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1.
Genet Test Mol Biomarkers ; 28(9): 373-383, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39185556

RESUMEN

Kawasaki disease (KD), a systemic vasculitic condition predominantly affecting children, remains a significant challenge in pediatric health care. First identified in 1967, KD is now recognized as the primary cause of pediatric ischemic heart disease in developed countries. This review provides a comprehensive update of KD, focusing on biomarkers, pathophysiology, and genetic associations. KD's clinical manifestation, including symptoms such as persistent fever and mucocutaneous changes, often overlaps with other pediatric conditions, complicating its diagnosis. This ambiguity, especially in cases of incomplete KD, highlights the critical need for specific biomarkers and more precise diagnostic methods. Recent studies have made promising advancements in identifying serum biomarkers and microRNAs, contributing to the development of rapid diagnostic tools. However, these are yet to be fully integrated into clinical practice. The article focuses on the pathophysiological aspects of KD, highlighting the potential for targeted therapies and personalized medicine approaches based on genetic predispositions. Collaborative efforts in global research and raising public awareness about KD are emphasized as key strategies for improving its management. This review presents the current understanding of KD while pointing out the gaps and future directions in research and clinical care. The ultimate goal is to enhance diagnostic accuracy, optimize treatment strategies, and improve patient outcomes, thereby addressing the complexities of this enigmatic and potentially life-threatening condition in pediatric medicine.


Asunto(s)
Predisposición Genética a la Enfermedad , Síndrome Mucocutáneo Linfonodular , Síndrome Mucocutáneo Linfonodular/genética , Síndrome Mucocutáneo Linfonodular/diagnóstico , Síndrome Mucocutáneo Linfonodular/fisiopatología , Humanos , Biomarcadores/sangre , Niño , MicroARNs/genética , Medicina de Precisión/métodos
2.
Ethn Dis ; 34(2): 103-112, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38973806

RESUMEN

Intracranial volume (ICV) reflects maximal brain development and is associated with later-life cognitive abilities. We quantified ICV among first- and second-generation Hispanic and Latino adults from the Study of Latinos-Investigation of Cognitive Aging - MRI (SOL-INCA-MRI), estimated ICV heritability, and tested its associations with previously reported genetic variants, both individually and as a genetic risk score (GRS). We also estimated the association of ICV with early life environmental measures: nativity or age of immigration and parental education. The estimated heritability of ICV was 19% (95% CI, 0.1%-56%) in n=1781 unrelated SOL-INCA-MRI individuals. Four of 10 tested genetic variants were associated with ICV and an increase of 1 SD of the ICV-GRS was associated with an increase of 10.37 cm3 in the ICV (95% CI, 5.29-15.45). Compared to being born in the continental United States, immigrating to the United States at age 11 years or older was associated with 24 cm3 smaller ICV (95% CI, -39.97 to -8.06). Compared to both parents having less than high-school education, at least 1 parent completing high-school education was associated with 15.4 cm3 greater ICV (95% CI, 4.46-26.39). These data confirm the importance of early life health on brain development.


Asunto(s)
Encéfalo , Hispánicos o Latinos , Imagen por Resonancia Magnética , Humanos , Femenino , Masculino , Encéfalo/diagnóstico por imagen , Adulto , Persona de Mediana Edad , Estados Unidos , Tamaño de los Órganos , Anciano , Niño
3.
Biomedicines ; 12(7)2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-39062002

