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2.
Sci Rep ; 13(1): 18532, 2023 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-37898691

RESUMO

Clostridioides difficile (C. diff.) infection (CDI) is a leading cause of hospital acquired diarrhea in North America and Europe and a major cause of morbidity and mortality. Known risk factors do not fully explain CDI susceptibility, and genetic susceptibility is suggested by the fact that some patients with colons that are colonized with C. diff. do not develop any infection while others develop severe or recurrent infections. To identify common genetic variants associated with CDI, we performed a genome-wide association analysis in 19,861 participants (1349 cases; 18,512 controls) from the Electronic Medical Records and Genomics (eMERGE) Network. Using logistic regression, we found strong evidence for genetic variation in the DRB locus of the MHC (HLA) II region that predisposes individuals to CDI (P > 1.0 × 10-14; OR 1.56). Altered transcriptional regulation in the HLA region may play a role in conferring susceptibility to this opportunistic enteric pathogen.


Assuntos
Infecções por Clostridium , Estudo de Associação Genômica Ampla , Humanos , Infecções por Clostridium/genética , Diarreia , Antígenos de Histocompatibilidade , Antígenos HLA/genética , Antígenos de Histocompatibilidade Classe II , Variação Genética
3.
Cornea ; 42(9): 1140-1149, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37170406

RESUMO

PURPOSE: The aim of this study was to assess risk for demographic variables and other health conditions that are associated with Fuchs endothelial corneal dystrophy (FECD). METHODS: We developed a FECD case-control algorithm based on structured electronic health record data and confirmed accuracy by individual review of charts at 3 Veterans Affairs (VA) Medical Centers. This algorithm was applied to the Department of VA Million Veteran Program cohort from whom sex, genetic ancestry, comorbidities, diagnostic phecodes, and laboratory values were extracted. Single-variable and multiple variable logistic regression models were used to determine the association of these risk factors with FECD diagnosis. RESULTS: Being a FECD case was associated with female sex, European genetic ancestry, and a greater number of comorbidities. Of 1417 diagnostic phecodes evaluated, 213 had a significant association with FECD, falling in both ocular and nonocular conditions, including diabetes mellitus (DM). Five of 69 laboratory values were associated with FECD, with the direction of change for 4 being consistent with DM. Insulin dependency and type 1 DM raised risk to a greater degree than type 2 DM, like other microvascular diabetic complications. CONCLUSIONS: Female sex, European ancestry, and multimorbidity increased FECD risk. Endocrine/metabolic clinic encounter codes and altered patterns of laboratory values support DM increasing FECD risk. Our results evoke a threshold model in which the FECD phenotype is intensified by DM and potentially other health conditions that alter corneal physiology. Further studies to better understand the relationship between FECD and DM are indicated and may help identify opportunities for slowing FECD progression.


Assuntos
Diabetes Mellitus , Distrofia Endotelial de Fuchs , Feminino , Humanos , Distrofia Endotelial de Fuchs/epidemiologia , Distrofia Endotelial de Fuchs/genética , Distrofia Endotelial de Fuchs/diagnóstico , Multimorbidade , Córnea , Fatores de Risco , Endotélio Corneano , Diabetes Mellitus/epidemiologia
4.
Annu Rev Biomed Data Sci ; 6: 339-356, 2023 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-37196357

RESUMO

Genome-wide association studies (GWAS) revolutionized our understanding of common genetic variation and its impact on common human disease and traits. Developed and adopted in the mid-2000s, GWAS led to searchable genotype-phenotype catalogs and genome-wide datasets available for further data mining and analysis for the eventual development of translational applications. The GWAS revolution was swift and specific, including almost exclusively populations of European descent, to the neglect of the majority of the world's genetic diversity. In this narrative review, we recount the GWAS landscape of the early years that established a genotype-phenotype catalog that is now universally understood to be inadequate for a complete understanding of complex human genetics. We then describe approaches taken to augment the genotype-phenotype catalog, including the study populations, collaborative consortia, and study design approaches aimed to generalize and then ultimately discover genome-wide associations in non-European descent populations. The collaborations and data resources established in the efforts to diversify genomic findings undoubtedly provide the foundations of the next chapters of genetic association studies with the advent of budget-friendly whole-genome sequencing.


