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1.
Annu Rev Genomics Hum Genet ; 25(1): 287-308, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38599222

RESUMEN

Glaucoma is a clinically heterogeneous disease and the world's leading cause of irreversible blindness. Therapeutic intervention can prevent blindness but relies on early diagnosis, and current clinical risk factors are limited in their ability to predict who will develop sight-threatening glaucoma. The high heritability of glaucoma makes it an ideal substrate for genetic risk prediction, with the bulk of risk being polygenic in nature. Here, we summarize the foundations of glaucoma genetic risk, the development of polygenic risk prediction instruments, and emerging opportunities for genetic risk stratification. Although challenges remain, genetic risk stratification will significantly improve glaucoma screening and management.


Asunto(s)
Predisposición Genética a la Enfermedad , Glaucoma , Herencia Multifactorial , Humanos , Glaucoma/genética , Factores de Riesgo , Estudio de Asociación del Genoma Completo , Puntuación de Riesgo Genético
2.
Am J Hum Genet ; 111(6): 1006-1017, 2024 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-38703768

RESUMEN

We present shaPRS, a method that leverages widespread pleiotropy between traits or shared genetic effects across ancestries, to improve the accuracy of polygenic scores. The method uses genome-wide summary statistics from two diseases or ancestries to improve the genetic effect estimate and standard error at SNPs where there is homogeneity of effect between the two datasets. When there is significant evidence of heterogeneity, the genetic effect from the disease or population closest to the target population is maintained. We show via simulation and a series of real-world examples that shaPRS substantially enhances the accuracy of polygenic risk scores (PRSs) for complex diseases and greatly improves PRS performance across ancestries. shaPRS is a PRS pre-processing method that is agnostic to the actual PRS generation method, and as a result, it can be integrated into existing PRS generation pipelines and continue to be applied as more performant PRS methods are developed over time.


Asunto(s)
Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Polimorfismo de Nucleótido Simple , Herencia Multifactorial/genética , Humanos , Modelos Genéticos , Simulación por Computador , Pleiotropía Genética , Fenotipo
3.
Am J Hum Genet ; 110(1): 13-22, 2023 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-36460009

RESUMEN

Polygenic risk score (PRS) has demonstrated its great utility in biomedical research through identifying high-risk individuals for different diseases from their genotypes. However, the broader application of PRS to the general population is hindered by the limited transferability of PRS developed in Europeans to non-European populations. To improve PRS prediction accuracy in non-European populations, we develop a statistical method called SDPRX that can effectively integrate genome wide association study summary statistics from different populations. SDPRX automatically adjusts for linkage disequilibrium differences between populations and characterizes the joint distribution of the effect sizes of a variant in two populations to be both null, population specific, or shared with correlation. Through simulations and applications to real traits, we show that SDPRX improves the prediction performance over existing methods in non-European populations.


Asunto(s)
Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Humanos , Herencia Multifactorial/genética , Estudio de Asociación del Genoma Completo/métodos , Predisposición Genética a la Enfermedad , Factores de Riesgo , Genotipo
4.
Am J Hum Genet ; 110(10): 1673-1689, 2023 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-37716346

RESUMEN

Accurate polygenic scores (PGSs) facilitate the genetic prediction of complex traits and aid in the development of personalized medicine. Here, we develop a statistical method called multi-trait assisted PGS (mtPGS), which can construct accurate PGSs for a target trait of interest by leveraging multiple traits relevant to the target trait. Specifically, mtPGS borrows SNP effect size similarity information between the target trait and its relevant traits to improve the effect size estimation on the target trait, thus achieving accurate PGSs. In the process, mtPGS flexibly models the shared genetic architecture between the target and the relevant traits to achieve robust performance, while explicitly accounting for the environmental covariance among them to accommodate different study designs with various sample overlap patterns. In addition, mtPGS uses only summary statistics as input and relies on a deterministic algorithm with several algebraic techniques for scalable computation. We evaluate the performance of mtPGS through comprehensive simulations and applications to 25 traits in the UK Biobank, where in the real data mtPGS achieves an average of 0.90%-52.91% accuracy gain compared to the state-of-the-art PGS methods. Overall, mtPGS represents an accurate, fast, and robust solution for PGS construction in biobank-scale datasets.


