Polygenic Risk Scores

多基因风险评分
  • 文章类型: Journal Article
    背景:已经报道了代谢状态和代谢变化与心血管结局风险之间的关联。然而,遗传易感性在这些关联背后的作用仍未被探索.我们的目的是检查代谢状态,代谢转变,和遗传易感性共同影响不同体重指数(BMI)类别的心血管结局和全因死亡率.
    方法:在我们对英国生物库的分析中,基线时,我们共纳入481,576名参与者(平均年龄:56.55岁;男性:45.9%).代谢健康(MH)状态定义为存在<3个异常成分(腰部情况、血压,血糖,甘油三酯,和高密度脂蛋白胆固醇)。正常体重,超重,肥胖定义为18.5≤BMI<25kg/m2,25≤BMI<30kg/m2,BMI≥30kg/m2。使用多基因风险评分(PRS)估计遗传易感性。进行Cox回归以评估代谢状态的关联,代谢转变,和PRS与不同BMI类别的心血管结局和全因死亡率。
    结果:在14.38年的中位随访中,31,883(7.3%)全因死亡,8133例(1.8%)心血管疾病(CVD)死亡,记录了67,260例(14.8%)CVD病例。在那些具有高PRS的人中,与代谢不健康的肥胖人群相比,代谢健康超重人群的全因死亡率(风险比[HR]0.70;95%置信区间[CI]0.65,0.76)和CVD死亡率(HR0.57;95%CI0.50,0.64)风险最低。在中度和低度PRS组中,有益的关联似乎更大。代谢健康正常体重的个体患CVD的风险最低(HR0.54;95%CI0.51,0.57)。此外,不同BMI类别的代谢状态和PRS与心血管结局和全因死亡率的负相关在65岁以下的个体中更为显著(P交互作用<0.05).此外,在BMI类别中,观察到代谢转变和PRS对这些结局的综合保护作用.
    结论:MH状态和低PRS与所有BMI类别的不良心血管结局和全因死亡率的较低风险相关。这种保护作用在65岁以下的个体中尤其明显。需要进一步的研究来确认不同人群的这些发现,并调查所涉及的潜在机制。
    BACKGROUND: Associations between metabolic status and metabolic changes with the risk of cardiovascular outcomes have been reported. However, the role of genetic susceptibility underlying these associations remains unexplored. We aimed to examine how metabolic status, metabolic transitions, and genetic susceptibility collectively impact cardiovascular outcomes and all-cause mortality across diverse body mass index (BMI) categories.
    METHODS: In our analysis of the UK Biobank, we included a total of 481,576 participants (mean age: 56.55; male: 45.9%) at baseline. Metabolically healthy (MH) status was defined by the presence of < 3 abnormal components (waist circumstance, blood pressure, blood glucose, triglycerides, and high-density lipoprotein cholesterol). Normal weight, overweight, and obesity were defined as 18.5 ≤ BMI < 25 kg/m2, 25 ≤ BMI < 30 kg/m2, and BMI ≥ 30 kg/m2, respectively. Genetic predisposition was estimated using the polygenic risk score (PRS). Cox regressions were performed to evaluate the associations of metabolic status, metabolic transitions, and PRS with cardiovascular outcomes and all-cause mortality across BMI categories.
    RESULTS: During a median follow-up of 14.38 years, 31,883 (7.3%) all-cause deaths, 8133 (1.8%) cardiovascular disease (CVD) deaths, and 67,260 (14.8%) CVD cases were documented. Among those with a high PRS, individuals classified as metabolically healthy overweight had the lowest risk of all-cause mortality (hazard ratios [HR] 0.70; 95% confidence interval [CI] 0.65, 0.76) and CVD mortality (HR 0.57; 95% CI 0.50, 0.64) compared to those who were metabolically unhealthy obesity, with the beneficial associations appearing to be greater in the moderate and low PRS groups. Individuals who were metabolically healthy normal weight had the lowest risk of CVD morbidity (HR 0.54; 95% CI 0.51, 0.57). Furthermore, the inverse associations of metabolic status and PRS with cardiovascular outcomes and all-cause mortality across BMI categories were more pronounced among individuals younger than 65 years (Pinteraction < 0.05). Additionally, the combined protective effects of metabolic transitions and PRS on these outcomes among BMI categories were observed.