Assuntos
Estudo de Associação Genômica Ampla , Medicina de Precisão , Humanos , Fenótipo , Estudos de Associação Genética , Predisposição Genética para Doença/genética
5.
PeerJ ; 11: e14910, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37214096

RESUMO

Polygenic risk scores (PRS) based on genome-wide discoveries are promising predictors or classifiers of disease development, severity, and/or progression for common clinical outcomes. A major limitation of most risk scores is the paucity of genome-wide discoveries in diverse populations, prompting an emphasis to generate these needed data for trans-population and population-specific PRS construction. Given diverse genome-wide discoveries are just now being completed, there has been little opportunity for PRS to be evaluated in diverse populations independent from the discovery efforts. To fill this gap, we leverage here summary data from a recent genome-wide discovery study of lipid traits (HDL-C, LDL-C, triglycerides, and total cholesterol) conducted in diverse populations represented by African Americans, Hispanics, Asians, Native Hawaiians, Native Americans, and others by the Population Architecture using Genomics and Epidemiology (PAGE) Study. We constructed lipid trait PRS using PAGE Study published genetic variants and weights in an independent African American adult patient population linked to de-identified electronic health records and genotypes from the Illumina Metabochip (n = 3,254). Using multi-population lipid trait PRS, we assessed levels of association for their respective lipid traits, clinical outcomes (cardiovascular disease and type 2 diabetes), and common clinical labs. While none of the multi-population PRS were strongly associated with the tested trait or outcome, PRSLDL-Cwas nominally associated with cardiovascular disease. These data demonstrate the complexity in applying PRS to real-world clinical data even when data from multiple populations are available.


Assuntos
Doenças Cardiovasculares , Diabetes Mellitus Tipo 2 , Adulto , Humanos , Negro ou Afro-Americano/genética , LDL-Colesterol/genética , Doenças Cardiovasculares/epidemiologia , Estudo de Associação Genômica Ampla , Fatores de Risco
6.
Eur Urol ; 84(1): 13-21, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-36872133

RESUMO

BACKGROUND: Genetic factors play an important role in prostate cancer (PCa) susceptibility. OBJECTIVE: To discover common genetic variants contributing to the risk of PCa in men of African ancestry. DESIGN, SETTING, AND PARTICIPANTS: We conducted a meta-analysis of ten genome-wide association studies consisting of 19378 cases and 61620 controls of African ancestry. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Common genotyped and imputed variants were tested for their association with PCa risk. Novel susceptibility loci were identified and incorporated into a multiancestry polygenic risk score (PRS). The PRS was evaluated for associations with PCa risk and disease aggressiveness. RESULTS AND LIMITATIONS: Nine novel susceptibility loci for PCa were identified, of which seven were only found or substantially more common in men of African ancestry, including an African-specific stop-gain variant in the prostate-specific gene anoctamin 7 (ANO7). A multiancestry PRS of 278 risk variants conferred strong associations with PCa risk in African ancestry studies (odds ratios [ORs] >3 and >5 for men in the top PRS decile and percentile, respectively). More importantly, compared with men in the 40-60% PRS category, men in the top PRS decile had a significantly higher risk of aggressive PCa (OR = 1.23, 95% confidence interval = 1.10-1.38, p = 4.4 × 10-4). CONCLUSIONS: This study demonstrates the importance of large-scale genetic studies in men of African ancestry for a better understanding of PCa susceptibility in this high-risk population and suggests a potential clinical utility of PRS in differentiating between the risks of developing aggressive and nonaggressive disease in men of African ancestry. PATIENT SUMMARY: In this large genetic study in men of African ancestry, we discovered nine novel prostate cancer (PCa) risk variants. We also showed that a multiancestry polygenic risk score was effective in stratifying PCa risk, and was able to differentiate risk of aggressive and nonaggressive disease.