Asunto(s)
Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Humanos , Herencia Multifactorial/genética , Estudio de Asociación del Genoma Completo/métodos , Fenotipo , Algoritmos , Proyectos de Investigación
5.
Brief Bioinform ; 25(5)2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39207728

RESUMEN

East Asian populations exhibit a genetic predisposition to obesity, yet comprehensive research on these traits is limited. We conducted a genome-wide association study (GWAS) with 93,673 Korean subjects to uncover novel genetic loci linked to obesity, examining metrics such as body mass index, waist circumference, body fat ratio, and abdominal fat ratio. Participants were categorized into non-obese, metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO) groups. Using advanced computational methods, we developed a multifaceted polygenic risk scores (PRS) model to predict obesity. Our GWAS identified significant genetic effects with distinct sizes and directions within the MHO and MUO groups compared with the non-obese group. Gene-based and gene-set analyses, along with cluster analysis, revealed heterogeneous patterns of significant genes on chromosomes 3 (MUO group) and 11 (MHO group). In analyses targeting genetic predisposition differences based on metabolic health, odds ratios of high PRS compared with medium PRS showed significant differences between non-obese and MUO, and non-obese and MHO. Similar patterns were seen for low PRS compared with medium PRS. These findings were supported by the estimated genetic correlation (0.89 from bivariate GREML). Regional analyses highlighted significant local genetic correlations on chromosome 11, while single variant approaches suggested widespread pleiotropic effects, especially on chromosome 11. In conclusion, our study identifies specific genetic loci and risks associated with obesity in the Korean population, emphasizing the heterogeneous genetic factors contributing to MHO and MUO.


Asunto(s)
Puntuación de Riesgo Genético , Obesidad , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Índice de Masa Corporal , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Obesidad/genética , Polimorfismo de Nucleótido Simple , República de Corea/epidemiología , Pueblos del Este de Asia/genética
6.
Genet Epidemiol ; 48(2): 85-100, 2024 03.
Artículo en Inglés | MEDLINE | ID: mdl-38303123

RESUMEN

The use of polygenic risk score (PRS) models has transformed the field of genetics by enabling the prediction of complex traits and diseases based on an individual's genetic profile. However, the impact of genotype-environment interaction (GxE) on the performance and applicability of PRS models remains a crucial aspect to be explored. Currently, existing genotype-environment interaction polygenic risk score (GxE PRS) models are often inappropriately used, which can result in inflated type 1 error rates and compromised results. In this study, we propose novel GxE PRS models that jointly incorporate additive and interaction genetic effects although also including an additional quadratic term for nongenetic covariates, enhancing their robustness against model misspecification. Through extensive simulations, we demonstrate that our proposed models outperform existing models in terms of controlling type 1 error rates and enhancing statistical power. Furthermore, we apply the proposed models to real data, and report significant GxE effects. Specifically, we highlight the impact of our models on both quantitative and binary traits. For quantitative traits, we uncover the GxE modulation of genetic effects on body mass index by alcohol intake frequency. In the case of binary traits, we identify the GxE modulation of genetic effects on hypertension by waist-to-hip ratio. These findings underscore the importance of employing a robust model that effectively controls type 1 error rates, thus preventing the occurrence of spurious GxE signals. To facilitate the implementation of our approach, we have developed an innovative R software package called GxEprs, specifically designed to detect and estimate GxE effects. Overall, our study highlights the importance of accurate GxE modeling and its implications for genetic risk prediction, although providing a practical tool to support further research in this area.