RESUMEN

Background: Celiac disease, a gluten-triggered autoimmune disorder, is known for its systemic inflammatory effects. Its genetic associations with type 2 inflammatory diseases like asthma, allergic rhinitis, and atopic dermatitis remain unclear, prompting this study to explore their potential genetic interplay. Methods: Utilizing two-sample Mendelian randomization (TSMR), we examined the genetic associations using 15 genetic instruments from GWAS datasets. Our analysis focused on celiac disease and its relation to asthma, allergic rhinitis, atopic dermatitis, and IgE-mediated food allergies. A power analysis was conducted to determine the study's detection capabilities, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using various MR methods. Results: Our Mendelian randomization analysis identified statistically significant genetic associations between celiac disease and several type 2 inflammatory diseases, although these were practically insignificant. Specifically, celiac disease was associated with a slight increase in the risk of atopic dermatitis (OR = 1.037) and a minor protective effect against asthma (OR = 0.97). The link with allergic rhinitis was statistically detectable (OR = 1.002) but practically negligible. Despite robust statistical confirmation through various sensitivity analyses, all observed effects remained within the range of practical equivalence (ROPE). Conclusions: Our study identifies potential genetic associations between celiac disease and certain type 2 inflammatory diseases. However, these associations, predominantly within the ROPE range, suggest only limited clinical implications. These findings highlight the need for cautious interpretation and indicate that further exploration for clinical applications may not be warranted at this stage.

4.
Oncologist ; 29(9): e1228-e1230, 2024 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-38886182

RESUMEN

Colorectal cancer (CRC) is a common cancer in younger adults. In patients undergoing liver resection with RAS-altered CRCs, there is evidence suggesting younger patients have worse outcomes than older patients. To explain this pattern, differences in associations between RAS status and other cancer-related biomarkers in tumors from younger versus older patients with CRC were evaluated in a cohort of 925 patients with CRC, 277 (30.0%) of whom were ≤50 years old, and 454 (49.1%) who had RAS-altered tumors. For 3 biomarkers, RNF43, APC, and microsatellite instability (MSI), the association with RAS status was significantly modified by age after adjustment for multiple testing. Specifically, younger patients with RAS-altered tumors were more likely to be MSI-high, RNF43 mutated, and APC wild type. These differences might contribute to the observed pattern of diminished survival in younger versus older patients with CRC with RAS-mutated tumors undergoing liver metastasis resection.


Asunto(s)
Biomarcadores de Tumor , Neoplasias Colorrectales , Inestabilidad de Microsatélites , Humanos , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Neoplasias Colorrectales/cirugía , Neoplasias Colorrectales/mortalidad , Masculino , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Persona de Mediana Edad , Femenino , Adulto , Anciano , Mutación , Factores de Edad , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patología , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Proteínas ras/genética , Proteínas ras/metabolismo , Pronóstico , Proteína de la Poliposis Adenomatosa del Colon/genética
5.
Cell Genom ; 4(6): 100562, 2024 Jun 12.
Artículo en Inglés | MEDLINE | ID: mdl-38749448

RESUMEN

The phenotypic impact of genetic variation of repetitive features in the human genome is currently understudied. One such feature is the multi-copy 47S ribosomal DNA (rDNA) that codes for rRNA components of the ribosome. Here, we present an analysis of rDNA copy number (CN) variation in the UK Biobank (UKB). From the first release of UKB whole-genome sequencing (WGS) data, a discovery analysis in White British individuals reveals that rDNA CN associates with altered counts of specific blood cell subtypes, such as neutrophils, and with the estimated glomerular filtration rate, a marker of kidney function. Similar trends are observed in other ancestries. A range of analyses argue against reverse causality or common confounder effects, and all core results replicate in the second UKB WGS release. Our work demonstrates that rDNA CN is a genetic influence on trait variance in humans.


Asunto(s)
Bancos de Muestras Biológicas , Variaciones en el Número de Copia de ADN , Humanos , Variaciones en el Número de Copia de ADN/genética , Reino Unido , Tasa de Filtración Glomerular/genética , ADN Ribosómico/genética , Riñón/metabolismo , Masculino , Femenino , Secuenciación Completa del Genoma , Genoma Humano , Biobanco del Reino Unido
6.
Int J Mol Sci ; 25(10)2024 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-38791322