    CONCLUSIONS: MH status and a low PRS are associated with a lower risk of adverse cardiovascular outcomes and all-cause mortality across all BMI categories. This protective effect is particularly pronounced in individuals younger than 65 years. Further research is required to confirm these findings in diverse populations and to investigate the underlying mechanisms involved.
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  • 文章类型: Journal Article
    许多但不是所有的双相情感障碍患者由于严重的情绪发作需要住院治疗。同样,一些但并非所有患者都经历了超出急性情绪发作的长期职业功能障碍。尚不清楚双相情感障碍的这些不同结果是否由不同的多基因谱驱动。这里,我们评估了主要精神疾病的多基因评分(PGSs)和受教育程度与双相情感障碍患者的职业功能和精神科住院率的关联.
    对4,782名双相情感障碍患者和2,963名对照受试者进行了基因分型,并与瑞典国家登记册相关联。使用至少10年登记数据的纵向测量得出不就业年份的百分比,长期病假的百分比,和平均每年精神病住院人数。序数回归用于测试结果与双相情感障碍的PGS之间的关联。精神分裂症,重度抑郁症,注意缺陷多动障碍(ADHD),和教育程度。使用来自双相情感障碍研究网络队列(N=4,219)的数据对住院患者进行复制分析。
    双相情感障碍的长期病假和失业与精神分裂症的PGS显著相关,多动症,重度抑郁症,和教育程度,但不能用PGS治疗双相情感障碍.相比之下,每年住院人数与双相情感障碍和精神分裂症的较高PGS相关,但不是与其他发电系统。
    双相情感障碍的严重程度(以住院人数为指标)与长期职业功能障碍不同的多基因特征相关。这些发现具有临床意义,这表明减轻职业功能障碍需要采取干预措施,而不是预防情绪发作的干预措施。
    UNASSIGNED: Many but not all persons with bipolar disorder require hospital care because of severe mood episodes. Likewise, some but not all patients experience long-term occupational dysfunction that extends beyond acute mood episodes. It is not known whether these dissimilar outcomes of bipolar disorder are driven by different polygenic profiles. Here, polygenic scores (PGSs) for major psychiatric disorders and educational attainment were assessed for associations with occupational functioning and psychiatric hospital admissions in bipolar disorder.
    UNASSIGNED: A total of 4,782 patients with bipolar disorder and 2,963 control subjects were genotyped and linked to Swedish national registers. Longitudinal measures from at least 10 years of registry data were used to derive percentage of years without employment, percentage of years with long-term sick leave, and mean number of psychiatric hospital admissions per year. Ordinal regression was used to test associations between outcomes and PGSs for bipolar disorder, schizophrenia, major depressive disorder, attention deficit hyperactivity disorder (ADHD), and educational attainment. Replication analyses of hospital admissions were conducted with data from the Bipolar Disorder Research Network cohort (N=4,219).
    UNASSIGNED: Long-term sick leave and unemployment in bipolar disorder were significantly associated with PGSs for schizophrenia, ADHD, major depressive disorder, and educational attainment, but not with the PGS for bipolar disorder. By contrast, the number of hospital admissions per year was associated with higher PGSs for bipolar disorder and schizophrenia, but not with the other PGSs.
    UNASSIGNED: Bipolar disorder severity (indexed by hospital admissions) was associated with a different polygenic profile than long-term occupational dysfunction. These findings have clinical implications, suggesting that mitigating occupational dysfunction requires interventions other than those deployed to prevent mood episodes.