Asunto(s)
Interacción Gen-Ambiente , Puntuación de Riesgo Genético , Humanos , Modelos Genéticos , Fenotipo , Factores de Riesgo
7.
Plant J ; 120(1): 253-271, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39166483

RESUMEN

Drought is one of the most important abiotic stresses, and seriously threatens plant development and productivity. Increasing evidence indicates that chromatin remodelers are pivotal for plant drought response. However, molecular mechanisms of chromatin remodelers-mediated plant drought responses remain obscure. In this study, we found a novel interactor of BRM called BRM-associated protein involved in drought response (BAPID), which interacted with SWI/SNF chromatin remodeler BRM and drought-induced transcription factor Di19. Our findings demonstrated that BAPID acted as a positive drought regulator since drought tolerance was increased in BAPID-overexpressing plants, but decreased in BAPID-deficient plants, and physically bound to PR1, PR2, and PR5 promoters to mediate expression of PR genes to defend against dehydration stress. Genetic approaches demonstrated that BRM acted epistatically to BAPID and Di19 in drought response in Arabidopsis. Furthermore, the BAPID protein-inhibited interaction between BRM and Di19, and suppressed the inhibition of BRM on the Di19-PR module by mediating the H3K27me3 deposition at PR loci, thus changing nucleosome accessibility of Di19 and activating transcription of PR genes in response to drought. Our results shed light on the molecular mechanism whereby the BAPID-BRM-Di19-PRs pathway mediates plant drought responses. We provide data improving our understanding of chromatin remodeler-mediated plant drought regulation network.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Sequías , Regulación de la Expresión Génica de las Plantas , Factores de Transcripción , Arabidopsis/genética , Arabidopsis/fisiología , Arabidopsis/metabolismo , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Estrés Fisiológico , Ensamble y Desensamble de Cromatina , Regiones Promotoras Genéticas/genética , Plantas Modificadas Genéticamente , Adenosina Trifosfatasas
8.
Am J Hum Genet ; 109(11): 1998-2008, 2022 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-36240765

RESUMEN

As most existing genome-wide association studies (GWASs) were conducted in European-ancestry cohorts, and as the existing polygenic risk score (PRS) models have limited transferability across ancestry groups, PRS research on non-European-ancestry groups needs to make efficient use of available data until we attain large sample sizes across all ancestry groups. Here we propose a PRS method using transfer learning techniques. Our approach, TL-PRS, uses gradient descent to fine-tune the baseline PRS model from an ancestry group with large sample GWASs to the dataset of target ancestry. In our application of constructing PRS for seven quantitative and two dichotomous traits for 10,285 individuals of South Asian ancestry and 8,168 individuals of African ancestry in UK Biobank, TL-PRS using PRS-CS as a baseline method obtained 25% average relative improvement for South Asian samples and 29% for African samples compared to the standard PRS-CS method in terms of predicted R2. Our approach increases the transferability of PRSs across ancestries and thereby helps reduce existing inequities in genetics research.


Asunto(s)
Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Humanos , Herencia Multifactorial/genética , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple/genética , Factores de Riesgo , Aprendizaje Automático
9.
Am J Hum Genet ; 109(10): 1742-1760, 2022 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-36152628

RESUMEN

Complex traits are influenced by genetic risk factors, lifestyle, and environmental variables, so-called exposures. Some exposures, e.g., smoking or lipid levels, have common genetic modifiers identified in genome-wide association studies. Because measurements are often unfeasible, exposure polygenic risk scores (ExPRSs) offer an alternative to study the influence of exposures on various phenotypes. Here, we collected publicly available summary statistics for 28 exposures and applied four common PRS methods to generate ExPRSs in two large biobanks: the Michigan Genomics Initiative and the UK Biobank. We established ExPRSs for 27 exposures and demonstrated their applicability in phenome-wide association studies and as predictors for common chronic conditions. Especially the addition of multiple ExPRSs showed, for several chronic conditions, an improvement compared to prediction models that only included traditional, disease-focused PRSs. To facilitate follow-up studies, we share all ExPRS constructs and generated results via an online repository called ExPRSweb.


