , Pacientes Ambulatorios , Neumonía Viral/patología , Neumonía Viral/fisiopatología , Polimorfismo de Nucleótido Simple/genética , Análisis de Componente Principal , Enfermedad Pulmonar Obstructiva Crónica/genética , Reproducibilidad de los Resultados , Reino Unido
11.
Hum Genet ; 137(9): 689-703, 2018 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-30046887

RESUMEN

Tooth agenesis (TA), the failure of development of one or more permanent teeth, is a common craniofacial abnormality observed in different world populations. The genetic etiology of TA is heterogeneous; more than a dozen genes have been associated with isolated or nonsyndromic TA, and more than 80 genes with syndromic forms. In this study, we applied whole exome sequencing (WES) to identify candidate genes contributing to TA in four Turkish families. Likely pathogenic variants with a low allele frequency in the general population were identified in four disease-associated genes, including two distinct variants in TSPEAR, associated with syndromic and isolated TA in one family each; a variant in LAMB3 associated with syndromic TA in one family; and a variant in BCOR plus a disease-associated WNT10A variant in one family with syndromic TA. With the notable exception of WNT10A (Tooth agenesis, selective, 4, MIM #150400), the genotype-phenotype relationships described in the present cohort represent an expansion of the clinical spectrum associated with these genes: TSPEAR (Deafness, autosomal recessive 98, MIM #614861), LAMB3 (Amelogenesis imperfecta, type IA, MIM #104530; Epidermolysis bullosa, junctional, MIMs #226700 and #226650), and BCOR (Microphthalmia, syndromic 2, MIM #300166). We provide evidence supporting the candidacy of these genes with TA, and propose TSPEAR as a novel nonsyndromic TA gene. Our data also suggest potential multilocus genomic variation, or mutational burden, in a single family, involving the BCOR and WNT10A loci, underscoring the complexity of the genotype-phenotype relationship in the common complex trait of TA.


Asunto(s)
Anodoncia/genética , Moléculas de Adhesión Celular/genética , Marcadores Genéticos , Mutación , Proteínas/genética , Proteínas Proto-Oncogénicas/genética , Proteínas Represoras/genética , Proteínas Wnt/genética , Anodoncia/epidemiología , Anodoncia/patología , Niño , Preescolar , Femenino , Humanos , Masculino , Linaje , Fenotipo , Turquía/epidemiología , Kalinina
12.
Am J Respir Cell Mol Biol ; 58(3): 391-401, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29077507

RESUMEN

Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single ethnic groups, and a large proportion of the heritability remains unexplained. The apnea-hypopnea index (AHI) is a commonly used quantitative measure characterizing OSA severity. Because OSA differs by sex, and the pathophysiology of obstructive events differ in rapid eye movement (REM) and non-REM (NREM) sleep, we hypothesized that additional genetic association signals would be identified by analyzing the NREM/REM-specific AHI and by conducting sex-specific analyses in multiethnic samples. We performed genome-wide association tests for up to 19,733 participants of African, Asian, European, and Hispanic/Latino American ancestry in 7 studies. We identified rs12936587 on chromosome 17 as a possible quantitative trait locus for NREM AHI in men (N = 6,737; P = 1.7 × 10-8) but not in women (P = 0.77). The association with NREM AHI was replicated in a physiological research study (N = 67; P = 0.047). This locus overlapping the RAI1 gene and encompassing genes PEMT1, SREBF1, and RASD1 was previously reported to be associated with coronary artery disease, lipid metabolism, and implicated in Potocki-Lupski syndrome and Smith-Magenis syndrome, which are characterized by abnormal sleep phenotypes. We also identified gene-by-sex interactions in suggestive association regions, suggesting that genetic variants for AHI appear to vary by sex, consistent with the clinical observations of strong sexual dimorphism.


Asunto(s)
Estudio de Asociación del Genoma Completo , Sitios de Carácter Cuantitativo/genética , Apnea Obstructiva del Sueño/genética , Sueño REM/fisiología , Factores de Transcripción/genética , Adulto , Anciano , Femenino , Humanos , Masculino , Persona de Mediana Edad , Fosfatidiletanolamina N-Metiltransferasa/genética , Caracteres Sexuales , Proteína 1 de Unión a los Elementos Reguladores de Esteroles/genética , Transactivadores , Proteínas ras/genética
13.
Sci Rep ; 7(1): 17075, 2017 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-29213071

RESUMEN

QT interval prolongation is a heritable risk factor for ventricular arrhythmias and can predispose to sudden death. Most genome-wide association studies (GWAS) of QT were performed in European ancestral populations, leaving other groups uncharacterized. Herein we present the first QT GWAS of Hispanic/Latinos using data on 15,997 participants from four studies. Study-specific summary results of the association between 1000 Genomes Project (1000G) imputed SNPs and electrocardiographically measured QT were combined using fixed-effects meta-analysis. We identified 41 genome-wide significant SNPs that mapped to 13 previously identified QT loci. Conditional analyses distinguished six secondary signals at NOS1AP (n = 2), ATP1B1 (n = 2), SCN5A (n = 1), and KCNQ1 (n = 1). Comparison of linkage disequilibrium patterns between the 13 lead SNPs and six secondary signals with previously reported index SNPs in 1000G super populations suggested that the SCN5A and KCNE1 lead SNPs were potentially novel and population-specific. Finally, of the 42 suggestively associated loci, AJAP1 was suggestively associated with QT in a prior East Asian GWAS; in contrast BVES and CAP2 murine knockouts caused cardiac conduction defects. Our results indicate that whereas the same loci influence QT across populations, population-specific variation exists, motivating future trans-ethnic and ancestrally diverse QT GWAS.