Assuntos
Predisposição Genética para Doença , Neoplasias da Próstata , Masculino , Humanos , Estudo de Associação Genômica Ampla , Neoplasias da Próstata/genética , Neoplasias da Próstata/epidemiologia , Fatores de Risco , População Negra/genética
7.
Pac Symp Biocomput ; 28: 257-262, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36540982

RESUMO

Precision medicine requires a deep understanding of complex biomedical and healthcare data, which is being generated at exponential rates and increasingly made available through public biobanks, electronic medical record systems and biomedical databases and knowledgebases. The complexity and sheer amount of data prohibit manual manipulation. Instead, the field depends on artificial intelligence approaches to parse, annotate, evaluate and interpret the data to enable applications to patient healthcare At the 2023 Pacific Symposium on Biocomputing (PSB) session entitled "Precision Medicine: Using Artificial Intelligence (AI) to improve diagnostics and healthcare", we spotlight research that develops and applies computational methodologies to solve biomedical problems.


Assuntos
Inteligência Artificial , Medicina de Precisão , Humanos , Biologia Computacional , Software , Atenção à Saúde
8.
Pediatr Nephrol ; 38(4): 1115-1126, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-35943576

RESUMO

BACKGROUND: Minimal change disease (MCD) is the major cause of childhood idiopathic nephrotic syndrome, which is characterized by massive proteinuria and debilitating edema. Proteinuria in MCD is typically rapidly reversible with corticosteroid therapy, but relapses are common, and children often have many adverse events from the repeated courses of immunosuppressive therapy. The pathobiology of MCD remains poorly understood. Prior clinical observations suggest that abnormal T-cell function may play a central role in MCD pathogenesis. Based on these observations, we hypothesized that T-cell responses to specific exposures or antigens lead to a clonal expansion of T-cell subsets, a restriction in the T-cell repertoire, and an elaboration of specific circulating factors that trigger disease onset and relapses. METHODS: To test these hypotheses, we sequenced T-cell receptors in fourteen MCD, four focal segmental glomerulosclerosis (FSGS), and four membranous nephropathy (MN) patients with clinical data and blood samples drawn during active disease and during remission collected by the Nephrotic Syndrome Study Network (NEPTUNE). We calculated several T-cell receptor diversity metrics to assess possible differences between active disease and remission states in paired samples. RESULTS: Median productive clonality did not differ between MCD active disease (0.0083; range: 0.0042, 0.0397) and remission (0.0088; range: 0.0038, 0.0369). We did not identify dominant clonotypes in MCD active disease, and few clonotypes were shared with FSGS and MN patients. CONCLUSIONS: While these data do not support an obvious role of the adaptive immune system T-cells in MCD pathogenesis, further study is warranted given the limited sample size. A higher resolution version of the Graphical abstract is available as Supplementary information.


Assuntos
Glomerulonefrite Membranosa , Glomerulosclerose Segmentar e Focal , Nefrose Lipoide , Síndrome Nefrótica , Criança , Humanos , Nefrose Lipoide/tratamento farmacológico , Glomerulosclerose Segmentar e Focal/complicações , Netuno , Síndrome Nefrótica/tratamento farmacológico , Proteinúria/etiologia , Glomerulonefrite Membranosa/complicações , Receptores de Antígenos de Linfócitos T/uso terapêutico , Recidiva
9.
Pac Symp Biocomput ; 28: 413-424, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36540996

RESUMO

A major goal of precision medicine is to stratify patients based on their genetic risk for a disease to inform future screening and intervention strategies. For conditions like primary open-angle glaucoma (POAG), the genetic risk architecture is complicated with multiple variants contributing small effects on risk. Following the tepid success of genome-wide association studies for high-effect disease risk variant discovery, genetic risk scores (GRS), which collate effects from multiple genetic variants into a single measure, have shown promise for disease risk stratification. We assessed the application of GRS for POAG risk stratification in Hispanic-descent (HIS) and European-descent (EUR) Veterans in the Million Veteran Program. Unweighted and cross-ancestry meta-weighted GRS were calculated based on 127 genomic variants identified in the most recent report of cross-ancestry POAG meta-analyses. We found that both GRS types were associated with POAG case-control status and performed similarly in HIS and EUR Veterans. This trend was also seen in our subset analysis of HIS Veterans with less than 50% EUR global genetic ancestry. Our findings highlight the importance of evaluating GRS based on known POAG risk variants in different ancestry groups and emphasize the need for more multi-ancestry POAG genetic studies.