Asunto(s)
Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Lípidos , Herencia Multifactorial/genética , Factores de Riesgo
10.
Hum Genomics ; 18(1): 4, 2024 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-38281958

RESUMEN

This review discusses the landscape of personalized prevention and management of obesity from a nutrigenetics perspective. Focusing on macronutrient tailoring, we discuss the impact of genetic variation on responses to carbohydrate, lipid, protein, and fiber consumption. Our bioinformatic analysis of genomic variants guiding macronutrient intake revealed enrichment of pathways associated with circadian rhythm, melatonin metabolism, cholesterol and lipoprotein remodeling and PPAR signaling as potential targets of macronutrients for the management of obesity in relevant genetic backgrounds. Notably, our data-based in silico predictions suggest the potential of repurposing the SYK inhibitor fostamatinib for obesity treatment in relevant genetic profiles. In addition to dietary considerations, we address genetic variations guiding lifestyle changes in weight management, including exercise and chrononutrition. Finally, we emphasize the need for a refined understanding and expanded research into the complex genetic landscape underlying obesity and its management.


Asunto(s)
Dieta , Obesidad , Humanos , Obesidad/genética , Obesidad/terapia , Obesidad/metabolismo , Genómica , Estilo de Vida
11.
Hum Genomics ; 18(1): 75, 2024 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-38956648

RESUMEN

BACKGROUND: Aging represents a significant risk factor for the occurrence of cerebral small vessel disease, associated with white matter (WM) lesions, and to age-related cognitive alterations, though the precise mechanisms remain largely unknown. This study aimed to investigate the impact of polygenic risk scores (PRS) for WM integrity, together with age-related DNA methylation, and gene expression alterations, on cognitive aging in a cross-sectional healthy aging cohort. The PRSs were calculated using genome-wide association study (GWAS) summary statistics for magnetic resonance imaging (MRI) markers of WM integrity, including WM hyperintensities, fractional anisotropy (FA), and mean diffusivity (MD). These scores were utilized to predict age-related cognitive changes and evaluate their correlation with structural brain changes, which distinguish individuals with higher and lower cognitive scores. To reduce the dimensionality of the data and identify age-related DNA methylation and transcriptomic alterations, Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) was used. Subsequently, a canonical correlation algorithm was used to integrate the three types of omics data (PRS, DNA methylation, and gene expression data) and identify an individual "omics" signature that distinguishes subjects with varying cognitive profiles. RESULTS: We found a positive association between MD-PRS and long-term memory, as well as a correlation between MD-PRS and structural brain changes, effectively discriminating between individuals with lower and higher memory scores. Furthermore, we observed an enrichment of polygenic signals in genes related to both vascular and non-vascular factors. Age-related alterations in DNA methylation and gene expression indicated dysregulation of critical molecular features and signaling pathways involved in aging and lifespan regulation. The integration of multi-omics data underscored the involvement of synaptic dysfunction, axonal degeneration, microtubule organization, and glycosylation in the process of cognitive aging. CONCLUSIONS: These findings provide valuable insights into the biological mechanisms underlying the association between WM coherence and cognitive aging. Additionally, they highlight how age-associated DNA methylation and gene expression changes contribute to cognitive aging.


Asunto(s)
Envejecimiento Cognitivo , Metilación de ADN , Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Humanos , Metilación de ADN/genética , Femenino , Masculino , Herencia Multifactorial/genética , Anciano , Persona de Mediana Edad , Estudios Transversales , Sustancia Blanca/diagnóstico por imagen , Sustancia Blanca/patología , Factores de Riesgo , Imagen por Resonancia Magnética , Envejecimiento/genética , Envejecimiento/patología , Encéfalo/diagnóstico por imagen , Encéfalo/metabolismo , Encéfalo/patología , Puntuación de Riesgo Genético
12.
Cancer ; 130(17): 2978-2987, 2024 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-38718029