Asunto(s)
Electrocardiografía , Estudio de Asociación del Genoma Completo , Hispánicos o Latinos/genética , Síndrome de QT Prolongado/patología , Sitios Genéticos , Genotipo , Humanos , Canal de Potasio KCNQ1/genética , Desequilibrio de Ligamiento , Síndrome de QT Prolongado/etnología , Síndrome de QT Prolongado/genética , Canal de Sodio Activado por Voltaje NAV1.5/genética , Polimorfismo de Nucleótido Simple , ATPasa Intercambiadora de Sodio-Potasio/genética
14.
Am J Hum Genet ; 98(6): 1146-1158, 2016 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-27259050

RESUMEN

Ataxia-pancytopenia (AP) syndrome is characterized by cerebellar ataxia, variable hematologic cytopenias, and predisposition to marrow failure and myeloid leukemia, sometimes associated with monosomy 7. Here, in the four-generation family UW-AP, linkage analysis revealed four regions that provided the maximal LOD scores possible, one of which was in a commonly microdeleted chromosome 7q region. Exome sequencing identified a missense mutation (c.2640C>A, p.His880Gln) in the sterile alpha motif domain containing 9-like gene (SAMD9L) that completely cosegregated with disease. By targeted sequencing of SAMD9L, we subsequently identified a different missense mutation (c.3587G>C, p.Cys1196Ser) in affected members of the first described family with AP syndrome, Li-AP. Neither variant is reported in the public databases, both affect highly conserved amino acid residues, and both are predicted to be damaging. With time in culture, lymphoblastic cell lines (LCLs) from two affected individuals in family UW-AP exhibited copy-neutral loss of heterozygosity for large portions of the long arm of chromosome 7, resulting in retention of only the wild-type SAMD9L allele. Newly established LCLs from both individuals demonstrated the same phenomenon. In addition, targeted capture and sequencing of SAMD9L in uncultured blood DNA from both individuals showed bias toward the wild-type allele. These observations indicate in vivo hematopoietic mosaicism. The hematopoietic cytopenias that characterize AP syndrome and the selective advantage for clones that have lost the mutant allele support the postulated role of SAMD9L in the regulation of cell proliferation. Furthermore, we show that AP syndrome is distinct from the dyskeratoses congenita telomeropathies, with which it shares some clinical characteristics.


Asunto(s)
Ataxia Cerebelosa/genética , Aberraciones Cromosómicas , Mutación Missense/genética , Pancitopenia/genética , Proteínas/genética , Adolescente , Adulto , Ataxia Cerebelosa/patología , Niño , Cromosomas Humanos Par 7/genética , Exoma/genética , Femenino , Ligamiento Genético , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Péptidos y Proteínas de Señalización Intracelular , Pérdida de Heterocigocidad , Masculino , Persona de Mediana Edad , Pancitopenia/patología , Linaje , Proteínas Supresoras de Tumor/genética , Adulto Joven
15.
Hum Mol Genet ; 25(10): 2070-2081, 2016 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-26911676

RESUMEN

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci.


Asunto(s)
Mapeo Cromosómico , Diabetes Mellitus Tipo 2/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Negro o Afroamericano/genética , Alelos , Pueblo Asiatico/genética , Inhibidor p16 de la Quinasa Dependiente de Ciclina , Inhibidor p18 de las Quinasas Dependientes de la Ciclina/genética , Diabetes Mellitus Tipo 2/patología , Femenino , Humanos , Canal de Potasio KCNQ1/genética , Desequilibrio de Ligamiento , Masculino , Polimorfismo de Nucleótido Simple , Proteínas de Unión al ARN/genética , Elementos Reguladores de la Transcripción/genética , Población Blanca/genética , ARNt Metiltransferasas/genética
16.
Hum Mutat ; 35(7): 824-7, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-24753205

RESUMEN

Severe congenital neutropenia (SCN) is a rare hematopoietic disorder, with estimated incidence of 1 in 200,000 individuals of European descent, many cases of which are inherited in an autosomal dominant pattern. Despite the fact that several causal genes have been identified, the genetic basis for >30% of cases remains unknown. We report a five-generation family segregating a novel single nucleotide variant (SNV) in TCIRG1. There is perfect cosegregation of the SNV with congenital neutropenia in this family; all 11 affected, but none of the unaffected, individuals carry this novel SNV. Western blot analysis show reduced levels of TCIRG1 protein in affected individuals, compared to healthy controls. Two unrelated patients with SCN, identified by independent investigators, are heterozygous for different, rare, highly conserved, coding variants in TCIRG1.