RESUMEN

A keloid is a benign fibroproliferative hypertrophy of scar tissue that extends outside the original wound and invades adjacent healthy skin. Keloid formation is thought to be a complex process including overactivity of the interleukin-6 signaling pathway and genetic susceptibility. The aim of the study was to investigate possible associations between rs1800797, rs1800796, and rs1800795 polymorphisms in the promoter of the IL6 gene encoding interleukin-6 and the rs2228145 polymorphism in the IL6R gene encoding the interleukin-6 receptor subunit alpha with the predisposition to keloids in Polish patients. The genetic polymorphisms were identified either using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) or sequencing of samples of genomic DNA extracted from blood leukocytes of 86 adult patients with keloids and 100 newborns comprising a control group. No significant differences in the distributions of IL6 or IL6R alleles or genotypes were found between keloid patients and newborn controls. There were also no significant differences between both groups in the distribution of IL6 haplotypes. The IL6 rs1800797, rs1800796 and rs1800795 and IL6R rs2228145 polymorphisms were not found to predispose individuals in the study group to keloids. IL6 promoter haplotypes were not found to be associated with a higher risk of keloids in the studied group.


Asunto(s)
Predisposición Genética a la Enfermedad , Interleucina-6 , Queloide , Polimorfismo de Nucleótido Simple , Receptores de Interleucina-6 , Humanos , Queloide/genética , Queloide/patología , Interleucina-6/genética , Receptores de Interleucina-6/genética , Masculino , Femenino , Adulto , Polonia , Persona de Mediana Edad , Regiones Promotoras Genéticas , Estudios de Casos y Controles , Haplotipos , Alelos , Adolescente , Adulto Joven , Frecuencia de los Genes , Genotipo , Recién Nacido , Estudios de Asociación Genética
7.
Clin Exp Med ; 24(1): 94, 2024 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-38703294

RESUMEN

Prior research has established associations between immune cells, inflammatory proteins, and chronic kidney disease (CKD). Our Mendelian randomization study aims to elucidate the genetic causal relationships among these factors and CKD. We applied Mendelian randomization using genetic variants associated with CKD from a large genome-wide association study (GWAS) and inflammatory markers from a comprehensive GWAS summary. The causal links between exposures (immune cell subtypes and inflammatory proteins) and CKD were primarily analyzed using the inverse variance-weighted, supplemented by sensitivity analyses, including MR-Egger, weighted median, weighted mode, and MR-PRESSO. Our analysis identified both absolute and relative counts of CD28 + CD45RA + CD8 + T cell (OR = 1.01; 95% CI = 1.01-1.02; p < 0.001, FDR = 0.018) (OR = 1.01; 95% CI = 1.00-1.01; p < 0.001, FDR = 0.002), CD28 on CD39 + CD8 + T cell(OR = 0.97; 95% CI = 0.96-0.99; p < 0.001, FDR = 0.006), CD16 on CD14-CD16 + monocyte (OR = 1.02; 95% CI = 1.01-1.03; p < 0.001, FDR = 0.004) and cytokines, such as IL-17A(OR = 1.11, 95% CI = 1.06-1.16, p < 0.001, FDR = 0.001), and LIF-R(OR = 1.06, 95% CI = 1.02-1.10, p = 0.005, FDR = 0.043) that are genetically predisposed to influence the risk of CKD. Moreover, the study discovered that CKD itself may causatively lead to alterations in certain proteins, including CST5(OR = 1.16, 95% CI = 1.09-1.24, p < 0.001, FDR = 0.001). No evidence of reverse causality was found for any single biomarker and CKD. This comprehensive MR investigation supports a genetic causal nexus between certain immune cell subtypes, inflammatory proteins, and CKD. These findings enhance the understanding of CKD's immunological underpinnings and open avenues for targeted treatments.


