Genome-wide polygenic score to predict chronic kidney disease across ancestries

Performance of Current Chronic Kidney Disease Screening Criteria in Women and Men Across Ethnic Groups: The HELIUS Study

Objective

To investigate whether the currently recommended screening criteria in Kidney Disease: Improving Global Outcomes 2024 guidelines (hypertension, diabetes mellitus, and cardiovascular disease) equally detect women and men across ethnic groups and whether consideration of optional criteria (education level, occupation, obesity, and genetic risk factors) listed in the guideline improves performance.

Patients and Methods

We included 12,384 women and 9046 men of Dutch, South Asian and African Surinamese, Ghanaian, Turkish, and Moroccan origin from the baseline HELIUS Study (January 1, 2011, through December 31, 2015, Amsterdam, the Netherlands). Chronic kidney disease (CKD) was defined as estimated glomerular filtration rate of <60 mL/min/1.73 m2 or albumin-to-creatinine ratio of >3 mg/mmol. Poisson regression analyses estimated associations between CKD and optional criteria on top of current screening criteria. Model comparisons were made with likelihood ratio tests and Akaike information criterion estimations in women and men. Area under the curve (AUC), sensitivity, specificity, and positive and negative predictive values were calculated by sex and ethnicity.

Results

Chronic kidney disease prevalence ranged from 2.9% to 8.8% in women and 3.2% to 8.6% in men. Low educational level (women only) and obesity significantly improved the models with current criteria with CKD. High-risk occupations and polygenic risk score did not improve the model. However, these criteria did not improve predictive measures across ethnic groups. Overall, the AUCs for the current screening criteria were acceptable in men (AUC, 0.75; 95% CI, 0.73-0.77) and poor in women (AUC, 0.65; 95% CI, 0.63-0.67), and showed minimal change after adding the optional criteria.

Conclusion

Current screening criteria may not be equally detecting women and men across ethnic groups with CKD. Optional criteria had limited added value.

A review of deoxyribonucleic acid-based single-nucleotide polymorphisms in diabetic kidney disease among Asian populations: Challenges and future directions

Diabetic kidney disease (DKD) is a persistent disorder that occurs as a result of long-term diabetes mellitus with genetic and environmental risk factors. The identification of DKD associated single-nucleotide polymorphisms (SNPs) is pivotal for patient screening. This manuscript briefly outlines the pathophysiology and the role of genetic factors in DKD expansion. The utility of bioinformatic tools and laboratory techniques in the identification of DKD-specific SNPs along with integrated data analysis pipelines valuable to enhance the accuracy of genetic interpretation is also presented. A comparative analysis of various SNPs across diverse Asian populations in conjunction with environmental and lifestyle factors was performed. The clinical relevance of SNPs in predicting DKD progression and stratifying patient risk is highlighted, with focus on gene-specific pathways and associated functional outcomes. The advances in genetic screening, gene-specific therapies, and microbiome-based therapy can facilitate the utility of SNPs-based identification of DKD in clinical settings. A structured clinical decision-making framework is proposed to support customized treatment based on SNP profiles. However, this domain is yet to gain widespread recognition with regard to variability in the effects of SNPs across diverse demographies, challenges in clinical translation, and ethical considerations in genetic testing.

Emerging Biomarkers and Advanced Diagnostics in Chronic Kidney Disease: Early Detection Through Multi-Omics and AI

Chronic kidney disease (CKD) remains a significant global health burden, often diagnosed at advanced stages due to the limitations of traditional biomarkers such as serum creatinine and estimated glomerular filtration rate (eGFR). This review aims to critically evaluate recent advancements in novel biomarkers, multi-omics technologies, and artificial intelligence (AI)-driven diagnostic strategies, specifically addressing existing gaps in early CKD detection and personalized patient management. We specifically explore key advancements in CKD diagnostics, focusing on emerging biomarkers-including neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), soluble urokinase plasminogen activator receptor (suPAR), and cystatin C-and their clinical applications. Additionally, multi-omics approaches integrating genomics, proteomics, metabolomics, and transcriptomics are reshaping disease classification and prognosis. Artificial intelligence (AI)-driven predictive models further enhance diagnostic accuracy, enabling real-time risk assessment and treatment optimization. Despite these innovations, challenges remain in biomarker standardization, large-scale validation, and integration into clinical practice. Future research should focus on refining multi-biomarker panels, improving assay standardization, and facilitating the clinical adoption of precision-driven diagnostics. By leveraging these advancements, CKD diagnostics can transition toward earlier intervention, individualized therapy, and improved patient outcomes.

Contributions of common and rare genetic variation to different measures of mood and anxiety disorder in the UK Biobank

BACKGROUND

Mood and anxiety disorders co-occur and share symptoms, treatments and genetic risk, but it is unclear whether combining them into a single phenotype would better capture genetic variation. The contribution of common genetic variation to these disorders has been investigated using a range of measures; however, the differences in their ability to capture variation remain unclear, while the impact of rare variation is mostly unexplored.