RESUMEN

BACKGROUND: The polygenic risk score (PRS) allows the quantification of the polygenic effect of many low-penetrance alleles on the risk of breast cancer (BC). This study aimed to evaluate the performance of two sets comprising 77 or 313 low-penetrance loci (PRS77 and PRS313) in patients with BC in the Czech population. METHODS: In a retrospective case-control study, variants were genotyped from both the PRS77 and PRS313 sets in 1329 patients with BC and 1324 noncancer controls, all women without germline pathogenic variants in BC predisposition genes. Odds ratios (ORs) were calculated according to the categorical PRS in individual deciles. Weighted Cox regression analysis was used to estimate the hazard ratio (HR) per standard deviation (SD) increase in PRS. RESULTS: The distributions of standardized PRSs in patients and controls were significantly different (p < 2.2 × 10-16) with both sets. PRS313 outperformed PRS77 in categorical and continuous PRS analyses. For patients in the highest 2.5% of PRS313, the risk reached an OR of 3.05 (95% CI, 1.66-5.89; p = 1.76 × 10-4). The continuous risk was estimated as an HRper SD of 1.64 (95% CI, 1.49-1.81; p < 2.0 × 10-16), which resulted in an absolute risk of 21.03% at age 80 years for individuals in the 95th percentile of PRS313. Discordant categorization into PRS deciles was observed in 248 individuals (9.3%). CONCLUSIONS: Both PRS77 and PRS313 are able to stratify individuals according to their BC risk in the Czech population. PRS313 shows better discriminatory ability. The results support the potential clinical utility of using PRS313 in individualized BC risk prediction.


Asunto(s)
Neoplasias de la Mama , Predisposición Genética a la Enfermedad , Humanos , Femenino , Neoplasias de la Mama/genética , Estudios de Casos y Controles , Persona de Mediana Edad , Estudios Retrospectivos , Anciano , Herencia Multifactorial/genética , Adulto , Medición de Riesgo/métodos , República Checa/epidemiología , Factores de Riesgo , Puntuación de Riesgo Genético
13.
Am J Hum Genet ; 108(6): 1001-1011, 2021 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-33964208

RESUMEN

The accuracy of polygenic risk scores (PRSs) to predict complex diseases increases with the training sample size. PRSs are generally derived based on summary statistics from large meta-analyses of multiple genome-wide association studies (GWASs). However, it is now common for researchers to have access to large individual-level data as well, such as the UK Biobank data. To the best of our knowledge, it has not yet been explored how best to combine both types of data (summary statistics and individual-level data) to optimize polygenic prediction. The most widely used approach to combine data is the meta-analysis of GWAS summary statistics (meta-GWAS), but we show that it does not always provide the most accurate PRS. Through simulations and using 12 real case-control and quantitative traits from both iPSYCH and UK Biobank along with external GWAS summary statistics, we compare meta-GWAS with two alternative data-combining approaches, stacked clumping and thresholding (SCT) and meta-PRS. We find that, when large individual-level data are available, the linear combination of PRSs (meta-PRS) is both a simple alternative to meta-GWAS and often more accurate.


Asunto(s)
Enfermedad/genética , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Modelos Estadísticos , Herencia Multifactorial , Polimorfismo de Nucleótido Simple , Estudios de Casos y Controles , Humanos , Fenotipo
14.
Gastroenterology ; 165(5): 1151-1167, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37541527