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  • 文章类型: Journal Article
    背景:关于轻度体力活动(LPA)的混合效应和重量的信息有限,适度的身体活动(MPA),和剧烈的体力活动(VPA)对痴呆症的风险。
    方法:基于UKBiobank数据集进行前瞻性队列研究。我们纳入了2006-2010年间基线年龄至少45岁无痴呆的参与者。采用加权分位数和回归分析三种体力活动对痴呆风险的混合效应和权重。
    结果:这项研究包括354,123名参与者,平均基线年龄为58.0岁,女性参与者占52.4%。在12.5年的中位随访时间内,观察到5,136例痴呆。LPA的混合效应,MPA,和VPA对痴呆有统计学意义(β:-0.0924,95%置信区间(CI):(-0.1402,-0.0446),P<0.001),VPA(体重:0.7922)对降低痴呆症风险的贡献最大,其次是MPA(0.1939)。对于阿尔茨海默病,MPA贡献最大(0.8555);对于血管性痴呆,VPA贡献最大(0.6271)。
    结论:对于阿尔茨海默病,MPA被确定为最具影响力的因素,而VPA对血管性痴呆最有影响。
    BACKGROUND: There is limited information on the mixture effect and weights of light physical activity (LPA), moderate physical activity (MPA), and vigorous physical activity (VPA) on dementia risk.
    METHODS: A prospective cohort study was conducted based on the UK Biobank dataset. We included participants aged at least 45 years old without dementia at baseline between 2006-2010. The weighted quantile sum regression was used to explore the mixture effect and weights of three types of physical activity on dementia risk.
    RESULTS: This study includes 354,123 participants, with a mean baseline age of 58.0-year-old and 52.4 % of female participants. During a median follow-up time of 12.5 years, 5,136 cases of dementia were observed. The mixture effect of LPA, MPA, and VPA on dementia was statistically significant (β: -0.0924, 95 % Confidence Interval (CI): (-0.1402, -0.0446), P < 0.001), with VPA (weight: 0.7922) contributing most to a lower dementia risk, followed by MPA (0.1939). For Alzheimer\'s disease, MPA contributed the most (0.8555); for vascular dementia, VPA contributed the most (0.6271).
    CONCLUSIONS: For Alzheimer\'s disease, MPA was identified as the most influential factor, while VPA stood out as the most impactful for vascular dementia.
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  • 文章类型: Journal Article
    冠状动脉疾病(CAD)是一种高度可遗传的多因素疾病。许多全基因组关联研究(GWAS)促进了多基因风险评分(PRS)的构建,以预测CAD的未来发病率。然而,仅在欧洲人口中。此外,识别具有全因死亡风险升高的CAD患者是二级预防的关键挑战,这将在很大程度上有助于减轻公共医疗保健的负担。
    我们招募了1,776名中国CAD患者,并进行了长达11年的医学随访。使用修剪和阈值法计算CAD的PRS及其14个危险因素。通过Cox回归计算它们与全因死亡的相关性。
    我们发现CAD的PRS及其七个危险因素,即心肌梗塞,缺血性卒中,心绞痛,心力衰竭,低密度脂蛋白胆固醇,总胆固醇和C反应蛋白,与死亡显著相关(P≤0.05),而体重指数的PRS表现出中等相关性(P<0.1)。使用5倍交叉验证的Elastic-netCox回归将这9个PRS模型整合到一个meta评分中,metaPRS,在对不同死亡风险的患者进行分层方面表现良好(P<0.0001)。将metaPRS与临床危险因素相结合,进一步增加了辨别能力和4%的敏感性。由对CAD的遗传易感性及其危险因素产生的metaPRS可以很好地根据CAD患者的死亡风险对其进行分层。整合metaPRS和临床危险因素可能有助于确定预后不良风险较高的患者。
    UNASSIGNED: Coronary artery disease (CAD) is a highly heritable and multifactorial disease. Numerous genome-wide association studies (GWAS) facilitated the construction of polygenic risk scores (PRS) for predicting future incidence of CAD, however, exclusively in European populations. Furthermore, identifying CAD patients with elevated risks of all-cause death presents a critical challenge in secondary prevention, which will contribute largely to reducing the burden for public healthcare.