Assuntos
Glaucoma de Ângulo Aberto , Veteranos , Humanos , Estudo de Associação Genômica Ampla , Predisposição Genética para Doença , Glaucoma de Ângulo Aberto/genética , Glaucoma de Ângulo Aberto/diagnóstico , Biologia Computacional , Fatores de Risco , Hispânico ou Latino/genética , Polimorfismo de Nucleotídeo Único
11.
Ophthalmology ; 129(11): 1263-1274, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35718050

RESUMO

PURPOSE: Primary open-angle glaucoma (POAG) is a degenerative eye disease for which early treatment is critical to mitigate visual impairment and irreversible blindness. POAG-associated loci individually confer incremental risk. Genetic risk score(s) (GRS) could enable POAG risk stratification. Despite significantly higher POAG burden among individuals of African ancestry (AFR), GRS are limited in this population. A recent large-scale, multi-ancestry meta-analysis identified 127 POAG-associated loci and calculated cross-ancestry and ancestry-specific effect estimates, including in European ancestry (EUR) and AFR individuals. We assessed the utility of the 127-variant GRS for POAG risk stratification in EUR and AFR Veterans in the Million Veteran Program (MVP). We also explored the association between GRS and documented invasive glaucoma surgery (IGS). DESIGN: Cross-sectional study. PARTICIPANTS: MVP Veterans with imputed genetic data, including 5830 POAG cases (445 with IGS documented in the electronic health record) and 64 476 controls. METHODS: We tested unweighted and weighted GRS of 127 published risk variants in EUR (3382 cases and 58 811 controls) and AFR (2448 cases and 5665 controls) Veterans in the MVP. Weighted GRS were calculated using effect estimates from the most recently published report of cross-ancestry and ancestry-specific meta-analyses. We also evaluated GRS in POAG cases with documented IGS. MAIN OUTCOME MEASURES: Performance of 127-variant GRS in EUR and AFR Veterans for POAG risk stratification and association with documented IGS. RESULTS: GRS were significantly associated with POAG (P < 5 × 10-5) in both groups; a higher proportion of EUR compared with AFR were consistently categorized in the top GRS decile (21.9%-23.6% and 12.9%-14.5%, respectively). Only GRS weighted by ancestry-specific effect estimates were associated with IGS documentation in AFR cases; all GRS types were associated with IGS in EUR cases. CONCLUSIONS: Varied performance of the GRS for POAG risk stratification and documented IGS association in EUR and AFR Veterans highlights (1) the complex risk architecture of POAG, (2) the importance of diverse representation in genomics studies that inform GRS construction and evaluation, and (3) the necessity of expanding diverse POAG-related genomic data so that GRS can equitably aid in screening individuals at high risk of POAG and who may require more aggressive treatment.


Assuntos
Glaucoma de Ângulo Aberto , Veteranos , Humanos , Glaucoma de Ângulo Aberto/diagnóstico , Glaucoma de Ângulo Aberto/epidemiologia , Glaucoma de Ângulo Aberto/genética , Estudo de Associação Genômica Ampla , Predisposição Genética para Doença , Polimorfismo de Nucleotídeo Único , Estudos Transversais , Estudos de Casos e Controles , Fatores de Risco
12.
PLoS Genet ; 18(4): e1010113, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35482673

RESUMO

The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n = 35) or hospitalization (n = 42) due to severe COVID-19 using genome-wide association summary data from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828 = 53 and nrs505922 = 59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p = 1.32 x 10-199), and thrombosis ORrs505922 1.33, p = 2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p = 4.12 × 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p = 2.26× 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p = 6.48 x10-23, lupus OR 0.84, p = 3.97 x 10-06. PheWAS stratified by ancestry demonstrated differences in genotype-phenotype associations. LMNA (rs581342) associated with neutropenia OR 1.29 p = 4.1 x 10-13 among Veterans of African and Hispanic ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.