RESUMEN

BACKGROUND & AIMS: Dysregulation of alternative splicing is implicated in many human diseases, and understanding the genetic variation underlying transcript splicing is essential to dissect the molecular mechanisms of cancers. We aimed to provide a comprehensive functional dissection of splicing quantitative trait loci (sQTLs) in cancer and focus on elucidating its distinct role in colorectal cancer (CRC) mechanisms. METHODS: We performed a comprehensive sQTL analysis to identify genetic variants that control messenger RNA splicing across 33 cancer types from The Cancer Genome Atlas and independently validated in our 154 CRC tissues. Then, large-scale, multicenter, multi-ethnic case-control studies (34,585 cases and 76,023 controls) were conducted to examine the association of these sQTLs with CRC risk. A series of biological experiments in vitro and in vivo were performed to investigate the potential mechanisms of the candidate sQTLs and target genes. RESULTS: The molecular characterization of sQTL revealed its distinct role in cancer susceptibility. Tumor-specific sQTL further showed better response to cancer development. In addition, functionally informed polygenic risk score highlighted the potentiality of sQTLs in the CRC prediction. Complemented by large-scale population studies, we identified that the risk allele (T) of a multi-ancestry-associated sQTL rs61746794 significantly increased the risk of CRC in Chinese (odds ratio, 1.20; 95% CI, 1.12-1.29; P = 8.82 × 10-7) and European (odds ratio, 1.11; 95% CI, 1.07-1.16; P = 1.13 × 10-7) populations. rs61746794-T facilitated PRMT7 exon 16 splicing mediated by the RNA-binding protein PRPF8, thus increasing the level of canonical PRMT7 isoform (PRMT7-V2). Overexpression of PRMT7-V2 significantly enhanced the growth of CRC cells and xenograft tumors compared with PRMT7-V1. Mechanistically, PRMT7-V2 functions as an epigenetic writer that catalyzes the arginine methylation of H4R3 and H3R2, subsequently regulating diverse biological processes, including YAP, AKT, and KRAS pathway. A selective PRMT7 inhibitor, SGC3027, exhibited antitumor effects on human CRC cells. CONCLUSIONS: Our study provides an informative sQTLs resource and insights into the regulatory mechanisms linking splicing variants to cancer risk and serving as biomarkers and therapeutic targets.

15.
BMC Med ; 22(1): 230, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38853248

RESUMEN

BACKGROUND: Obesity and central obesity are multifactorial conditions with genetic and non-genetic (lifestyle and environmental) contributions. There is incomplete understanding of whether lifestyle modifies the translation from respective genetic risks into phenotypic obesity and central obesity, and to what extent genetic predisposition to obesity and central obesity is mediated via lifestyle factors. METHODS: This is a cross-sectional study of 201,466 (out of approximately 502,000) European participants from UK Biobank and tested for interactions and mediation role of lifestyle factors (diet quality; physical activity levels; total energy intake; sleep duration, and smoking and alcohol intake) between genetic risk for obesity and central obesity. BMI-PRS and WHR-PRS are exposures and obesity and central obesity are outcomes. RESULTS: Overall, 42.8% of the association between genetic predisposition to obesity and phenotypic obesity was explained by lifestyle: 0.9% by mediation and 41.9% by effect modification. A significant difference between men and women was found in central obesity; the figures were 42.1% (association explained by lifestyle), 1.4% (by mediation), and 40.7% (by modification) in women and 69.6% (association explained by lifestyle), 3.0% (by mediation), and 66.6% (by modification) in men. CONCLUSIONS: A substantial proportion of the association between genetic predisposition to obesity/central obesity and phenotypic obesity/central obesity was explained by lifestyles. Future studies with repeated measures of obesity and lifestyle would be needed to clarify causation.


Asunto(s)
Bancos de Muestras Biológicas , Predisposición Genética a la Enfermedad , Estilo de Vida , Obesidad , Fenotipo , Humanos , Masculino , Femenino , Estudios Transversales , Reino Unido/epidemiología , Persona de Mediana Edad , Obesidad/genética , Obesidad/epidemiología , Anciano , Adulto , Obesidad Abdominal/genética , Obesidad Abdominal/epidemiología , Biobanco del Reino Unido
16.
Brief Bioinform ; 23(6)2022 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-36326078