    UNASSIGNED: We recruited a cohort of 1,776 Chinese CAD patients and performed medical follow-up for up to 11 years. A pruning and thresholding method was used to calculate PRS of CAD and its 14 risk factors. Their correlations with all-cause death were computed via Cox regression.
    UNASSIGNED: We found that the PRS for CAD and its seven risk factors, namely myocardial infarction, ischemic stroke, angina, heart failure, low-density lipoprotein cholesterol, total cholesterol and C-reaction protein, were significantly associated with death (P ≤ 0.05), whereas the PRS of body mass index displayed moderate association (P < 0.1). Elastic-net Cox regression with 5-fold cross-validation was used to integrate these nine PRS models into a meta score, metaPRS, which performed well in stratifying patients at different risks for death (P < 0.0001). Combining metaPRS with clinical risk factors further increased the discerning power and a 4% increase in sensitivity. The metaPRS generated from the genetic susceptibility to CAD and its risk factors can well stratify CAD patients by their risks of death. Integrating metaPRS and clinical risk factors may contribute to identifying patients at higher risk of poor prognosis.
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  • 文章类型: Journal Article
    慢性阻塞性肺疾病(COPD)是一个主要的公共卫生问题,影响全球估计1.64亿人。早期发现和干预策略对于减轻COPD的负担至关重要。但目前的筛查方法在准确预测风险的能力上是有限的.机器学习(ML)模型通过结合遗传和电子病历数据,为提高COPD风险预测的准确性提供了希望。在这项研究中,我们利用常规筛查数据开发并评估了8个用于COPD初级筛查的ML模型,多基因风险评分(PRS),额外的临床数据,或者三者的组合。为了评估我们的模型,我们对UKBiobank数据库中的约329,396例患者进行了回顾性分析.结合个人信息和血液生化检测结果显著提高了模型预测COPD风险的准确性,实现0.8505AUC的最佳性能,特异性为0.8539,敏感性为0.7584。这些结果表明,ML模型可以有效地用于20至50岁个体的COPD风险的准确预测。为早期发现和干预提供了一个有价值的工具。
    Chronic obstructive pulmonary disease (COPD) is a major public health concern, affecting estimated 164 million people worldwide. Early detection and intervention strategies are essential to reduce the burden of COPD, but current screening approaches are limited in their ability to accurately predict risk. Machine learning (ML) models offer promise for improved accuracy of COPD risk prediction by combining genetic and electronic medical record data. In this study, we developed and evaluated eight ML models for primary screening of COPD utilizing routine screening data, polygenic risk scores (PRS), additional clinical data, or a combination of all three. To assess our models, we conducted a retrospective analysis of approximately 329,396 patients in the UK Biobank database. Incorporating personal information and blood biochemical test results significantly improved the model\'s accuracy for predicting COPD risk, achieving a best performance of 0.8505 AUC, a specificity of 0.8539 and a sensitivity of 0.7584. These results indicate that ML models can be effectively utilized for accurate prediction of COPD risk in individuals aged 20 to 50 years, providing a valuable tool for early detection and intervention.
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  • 文章类型: Journal Article
    基因测序技术的进步和成本的降低导致了基因组数据作为大数据不可或缺的组成部分的激增。大量基因组数据和更复杂的基因组分析技术的可用性促进了基因组学从实验室到临床环境的转变。更全面,更精确的DNA测序使患者能够在分子水平上解决健康问题。促进早期诊断,及时干预,和个性化的医疗保健管理策略。通过鉴定相关基因进一步探索疾病机制可能有助于发现治疗靶标。对个体疾病风险的预测允许改进分层和个性化预防措施。鉴于大量的基因组数据,人工智能,作为一种新兴的数据分析技术,有望对基因组学产生重大影响。
    Advances in gene sequencing technology and decreasing costs have resulted in a proliferation of genomic data as an integral component of big data. The availability of vast amounts of genomic data and more sophisticated genomic analysis techniques has facilitated the transition of genomics from the laboratory to clinical settings. More comprehensive and precise DNA sequencing empowers patients to address health issues at the molecular level, facilitating early diagnosis, timely intervention, and personalized healthcare management strategies. Further exploration of disease mechanisms through identification of associated genes may facilitate the discovery of therapeutic targets. The prediction of an individual\'s disease risk allows for improved stratification and personalized prevention measures. Given the vast amount of genomic data, artificial intelligence, as a burgeoning technology for data analysis, is poised to make a significant impact in genomics.