Assuntos
COVID-19 , Veteranos , COVID-19/epidemiologia , COVID-19/genética , Estudos de Associação Genética , Estudo de Associação Genômica Ampla/métodos , Humanos , Polimorfismo de Nucleotídeo Único/genética
13.
Genome Res ; 32(4): 778-790, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35210353

RESUMO

More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure-based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.


Assuntos
Doença de Alzheimer , Doença de Alzheimer/genética , Frequência do Gene , Predisposição Genética para Doença , Humanos , Proteínas Relacionadas a Receptor de LDL/genética , Proteínas Relacionadas a Receptor de LDL/metabolismo , Proteínas de Membrana Transportadoras/genética , Mutação de Sentido Incorreto , Fenótipo , Sequenciamento do Exoma
14.
Eur Urol ; 81(5): 458-462, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35031163

RESUMO

A rare African ancestry-specific germline deletion variant in HOXB13 (X285K, rs77179853) was recently reported in Martinican men with early-onset prostate cancer. Given the role of HOXB13 germline variation in prostate cancer, we investigated the association between HOXB13 X285K and prostate cancer risk in a large sample of 22 361 African ancestry men, including 11 688 prostate cancer cases. The risk allele was present only in men of West African ancestry, with an allele frequency in men that ranged from 0.40% in Ghana and 0.31% in Nigeria to 0% in Uganda and South Africa, with a range of frequencies in men with admixed African ancestry from North America and Europe (0-0.26%). HOXB13 X285K was associated with 2.4-fold increased odds of prostate cancer (95% confidence interval [CI] = 1.5-3.9, p = 2 × 10-4), with greater risk observed for more aggressive and advanced disease (Gleason ≥8: odds ratio [OR] = 4.7, 95% CI = 2.3-9.5, p = 2 × 10-5; stage T3/T4: OR = 4.5, 95% CI = 2.0-10.0, p = 2 × 10-4; metastatic disease: OR = 5.1, 95% CI = 1.9-13.7, p = 0.001). We estimated that the allele arose in West Africa 1500-4600 yr ago. Further analysis is needed to understand how the HOXB13 X285K variant impacts the HOXB13 protein and function in the prostate. Understanding who carries this mutation may inform prostate cancer screening in men of West African ancestry. PATIENT SUMMARY: A rare African ancestry-specific germline deletion in HOXB13, found only in men of West African ancestry, was reported to be associated with an increased risk of overall and advanced prostate cancer. Understanding who carries this mutation may help inform screening for prostate cancer in men of West African ancestry.


Assuntos
Detecção Precoce de Câncer , Neoplasias da Próstata , Estudos de Casos e Controles , Predisposição Genética para Doença , Células Germinativas/patologia , Mutação em Linhagem Germinativa , Proteínas de Homeodomínio/genética , Humanos , Masculino , Antígeno Prostático Específico/genética , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia
15.
Trends Genet ; 38(4): 353-363, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-34991903

RESUMO

In the past 10 years since its introduction, phenome-wide association studies (PheWAS) have uncovered novel genotype-phenotype relationships. Along the way, PheWAS have evolved in many aspects as a study design with the expanded availability of large data repositories with genome-wide data linked to detailed phenotypic data. Advancement in methods, including algorithms, software, and publicly available integrated resources, makes it feasible to more fully realize the potential of PheWAS, overcoming the previous computational and analytical limitations. We review here the most recent improvements and notable applications of PheWAS since the second half of the decade from its inception. We also note the challenges that remain embedded along the entire PheWAS analytical pipeline that necessitate further development of tools and resources to further advance the understanding of the complex genetic architecture underlying human diseases and traits.