RESUMEN

Most polygenic risk score (PRS)models have been based on data from populations of European origins (accounting for the majority of the large genomics datasets, e.g. >78% in the UK Biobank and >85% in the GTEx project). Although several large-scale Asian biobanks were initiated (e.g. Japanese, Korean, Han Chinese biobanks), most other Asian countries have little or near-zero genomics data. To implement PRS models for under-represented populations, we explored transfer learning approaches, assuming that information from existing large datasets can compensate for the small sample size that can be feasibly obtained in developing countries, like Vietnam. Here, we benchmark 13 common PRS methods in meta-population strategy (combining individual genotype data from multiple populations) and multi-population strategy (combining summary statistics from multiple populations). Our results highlight the complementarity of different populations and the choice of methods should depend on the target population. Based on these results, we discussed a set of guidelines to help users select the best method for their datasets. We developed a robust and comprehensive software to allow for benchmarking comparisons between methods and proposed a computational framework for improving PRS performance in a dataset with a small sample size. This work is expected to inform the development of genomics applications in under-represented populations. PRSUP framework is available at: https://github.com/BiomedicalMachineLearning/VGP.


Asunto(s)
Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Humanos , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple , Vietnam , Genómica/métodos , Factores de Riesgo
17.
Behav Genet ; 54(1): 34-41, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37801150

RESUMEN

Polygenic scores (PGS) are increasingly being used for prediction of social and behavioral traits, but suffer from many methodological, theoretical, and ethical concerns that profoundly limit their value. Primarily, these scores are derived from statistical correlations, carrying no inherent biological meaning, and thus may capture indirect effects. Further, the performance of these scores depends upon the diversity of the reference populations and the genomic panels from which they were derived, which consistently underrepresent minoritized populations, leading to poor fit when applied to diverse groups. There is also inherent danger of eugenic applications for the information gained from these scores, and general risk of misunderstandings that could lead to stigmatization for underrepresented groups. We urge extreme caution in use of PGS particularly for social/behavioral outcomes fraught for misinterpretation, with potential harm for the minoritized groups least likely to benefit from their use.


Asunto(s)
Estudio de Asociación del Genoma Completo , Herencia Multifactorial , Herencia Multifactorial/genética , Fenotipo , Genómica
18.
Am J Med Genet A ; 194(7): e63584, 2024 07.
Artículo en Inglés | MEDLINE | ID: mdl-38450933

RESUMEN

Debates about the prospective clinical use of polygenic risk scores (PRS) have grown considerably in the last years. The potential benefits of PRS to improve patient care at individual and population levels have been extensively underlined. Nonetheless, the use of PRS in clinical contexts presents a number of unresolved ethical challenges and consequent normative gaps that hinder their optimal implementation. Here, we conducted a systematic review of reasons of the normative literature discussing ethical issues and moral arguments related to the use of PRS for the prevention and treatment of common complex diseases. In total, we have included and analyzed 34 records, spanning from 2013 to 2023. The findings have been organized in three major themes: in the first theme, we consider the potential harms of PRS to individuals and their kin. In the theme "Threats to health equity," we consider ethical concerns of social relevance, with a focus on justice issues. Finally, the theme "Towards best practices" collects a series of research priorities and provisional recommendations to be considered for an optimal clinical translation of PRS. We conclude that the use of PRS in clinical care reinvigorates old debates in matters of health justice; however, open questions, regarding best practices in clinical counseling, suggest that the ethical considerations applicable in monogenic settings will not be sufficient to face PRS emerging challenges.