Asunto(s)
Estudio de Asociación del Genoma Completo , Análisis de la Aleatorización Mendeliana , Insuficiencia Renal Crónica , Humanos , Insuficiencia Renal Crónica/genética , Insuficiencia Renal Crónica/inmunología , Mediadores de Inflamación/metabolismo , Predisposición Genética a la Enfermedad
8.
ESC Heart Fail ; 2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38714485

RESUMEN

AIMS: This study aimed to explore the causal relationships between cathepsins and cardiovascular diseases (CVDs) by Mendelian randomization (MR) analysis. METHODS AND RESULTS: Single nucleotide polymorphisms (SNPs) associated with nine cathepsin types (cathepsins B, E, F, G, H, O, S, L2, and Z) were obtained from the INTERVAL study (3301 individuals). CVDs data were acquired from the UK Biobank (coronary atherosclerosis: 14 334 cases, 346 860 controls) and a genome-wide association study (GWAS) (myocardial infarction: 20 917 cases, 440 906 controls; myocarditis: 633 cases, 427 278 controls; chronic heart failure: 14 262 cases, 471 898 controls; angina pectoris: 30 025 cases, 440 906 controls; stable angina pectoris: 17 894 cases, 325 132 controls; unstable angina pectoris: 9481 cases, 446 987 controls; pericarditis: 1795 cases, 453 370 controls). Inverse variance weighted (IVW), MR-Egger, weighted median methods were adopted to conduct univariable MR (UVMR), reverse MR, multivariable MR (MVMR) analyses to estimate causality. The UVMR analyses demonstrated significant causal relationships between higher cathepsin E levels and increased risk of coronary atherosclerosis [IVW: P = 0.0051, odds ratio (OR) = 1.0033, 95% confidence interval (CI) = 1.0010-1.0056] and myocardial infarction (IVW: P = 0.0097, OR = 1.0553, 95% CI = 1.0131-1.0993), while elevated cathepsin L2 levels were causally related to reduced risk of myocarditis (IVW: P = 0.0120, OR = 0.6895, 95% CI = 0.5158-0.9216) and chronic heart failure (IVW: P = 0.0134, OR = 0.9316, 95% CI = 0.8807-0.9854). Reverse MR analyses revealed that myocardial infarction increased cathepsin O levels (IVW: P = 0.0400, OR = 1.0708, 95% CI = 1.0031-1.1431). MVMR analyses treating nine cathepsins together revealed that the positive causality between cathepsin E levels and coronary atherosclerosis risk (IVW: P = 0.0390, OR = 1.0030, 95% CI = 1.0000-1.0060), and the protective effect of cathepsin L2 levels on myocarditis (IVW: P = 0.0030, OR = 0.6610, 95% CI = 0.5031-0.8676) and chronic heart failure (IVW: P = 0.0090, OR = 0.9259, 95% CI = 0.8737-0.9812) remained, as higher cathepsin O levels were found to be causally related to increased risks of myocarditis (IVW: P = 0.0030, OR = 1.6145, 95% CI = 1.1829-2.2034) and chronic heart failure (IVW: P = 0.0300, OR = 1.0779, 95% CI = 1.0070-1.1537). CONCLUSIONS: The study highlights the causalities of cathepsin E, L2, and O on CVDs, offering insights into their roles in cardiovascular biomarkers and therapeutic targets development. Further research is required to apply these genetic findings clinically.

9.
Genes (Basel) ; 15(2)2024 01 23.
Artículo en Inglés | MEDLINE | ID: mdl-38397132

RESUMEN

Pigment Dispersion Syndrome (PDS) and Pigmentary Glaucoma (PG) comprise a spectrum of ocular disorders characterized by iris pigment dispersion and trabecular meshwork changes, resulting in increased intraocular pressure and potential glaucomatous optic neuropathy. This review summarizes recent progress in PDS/PG genetics including rare pathogenic protein coding alterations (PMEL) and susceptibility loci identified from genome-wide association studies (GSAP and GRM5/TYR). Areas for future research are also identified, especially the development of efficient model systems. While substantial strides have been made in understanding the genetics of PDS/PG, our review identifies key gaps and outlines the future directions necessary for further advancing this important field of ocular genetics.