Assuntos
Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Algoritmos , Fenótipo , Software
16.
Prostate Cancer Prostatic Dis ; 25(2): 229-237, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34127801

RESUMO

BACKGROUND: We previously developed an African-ancestry-specific polygenic hazard score (PHS46+African) that substantially improved prostate cancer risk stratification in men with African ancestry. The model consists of 46 SNPs identified in Europeans and 3 SNPs from 8q24 shown to improve model performance in Africans. Herein, we used principal component (PC) analysis to uncover subpopulations of men with African ancestry for whom the utility of PHS46+African may differ. MATERIALS AND METHODS: Genotypic data were obtained from the PRACTICAL consortium for 6253 men with African genetic ancestry. Genetic variation in a window spanning 3 African-specific 8q24 SNPs was estimated using 93 PCs. A Cox proportional hazards framework was used to identify the pair of PCs most strongly associated with the performance of PHS46+African. A calibration factor (CF) was formulated using Cox coefficients to quantify the extent to which the performance of PHS46+African varies with PC. RESULTS: CF of PHS46+African was strongly associated with the first and twentieth PCs. Predicted CF ranged from 0.41 to 2.94, suggesting that PHS46+African may be up to 7 times more beneficial to some African men than others. The explained relative risk for PHS46+African varied from 3.6% to 9.9% for individuals with low and high CF values, respectively. By cross-referencing our data set with 1000 Genomes, we identified significant associations between continental and calibration groupings. CONCLUSION: We identified PCs within 8q24 that were strongly associated with the performance of PHS46+African. Further research to improve the clinical utility of polygenic risk scores (or models) is needed to improve health outcomes for men of African ancestry.


Assuntos
População Negra , Cromossomos Humanos Par 8 , Predisposição Genética para Doença , Herança Multifatorial , Neoplasias da Próstata , População Negra/genética , Estudos de Casos e Controles , Cromossomos Humanos Par 8/genética , Humanos , Masculino , Polimorfismo de Nucleotídeo Único , Neoplasias da Próstata/etnologia , Neoplasias da Próstata/genética , Medição de Risco , População Branca/genética
17.
Ophthalmic Epidemiol ; 29(6): 640-648, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-34822319

RESUMO

The availability of electronic health record (EHR)-linked biobank data for research presents opportunities to better understand complex ocular diseases. Developing accurate computable phenotypes for ocular diseases for which gold standard diagnosis includes imaging remains inaccessible in most biobank-linked EHRs. The objective of this study was to develop and validate a computable phenotype to identify primary open-angle glaucoma (POAG) through accessing the Department of Veterans Affairs (VA) Computerized Patient Record System (CPRS) and Million Veteran Program (MVP) biobank. Accessing CPRS clinical ophthalmology data from VA Medical Center Eye Clinic (VAMCEC) patients, we developed and iteratively refined POAG case and control algorithms based on clinical, prescription, and structured diagnosis data (ICD-CM codes). Refinement was performed via detailed chart review, initially at a single VAMCEC (n = 200) and validated at two additional VAMCECs (n = 100 each). Positive and negative predictive values (PPV, NPV) were computed as the proportion of CPRS patients correctly classified with POAG or without POAG, respectively, by the algorithms, validated by ophthalmologists and optometrists with access to gold-standard clinical diagnosis data. The final algorithms performed better than previously reported approaches in assuring the accuracy and reproducibility of POAG classification (PPV >83% and NPV >97%) with consistent performance in Black or African American and in White Veterans. Applied to the MVP to identify cases and controls, genetic analysis of a known POAG-associated locus further validated the algorithms. We conclude that ours is a viable approach to use combined EHR-genetic data to study patients with complex diseases that require imaging confirmation.