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  • 文章类型: Journal Article
    帕金森病(PD)的早期检测对其治疗和管理具有重要意义。但对于哪些信息是必要的,以及应该使用哪些模型来最好地预测PD风险缺乏共识.在我们的研究中,我们首先根据PD相关因素的成本和可及性对其进行分组,然后逐渐将它们纳入风险预测中,它们是使用八种常用的机器学习模型构建的,以便进行全面评估。最后,Shapley加性解释(SHAP)方法用于研究各因素的贡献。我们发现用人口统计学变量建立的模型,入院检查,临床评估,多基因风险评分达到最佳预测性能,并且包含侵入性生物标志物不能进一步提高其准确性。在所考虑的八种机器学习模型中,惩罚逻辑回归和XGBoost是评估PD风险的最准确算法,惩罚逻辑回归曲线下面积为0.94,Brier得分为0.08。嗅觉功能和多基因风险评分是PD风险的最重要预测因子。我们的研究为PD风险评估提供了一个实用的框架,其中强调了必要的信息和高效的机器学习工具。
    The detection of Parkinson\'s disease (PD) in its early stages is of great importance for its treatment and management, but consensus is lacking on what information is necessary and what models should be used to best predict PD risk. In our study, we first grouped PD-associated factors based on their cost and accessibility, and then gradually incorporated them into risk predictions, which were built using eight commonly used machine learning models to allow for comprehensive assessment. Finally, the Shapley Additive Explanations (SHAP) method was used to investigate the contributions of each factor. We found that models built with demographic variables, hospital admission examinations, clinical assessment, and polygenic risk score achieved the best prediction performance, and the inclusion of invasive biomarkers could not further enhance its accuracy. Among the eight machine learning models considered, penalized logistic regression and XGBoost were the most accurate algorithms for assessing PD risk, with penalized logistic regression achieving an area under the curve of 0.94 and a Brier score of 0.08. Olfactory function and polygenic risk scores were the most important predictors for PD risk. Our research has offered a practical framework for PD risk assessment, where necessary information and efficient machine learning tools were highlighted.
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  • 文章类型: Journal Article
    双相情感障碍(BD)是一种常见且高度遗传性的精神疾病,对BD基因特征的研究有助于早期预防和个体化治疗。同时,BD是一种高度异质性的多基因遗传疾病,与其他精神疾病有显著的遗传重叠。近年来,来自全基因组关联研究(GWAS)数据的多基因风险评分(PRS)已广泛应用于各种复杂疾病的遗传研究,可用于探索疾病的遗传易感性。这篇综述讨论了基于PRS的BD与其他疾病的表型关联和遗传相关性,并为遗传研究和预防BD提供思路。
    Bipolar disorder (BD) is a common and highly heritable psychiatric disorder, the study of BD genetic characteristics can help with early prevention and individualized treatment. At the same time, BD is a highly heterogeneous polygenic genetic disorder with significant genetic overlap with other psychiatric disorders. In recent years, polygenic risk scores (PRS) derived from genome-wide association studies (GWAS) data have been widely used in genetic studies of various complex diseases and can be used to explore the genetic susceptibility of diseases. This review discusses phenotypic associations and genetic correlations with other conditions of BD based on PRS, and provides ideas for genetic studies and prevention of BD.