Asunto(s)
Estudio de Asociación del Genoma Completo , Glaucoma de Ángulo Abierto , Humanos , Glaucoma de Ángulo Abierto/patología , Malla Trabecular/patología , Cara/patología
10.
Genes (Basel) ; 15(2)2024 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-38397151

RESUMEN

The phenotypic similarities between exfoliation syndrome (XFS)/exfoliation glaucoma (XFG) and pigment dispersion syndrome (PDS)/pigmentary glaucoma (PG), particularly their association with material deposition in the eye's anterior segment, have prompted investigations into genetic commonalities. This study focuses on the LOXL1 gene, conducting a comprehensive meta-analysis of three candidate gene association studies. We analyzed three single nucleotide polymorphisms (SNPs) of LOXL1: rs1048661, rs3825942, and rs2165241. Our results reveal nominal significance for the exonic SNPs rs1048661 and rs3825942 (p ≤ 0.01), but show no significant association for the intronic SNP rs2165241 (p = 0.83) with PDS/PG. There was homogeneity across study cohorts (I2 = 0), and sensitivity analyses and funnel plots confirmed a lower likelihood of bias in our findings. The lack of a statistically significant association between LOXL1 variants and PDS/PG at p < 0.05 was attributable to the insufficient statistical power of the pooled data, which ranged from 5% to 37% for the three SNPs. This study suggests no association between LOXL1 variants and PDS/PG. Further validation and exploration of XFS/XFG-associated genes in larger and more diverse cohorts would be helpful to determine the genetic correlation or distinctiveness between these conditions.


Asunto(s)
Síndrome de Exfoliación , Glaucoma de Ángulo Abierto , Humanos , Aminoácido Oxidorreductasas/genética , Síndrome de Exfoliación/genética , Glaucoma de Ángulo Abierto/genética , Haplotipos
11.
Sci Total Environ ; 912: 168843, 2024 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-38029998

RESUMEN

Air pollution has been increasingly linked to cancer risk. However, the genetic causality between air pollution and cancer risk remains poorly understood. To elucidate the potential roles of air pollution (NOx, NO2, PM2.5, PM course, and PM10) in the risk of 18 specific-site cancers, large-scale genome-wide association studies with a novel Mendelian randomization (MR) method were employed. Our MR analyses revealed significant associations between certain air pollutants and specific types of cancer. Specifically, a positive association was observed between NOx exposure and squamous cell lung cancer (OR: 1.96, 95%CI: 1.07-3.59, p = 0.03) as well as esophageal cancer (OR: 1.002, 95%CI: 1.001-1.003, p = 0.005). Genetically predicted NO2 exposure was found to be a risk factor for endometrial cancer (OR 1.41, 95%CI: 1.03-1.94, p = 0.03) and ovarian cancer (OR: 1.49, 95%CI: 1.14-1.95, p = 0.0037). Additionally, genetically predicted PM2.5 exposure was associated with an increased risk of ER+ breast cancer (OR: 1.24, 95%CI: 1.03-1.5, p = 0.02) and ER- breast cancer (OR: 2.57, 95%CI: 1.05-6.3, p = 0.04). PM course exposure was identified as a risk factor for glioma (OR: 487.28, 95%CI: 13.08-18,153, p = 0.0008), while PM10 exposure exerted a detrimental effect on mesothelioma (OR: 114.75, 95%CI: 1.14-11,500.11, p = 0.04) and esophageal cancer (OR: 1.01, 95%CI: 1.007-1.02, p = 0.03). These findings underscored the importance of mitigating air pollution to reduce the burden of cancer and highlight the need for further investigations to elucidate the underlying mechanisms involved in these associations.


Asunto(s)
Contaminantes Atmosféricos , Contaminación del Aire , Neoplasias de la Mama , Neoplasias Esofágicas , Humanos , Femenino , Material Particulado/análisis , Estudio de Asociación del Genoma Completo , Exposición a Riesgos Ambientales/análisis , Contaminación del Aire/efectos adversos , Contaminación del Aire/análisis , Contaminantes Atmosféricos/análisis , Neoplasias Esofágicas/inducido químicamente , Dióxido de Nitrógeno/análisis
12.
Alzheimers Dement ; 20(2): 1123-1136, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-37881831