Assuntos
Glaucoma de Ângulo Aberto , Veteranos , Humanos , Glaucoma de Ângulo Aberto/diagnóstico , Glaucoma de Ângulo Aberto/epidemiologia , Reprodutibilidade dos Testes , Algoritmos , Registros Eletrônicos de Saúde
18.
Pac Symp Biocomput ; 27: 223-230, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34890151

RESUMO

The continued generation of large amounts of data within healthcare-from imaging to electronic medical health records to genomics and multi-omics -necessitates tools and methods to parse and interpret these data to improve healthcare outcomes. Artificial intelligence, and in particular deep learning, has enabled researchers to gain new insights from large scale and multimodal data. At the 2022 Pacific Symposium on Biocomputing (PSB) session entitled "Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare", we showcase the latest research, influenced and inspired by the idea of using technology to build a more fair, tailored, and cost-effective healthcare system after the COVID-19 pandemic.


Assuntos
Inteligência Artificial , COVID-19 , Biologia Computacional , Atenção à Saúde , Humanos , Pandemias , Medicina de Precisão , SARS-CoV-2
19.
PLoS One ; 16(11): e0259962, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34793544

RESUMO

OBJECTIVE: Hypertension is more prevalent in African Americans (AA) than other ethnic groups. Genome-wide association studies (GWAS) have identified loci associated with hypertension and other cardio-metabolic traits like type 2 diabetes, coronary artery disease, and body mass index (BMI), however the AA population is underrepresented in these studies. In this study, we examined a large AA cohort for the generalizability of 14 Metabochip array SNPs with previously reported European hypertension associations. METHODS: To evaluate associations, we analyzed genotype data of 14 SNPs for their associations with a diagnosis of hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) in a case-control study of an AA population (N = 9,534). We also performed an age-stratified analysis (>30, 30≥59 and ≥60 years) following the hypertension definition described by the 8th Joint National Committee (JNC). Associations were adjusted for BMI, age, age2, sex, clinical confounders, and genetic ancestry using multivariable regression models to estimate odds ratios (ORs) and beta-coefficients. Analyses stratified by sex were also conducted. Meta-analyses (including both BioVU and COGENT-BP cohorts) were performed using a random-effects model. RESULTS: We found rs880315 to be associated with systolic hypertension (SBP≥140 mmHg) in the entire cohort (OR = 1.14, p = 0.003) and within women only (OR = 1.16, p = 0.012). Variant rs17080093 associated with lower SBP and DBP (ß = -2.99, p = 0.0352 and - ß = 1.69, p = 0.0184) among younger individuals, particularly in younger women (ß = -3.92, p = 0.0025 and ß = -1.87, p = 0.0241 for SBP and DBP respectively). SNP rs1530440 associated with higher SBP and DBP measurements (younger individuals ß = 4.1, p = 0.039 and ß = 2.5, p = 0.043 for SBP and DBP; (younger women ß = 4.5, p = 0.025 and ß = 2.9, p = 0.028 for SBP and DBP), and hypertension risk in older women (OR = 1.4, p = 0.050). rs16948048 increases hypertension risk in younger individuals (OR = 1.31, p = 0.011). Among mid-age women rs880315 associated with higher risk of hypertension (OR = 1.20, p = 0.027). rs1361831 associated with DBP (ß = -1.96, p = 0.02) among individuals older than 60 years. rs3096277 increases hypertension risk among older individuals (OR = 1.26 p = 0.0015), however, this variant also reduces SBP among younger women (ß = -2.63, p = 0.0102). CONCLUSION: These findings suggest that European-descent and AA populations share genetic loci that contribute to blood pressure traits and hypertension. However, the OR and beta-coefficient estimates differ, and some are age-dependent. Additional genetic studies of hypertension in AA are warranted to identify new loci associated with hypertension and blood pressure traits in this population.


Assuntos
Negro ou Afro-Americano/genética , Estudo de Associação Genômica Ampla , Hipertensão/genética , Adulto , Pressão Sanguínea , Estudos de Coortes , Feminino , Humanos , Masculino , Análise em Microsséries , Polimorfismo de Nucleotídeo Único
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