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  • 文章类型: Journal Article
    尽管部署了特定的乳腺癌筛查策略,近几十年来,乳腺癌发病率显著上升。为了扭转这一趋势,科学家对乳腺癌患病率进行了广泛的流行病学研究,识别众多个体危险因素,促进全民健康教育。再加上基因检测的进步,已经开发了基于乳腺癌基因的风险预测模型,尽管有固有的局限性。在新的千年里,人工智能(AI)作为主导技术力量的出现表明,用AI开发的乳腺癌预测模型可能代表研究的下一个前沿。
    Despite the deployment of specific breast cancer screening strategies, breast cancer incidence rates have escalated significantly over recent decades. In a bid to reverse this trend, scientists have engaged in extensive epidemiological research into breast cancer prevalence, identifying numerous individual risk factors and promoting population-wide health education. Coupled with advances in genetic testing, risk prediction models based on breast cancer genes have been developed, albeit with inherent limitations. In the new millennium, the emergence of artificial intelligence (AI) as a dominant technological force suggests that breast cancer prediction models developed with AI may represent the next frontier in research.
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  • 文章类型: Journal Article
    背景:阿尔茨海默病(AD-PRS)的多基因风险评分与认知相关。然而,很少有研究检查过AD-PRS超出APOE基因的作用,以及与认知能力水平(COG-PRS)相关的遗传变异对一般老年人群认知表现的影响。
    方法:以人口为基础的样本,包括1930年出生的965个人,在六个心理测量测试中获得了遗传和标准化的认知数据(Thurstone的图片记忆,立即回忆10个字,块设计,单词流利,图识别,延迟召回12项),在70、75、79和85岁时进行检查。非APOEAD-PRS和COG-PRS(P<5e-8,P<1e-5,P<1e-3,P<1e-1)来自最近的全基因组关联研究。采用随机截距和斜率的线性混合效应模型分析APOEε4等位基因的效应,AD-PRS,和COG-PRS,认知表现和变化率。在不包括痴呆的样品中重复分析。
    结果:APOEε4和AD-PRS可预测认知能力的变化(APOEε4*年龄:β=-0.03,P<0.0001,AD-PRS*年龄:β=-0.01,P=0.02)。除痴呆症患者外,样本中的结果仍然相似。COG-PRS预测认知表现水平,而APOEε4和AD-PRS没有。COG-PRS不能预测认知表现的变化。
    结论:我们发现,在70岁的人群中,AD的遗传易感性可以预测16岁以上的认知能力下降。不管痴呆状态如何,而一般认知表现的多基因风险没有。
    BACKGROUND: Polygenic risk scores for Alzheimer\'s disease (AD-PRSs) have been associated with cognition. However, few studies have examined the effect of AD-PRS beyond the APOE gene, and the influence of genetic variants related to level of cognitive ability (COG-PRS) on cognitive performance over time in the general older population.
    METHODS: A population-based sample of 965 individuals born in 1930, with genetic and standardized cognitive data on six psychometric tests (Thurstone\'s picture memory, immediate recall of 10 words, Block design, word fluency, figure identification, delayed recall of 12 items), were examined at age 70, 75, 79, and 85 years. Non-APOE AD-PRSs and COG-PRSs (P < 5e-8, P < 1e-5, P < 1e-3, P < 1e-1) were generated from recent genome-wide association studies. Linear mixed effect models with random intercepts and slope were used to analyze the effect of APOE ε4 allele, AD-PRSs, and COG-PRSs, on cognitive performance and rate of change. Analyses were repeated in samples excluding dementia.
    RESULTS: APOE ε4 and AD-PRS predicted change in cognitive performance (APOE ε4*age: β = -0.03, P < 0.0001 and AD-PRS *age: β = -0.01, P = 0.02). The results remained similar in the sample excluding those with dementia. COG-PRS predicted level of cognitive performance, while APOE ε4 and AD-PRS did not. COG-PRSs did not predict change in cognitive performance.
    CONCLUSIONS: We found that genetic predisposition of AD predicted cognitive decline among 70-year-olds followed over 16 years, regardless of dementia status, while polygenic risk for general cognitive performance did not.
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