RESUMEN

INTRODUCTION: The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site Alzheimer's Genomics Database (GenomicsDB) is a public knowledge base of Alzheimer's disease (AD) genetic datasets and genomic annotations. METHODS: GenomicsDB uses a custom systems architecture to adopt and enforce rigorous standards that facilitate harmonization of AD-relevant genome-wide association study summary statistics datasets with functional annotations, including over 230 million annotated variants from the AD Sequencing Project. RESULTS: GenomicsDB generates interactive reports compiled from the harmonized datasets and annotations. These reports contextualize AD-risk associations in a broader functional genomic setting and summarize them in the context of functionally annotated genes and variants. DISCUSSION: Created to make AD-genetics knowledge more accessible to AD researchers, the GenomicsDB is designed to guide users unfamiliar with genetic data in not only exploring but also interpreting this ever-growing volume of data. Scalable and interoperable with other genomics resources using data technology standards, the GenomicsDB can serve as a central hub for research and data analysis on AD and related dementias. HIGHLIGHTS: The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) offers to the public a unique, disease-centric collection of AD-relevant GWAS summary statistics datasets. Interpreting these data is challenging and requires significant bioinformatics expertise to standardize datasets and harmonize them with functional annotations on genome-wide scales. The NIAGADS Alzheimer's GenomicsDB helps overcome these challenges by providing a user-friendly public knowledge base for AD-relevant genetics that shares harmonized, annotated summary statistics datasets from the NIAGADS repository in an interpretable, easily searchable format.


Asunto(s)
Enfermedad de Alzheimer , Estados Unidos , Humanos , Enfermedad de Alzheimer/genética , Estudio de Asociación del Genoma Completo , National Institute on Aging (U.S.) , Genómica , Bases de Datos Factuales , Predisposición Genética a la Enfermedad/genética
13.
Wellcome Open Res ; 8: 449, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37915953

RESUMEN

The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added or edited in the package since version 0.5.0, when we last described the package and its contents. The main additions to the package since that time are: 1) new robust methods for performing Mendelian randomization, particularly in the cases of bias from weak instruments and/or winner's curse, and pleiotropic variants, 2) methods for performing Mendelian randomization with correlated variants using dimension reduction to summarize large numbers of highly correlated variants into a limited set of principal components, 3) functions for calculating first-stage F statistics, representing instrument strength, in both univariable and multivariable contexts, and with uncorrelated and correlated genetic variants. We also discuss some pragmatic issues relating to the use of correlated variants in Mendelian randomization.

14.
Metab Syndr Relat Disord ; 21(10): 545-560, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37816229

RESUMEN

Metabolic syndrome (MetS) is a cluster of cardiometabolic risk factors that includes central obesity, hyperglycemia, hypertension, and dyslipidemias and whose inter-related occurrence may increase the odds of developing type 2 diabetes and cardiovascular diseases. MetS has become one of the most studied conditions, nevertheless, due to its complex etiology, this has not been fully elucidated. Recent evidence describes that both genetic and environmental factors play an important role on its development. With the advent of genomic-wide association studies, single nucleotide polymorphisms (SNPs) have gained special importance. In this review, we present an update of the genetics surrounding MetS as a single entity as well as its corresponding risk factors, considering SNPs and gene-diet interactions related to cardiometabolic markers. In this study, we focus on the conceptual aspects, diagnostic criteria, as well as the role of genetics, particularly on SNPs and polygenic risk scores (PRS) for interindividual analysis. In addition, this review highlights future perspectives of personalized nutrition with regard to the approach of MetS and how individualized multiomics approaches could improve the current outlook.