Asunto(s)
Neutropenia/congénito , ATPasas de Translocación de Protón Vacuolares/genética , Síndromes Congénitos de Insuficiencia de la Médula Ósea , Análisis Mutacional de ADN , Heterocigoto , Humanos , Mutación , Neutropenia/diagnóstico , Neutropenia/genética , Neutropenia/metabolismo , Linaje , ATPasas de Translocación de Protón Vacuolares/metabolismo
17.
Am J Hum Genet ; 92(1): 137-43, 2013 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-23273567

RESUMEN

Opsismodysplasia is a rare, autosomal-recessive skeletal dysplasia characterized by short stature, characteristic facial features, and in some cases severe renal phosphate wasting. We used linkage analysis and whole-genome sequencing of a consanguineous trio to discover that mutations in inositol polyphosphate phosphatase-like 1 (INPPL1) cause opsismodysplasia with or without renal phosphate wasting. Evaluation of 12 families with opsismodysplasia revealed that INPPL1 mutations explain ~60% of cases overall, including both of the families in our cohort with more than one affected child and 50% of the simplex cases.


Asunto(s)
Mutación , Osteocondrodisplasias/genética , Monoéster Fosfórico Hidrolasas/genética , Niño , Preescolar , Femenino , Genoma Humano , Humanos , Lactante , Recién Nacido , Masculino , Fosfatidilinositol-3,4,5-Trifosfato 5-Fosfatasas
18.
Nat Genet ; 43(10): 1022-5, 2011 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-21874000

RESUMEN

Because only a small fraction of asbestos-exposed individuals develop malignant mesothelioma, and because mesothelioma clustering is observed in some families, we searched for genetic predisposing factors. We discovered germline mutations in the gene encoding BRCA1 associated protein-1 (BAP1) in two families with a high incidence of mesothelioma, and we observed somatic alterations affecting BAP1 in familial mesotheliomas, indicating biallelic inactivation. In addition to mesothelioma, some BAP1 mutation carriers developed uveal melanoma. We also found germline BAP1 mutations in 2 of 26 sporadic mesotheliomas; both individuals with mutant BAP1 were previously diagnosed with uveal melanoma. We also observed somatic truncating BAP1 mutations and aberrant BAP1 expression in sporadic mesotheliomas without germline mutations. These results identify a BAP1-related cancer syndrome that is characterized by mesothelioma and uveal melanoma. We hypothesize that other cancers may also be involved and that mesothelioma predominates upon asbestos exposure. These findings will help to identify individuals at high risk of mesothelioma who could be targeted for early intervention.


Asunto(s)
Mutación de Línea Germinal , Mesotelioma/genética , Neoplasias Pleurales/genética , Proteínas Supresoras de Tumor/genética , Ubiquitina Tiolesterasa/genética , Amianto/toxicidad , Exposición a Riesgos Ambientales , Femenino , Ligamiento Genético , Predisposición Genética a la Enfermedad , Humanos , Masculino , Melanoma/genética , Mesotelioma/patología , Linaje , Neoplasias Pleurales/patología , Factores de Riesgo , Proteínas Supresoras de Tumor/metabolismo , Ubiquitina Tiolesterasa/metabolismo , Neoplasias de la Úvea/genética
19.
J Toxicol Environ Health B Crit Rev ; 14(1-4): 246-66, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21534090

RESUMEN

Asbestos and related fibers are associated with a number of adverse health effects, including malignant mesothelioma (MM), an aggressive cancer that generally develops in the surface serosal cells of the pleural, pericardial, and peritoneal cavities. Although approximately 80% of individuals with MM are exposed to asbestos, fewer than 5% of asbestos workers develop MM. In addition to asbestos, other mineralogical, environmental, genetic, and possibly viral factors might contribute to MM susceptibility. Given this complex etiology of MM, understanding susceptibility to MM needs to be a priority for investigators in order to reduce exposure of those most at risk to known environmental carcinogens. In this review, the current body of literature related to fiber-associated disease susceptibility including age, sex, nutrition, genetics, asbestos, and other mineral exposure is addressed with a focus on MM, and critical areas for further study are recommended.


Asunto(s)
Susceptibilidad a Enfermedades/inducido químicamente , Contaminantes Ambientales/toxicidad , Fibras Minerales/toxicidad , Factores de Edad , Animales , Amianto/toxicidad , Carcinógenos Ambientales/toxicidad , Aberraciones Cromosómicas/inducido químicamente , Cocarcinogénesis , Predisposición Genética a la Enfermedad , Humanos , Mesotelioma/inducido químicamente , Mesotelioma/epidemiología , Mesotelioma/genética , Estado Nutricional , Efectos de la Radiación , Riesgo , Caracteres Sexuales , Zeolitas/toxicidad
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