Asunto(s)
Predisposición Genética a la Enfermedad , Herencia Multifactorial , Humanos , Herencia Multifactorial/genética , Principios Morales , Pruebas Genéticas/ética , Medición de Riesgo , Asesoramiento Genético/ética , Factores de Riesgo , Puntuación de Riesgo Genético
19.
Vox Sang ; 119(1): 34-42, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38018286

RESUMEN

BACKGROUND AND OBJECTIVES: Although the genetic determinants of haemoglobin and ferritin have been widely studied, those of the clinically and globally relevant iron deficiency anaemia (IDA) and deferral due to hypohaemoglobinemia (Hb-deferral) are unclear. In this investigation, we aimed to quantify the value of genetic information in predicting IDA and Hb-deferral. MATERIALS AND METHODS: We analysed genetic data from up to 665,460 participants of the FinnGen, Blood Service Biobank and UK Biobank, and used INTERVAL (N = 39,979) for validation. We performed genome-wide association studies (GWASs) of IDA and Hb-deferral and utilized publicly available genetic associations to compute polygenic scores for IDA, ferritin and Hb. We fitted models to estimate the effect sizes of these polygenic risk scores (PRSs) on IDA and Hb-deferral risk while accounting for the individual's age, sex, weight, height, smoking status and blood donation history. RESULTS: Significant variants in GWASs of IDA and Hb-deferral appear to be a small subset of variants associated with ferritin and Hb. Effect sizes of genetic predictors of IDA and Hb-deferral are similar to those of age and weight which are typically used in blood donor management. A total genetic score for Hb-deferral was estimated for each individual. The odds ratio estimate between first decile against that at ninth decile of total genetic score distribution ranged from 1.4 to 2.2. CONCLUSION: The value of genetic data in predicting IDA or suitability to donate blood appears to be on a practically useful level.


Asunto(s)
Anemia Ferropénica , Humanos , Anemia Ferropénica/genética , Estudio de Asociación del Genoma Completo , Ferritinas/genética , Hemoglobinas/análisis
20.
Clin Transplant ; 38(5): e15336, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38762783

RESUMEN

BACKGROUND: Individual events during donation after circulatory death (DCD) procurement, such as hypotensive or hypoxic warm ischemia, or circulatory arrest are all a part of donor warm ischemia time (dWIT), and may have differing effects on the outcome of the liver graft. This study aimed to identify risk factors for postreperfusion syndrome (PRS), a state of severe hemodynamic derangement following graft reperfusion, and its impact on DCD liver transplantation (LT) outcomes. METHODS: This was a retrospective analysis using 106 DCD LT. Detailed information for events during procurement (withdrawal of life support; systolic blood pressure < 80 mmHg; oxygen saturation < 80%; circulatory arrest; aortic cold perfusion) and their association with the development of PRS were examined using logistic regression. RESULTS: The overall incidence of PRS was 26.4%, occurring in 28 patients. Independent risk factors for PRS were asystolic dWIT (odds ratio (OR) 3.65, 95% confidence interval (CI) 1.38-9.66) and MELD score (OR 1.06, 95% CI 1.01-1.10). Total bilirubin was significantly higher in the PRS group at postoperative day (POD) 1 (p = .02; 5.2 mg/dL vs. 3.4 mg/dL), POD 3 (p = .049; 4.5 mg/dL vs. 2.8 mg/dL), and POD 7 (p = .04; 3.1 mg/dL vs. 1.9 mg/dL). Renal replacement therapy after LT was more likely to be required in the PRS group (p = .01; 48.2% vs. 23.1%). CONCLUSION: Asystolic dWIT is a risk factor for the development of PRS in DCD LT. Our results suggest that asystolic dWIT should be considered when selecting DCD liver donors.


Asunto(s)
Trasplante de Hígado , Donantes de Tejidos , Isquemia Tibia , Humanos , Trasplante de Hígado/efectos adversos , Masculino , Femenino , Estudios Retrospectivos , Isquemia Tibia/efectos adversos , Persona de Mediana Edad , Factores de Riesgo , Pronóstico , Estudios de Seguimiento , Supervivencia de Injerto , Adulto , Obtención de Tejidos y Órganos , Complicaciones Posoperatorias/etiología , Daño por Reperfusión/etiología , Reperfusión/efectos adversos , Síndrome , Recolección de Tejidos y Órganos/efectos adversos
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