Asunto(s)
Diabetes Mellitus Tipo 2 , Síndrome Metabólico , Humanos , Síndrome Metabólico/diagnóstico , Síndrome Metabólico/epidemiología , Síndrome Metabólico/genética , Diabetes Mellitus Tipo 2/complicaciones , Obesidad/complicaciones , Dieta , Factores de Riesgo , Polimorfismo de Nucleótido Simple
15.
Cell ; 186(17): 3659-3673.e23, 2023 08 17.
Artículo en Inglés | MEDLINE | ID: mdl-37527660

RESUMEN

Many regions in the human genome vary in length among individuals due to variable numbers of tandem repeats (VNTRs). To assess the phenotypic impact of VNTRs genome-wide, we applied a statistical imputation approach to estimate the lengths of 9,561 autosomal VNTR loci in 418,136 unrelated UK Biobank participants and 838 GTEx participants. Association and statistical fine-mapping analyses identified 58 VNTRs that appeared to influence a complex trait in UK Biobank, 18 of which also appeared to modulate expression or splicing of a nearby gene. Non-coding VNTRs at TMCO1 and EIF3H appeared to generate the largest known contributions of common human genetic variation to risk of glaucoma and colorectal cancer, respectively. Each of these two VNTRs associated with a >2-fold range of risk across individuals. These results reveal a substantial and previously unappreciated role of non-coding VNTRs in human health and gene regulation.


Asunto(s)
Canales de Calcio , Neoplasias Colorrectales , Factor 3 de Iniciación Eucariótica , Glaucoma , Repeticiones de Minisatélite , Humanos , Canales de Calcio/genética , Neoplasias Colorrectales/genética , Genoma Humano , Glaucoma/genética , Polimorfismo Genético , Factor 3 de Iniciación Eucariótica/genética
16.
Genes (Basel) ; 14(3)2023 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-36980925

RESUMEN

The present study aimed to summarize and validate the genomic association signals for diabetic retinopathy (DR), proliferative DR, and diabetic macular edema/diabetic maculopathy. A systematic search of the genome-wide association study (GWAS) catalog and PubMed/MELINE databases was conducted to curate a comprehensive list of significant GWAS discoveries. The top signals were then subjected to meta-analysis using established protocols. The results indicate the need for improved consensus among DR GWASs, highlighting the importance of validation efforts. A subsequent meta-analysis confirmed the association of two SNPs, rs4462262 (ZWINT-MRPS35P3) (odds ratio = 1.38, p = 0.001) and rs7903146 (TCF7L2) (odd ratio = 1.30, p < 0.001), with DR in independent populations, strengthening the evidence of their true association. We also compiled a list of candidate SNPs for further validation. This study highlights the importance of consistent validation and replication efforts in the field of DR genetics. The two identified gene loci warrant further functional investigation to understand their role in DR pathogenesis.


Asunto(s)
Diabetes Mellitus , Retinopatía Diabética , Edema Macular , Humanos , Estudio de Asociación del Genoma Completo/métodos , Retinopatía Diabética/genética , Edema Macular/complicaciones , Edema Macular/genética , Polimorfismo de Nucleótido Simple , Oportunidad Relativa
17.
Cell Metab ; 35(4): 695-710.e6, 2023 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-36963395

RESUMEN

Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.


Asunto(s)
Diabetes Mellitus Tipo 2 , Humanos , Diabetes Mellitus Tipo 2/genética , Acceso a la Información , Estudios Prospectivos , Genómica/métodos , Fenotipo
18.
HGG Adv ; 4(1): 100159, 2023 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-36465187

RESUMEN

Over the last two decades, the human reference genome has undergone multiple updates as we complete a linear representation of our genome. Two versions of human references are currently used in the biomedical literature, GRCh37/hg19 and GRCh38. Conversions between these versions are critical for quality control, imputation, and association analysis. In the present study, we show that single-nucleotide variants (SNVs) in regions inverted between different builds of the reference genome are often mishandled bioinformatically. Depending on the array type, SNVs are found in approximately 2-5 Mb of the genome that are inverted between reference builds. Coordinate conversions of these variants are mishandled by both the TOPMed imputation server as well as routine in-house quality control pipelines, leading to underrecognized downstream analytical consequences. Specifically, we observe that undetected allelic conversion errors for palindromic (i.e., A/T or C/G) variants in these inverted regions would destabilize the local haplotype structure, leading to loss of imputation accuracy and power in association analyses. Though only a small proportion of the genome is affected, these regions include important disease susceptibility variants that would be affected. For example, the p value of a known locus associated with prostate cancer on chromosome 10 (chr10) would drop from 2.86 × 10-7 to 0.0011 in a case-control analysis of 20,286 Africans and African Americans (10,643 cases and 9,643 controls). We devise a straight-forward heuristic based on the popular tool, liftOver, that can easily detect and correct these variants in the inverted regions between genome builds to locally improve imputation accuracy.


Asunto(s)
Estudio de Asociación del Genoma Completo , Genómica , Masculino , Humanos , Genoma Humano/genética , Haplotipos/genética , Negro o Afroamericano
19.
Front Genet ; 14: 1274743, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38348408

RESUMEN

Introduction: Age-related macular degeneration (AMD) is the leading cause of central vision loss in the elderly. One-third of the genetic contribution to this disease remains unexplained. Methods: We analyzed targeted sequencing data from two independent cohorts (4,245 cases, 1,668 controls) which included genomic regions of known AMD loci in 49 genes. Results: At a false discovery rate of <0.01, we identified 11 low-frequency AMD variants (minor allele frequency <0.05). Two of those variants were present in the complement C4A gene, including the replacement of the residues that contribute to the Rodgers-1/Chido-1 blood group antigens: [VDLL1207-1210ADLR (V1207A)] with discovery odds ratio (OR) = 1.7 (p = 3.2 × 10-5) which was replicated in the UK Biobank dataset (3,294 cases, 200,086 controls, OR = 1.52, p = 0.037). A novel variant associated with reduced risk for AMD in our discovery cohort was P1120T, one of the four C4A-isotypic residues. Gene-based tests yielded aggregate effects of nonsynonymous variants in 10 genes including C4A, which were associated with increased risk of AMD. In human eye tissues, immunostaining demonstrated C4A protein accumulation in and around endothelial cells of retinal and choroidal vasculature, and total C4 in soft drusen. Conclusion: Our results indicate that C4A protein in the complement activation pathways may play a role in the pathogenesis of AMD.

20.
Genes (Basel) ; 13(12)2022 11 30.
Artículo en Inglés | MEDLINE | ID: mdl-36553520

RESUMEN

Complications endangering mother or fetus affect around one in seven pregnant women. Investigation of the genetic susceptibility to such diseases is of high importance for better understanding of the disease biology as well as for prediction of individual risk. In this study, we collected and analyzed GWAS summary statistics from the FinnGen cohort and UK Biobank for 24 pregnancy complications. In FinnGen, we identified 11 loci associated with pregnancy hypertension, excessive vomiting, and gestational diabetes. When UK Biobank and FinnGen data were combined, we discovered six loci reaching genome-wide significance in the meta-analysis. These include rs35954793 in FGF5 (p=6.1×10-9), rs10882398 in PLCE1 (p=8.9×10-9), and rs167479 in RGL3 (p=5.2×10-9) for pregnancy hypertension, rs10830963 in MTNR1B (p=4.5×10-41) and rs36090025 in TCF7L2 (p=3.4×10-15) for gestational diabetes, and rs2963457 in the EBF1 locus (p=6.5×10-9) for preterm birth. In addition to the identified genome-wide associations, we also replicated 14 out of 40 previously reported GWAS markers for pregnancy complications, including four more preeclampsia-related variants. Finally, annotation of the GWAS results identified a causal relationship between gene expression in the cervix and gestational hypertension, as well as both known and previously uncharacterized genetic correlations between pregnancy complications and other traits. These results suggest new prospects for research into the etiology and pathogenesis of pregnancy complications, as well as early risk prediction for these disorders.


Asunto(s)
Diabetes Gestacional , Hipertensión , Complicaciones del Embarazo , Nacimiento Prematuro , Recién Nacido , Humanos , Femenino , Embarazo , Estudio de Asociación del Genoma Completo , Diabetes Gestacional/genética , Bancos de Muestras Biológicas , Complicaciones del Embarazo/genética , Reino Unido
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