AIMS

We aimed to explore the contributions of common genetic variation and copy number variations associated with risk of psychiatric morbidity (P-CNVs) to different measures of internalising disorders.

METHOD

We investigated eight definitions of mood and anxiety disorder, and a combined internalising disorder, derived from self-report questionnaires, diagnostic assessments and electronic healthcare records (EHRs). Association of these definitions with polygenic risk scores (PRSs) of major depressive disorder and anxiety disorder, as well as presence of a P-CNV, was assessed.

RESULTS

The effect sizes of both PRSs and P-CNVs were similar for mood and anxiety disorder. Compared to mood and anxiety disorder, internalising disorder resulted in higher prediction accuracy for PRSs, and increased significance of associations with P-CNVs for most definitions. Comparison across the eight definitions showed that PRSs had higher prediction accuracy and effect sizes for stricter definitions, whereas P-CNVs were more strongly associated with EHR- and self-report-based definitions.

CONCLUSIONS

Future studies may benefit from using a combined internalising disorder phenotype, and may need to consider that different phenotype definitions may be more informative depending on whether common or rare variation is studied.

Clinical staging to guide management of metabolic disorders and their sequelae: a European Atherosclerosis Society consensus statement

Obesity rates have surged since 1990 worldwide. This rise is paralleled by increases in pathological processes affecting organs such as the heart, liver, and kidneys, here termed systemic metabolic disorders (SMDs). For clinical management of SMD, the European Atherosclerosis Society proposes a pathophysiology-based system comprising three stages: Stage 1, where metabolic abnormalities such as dysfunctional adiposity and dyslipidaemia occur without detectable organ damage; Stage 2, which involves early organ damage manifested as Type 2 diabetes, asymptomatic diastolic dysfunction, metabolic-associated steatohepatitis (MASH), and chronic kidney disease (CKD); and Stage 3, characterized by more advanced organ damage affecting multiple organs. Various forms of high-risk obesity, driven by maintained positive energy balance, are the most common cause of SMD, leading to ectopic lipid accumulation and insulin resistance. This progression affects various organs, promoting comorbidities such as hypertension and atherogenic dyslipidaemia. Genetic factors influence SMD susceptibility, and ethnic disparities in SMD are attributable to genetic and socioeconomic factors. Key SMD features include insulin resistance, inflammation, pre-diabetes, Type 2 diabetes, MASH, hypertension, CKD, atherogenic dyslipidaemia, and heart failure. Management strategies involve lifestyle changes, pharmacotherapy, and metabolic surgery in severe cases, with emerging treatments focusing on genetic approaches. The staging system provides a structured approach to understanding and addressing the multi-faceted nature of SMD, which is crucial for improving health outcomes. Categorization of SMD abnormalities by presence and progression is aimed to improve awareness of a multi-system trait and encourage a tailored and global approach to treatment, ultimately aiming to reduce the burden of obesity-related comorbidities.

Risk-directed management of chronic kidney disease

The timely and rational institution of therapy is a key step towards reducing the global burden of chronic kidney disease (CKD). CKD is a heterogeneous entity with varied aetiologies and diverse trajectories, which include risk of kidney failure but also cardiovascular events and death. Developments in the past decade include substantial progress in CKD risk prediction, driven in part by the accumulation of electronic health records data. In addition, large randomized clinical trials have demonstrated the effectiveness of sodium-glucose co-transporter 2 inhibitors, glucagon-like peptide 1 receptor agonists and mineralocorticoid receptor antagonists in reducing adverse events in CKD, greatly expanding the options for effective therapy. Alongside angiotensin-converting enzyme inhibitors and angiotensin receptor blockers, these classes of medication have been proposed to be the four pillars of CKD pharmacotherapy. However, all of these drug classes are underutilized, even in individuals at high risk. Leveraging prognostic estimates to guide therapy could help clinicians to prescribe CKD-related therapies to those who are most likely to benefit from their use. Risk-based CKD management thus aligns patient risk and care, allowing the prioritization of absolute benefit in determining therapeutic selection and timing. Here, we discuss CKD prognosis tools, evidence-based management and prognosis-guided therapies.

APOL1-associated kidney disease: modulators of the genotype-phenotype relationship

PURPOSE OF REVIEW

Apolipoprotein-L1 (APOL1) G1 and G2 risk variants, found in people of recent west sub-Saharan African ancestry, dramatically increase the likelihood of kidney disease, yet the incomplete penetrance an diverse clinical manifestations underscore the need to understand the molecular and environmental factors that modulate APOL1-mediated toxicity.

RECENT FINDINGS

Recent studies confirm that risk variants exert a toxic gain-of-function effect, exacerbated by inflammatory triggers such as HIV infection and COVID-19. Epigenetic mechanisms and microRNA pathways further modulate APOL1 expression, influencing disease penetrance. Multiple models have clarified how subcellular localization, signal peptide processing, and interactions with the endoplasmic reticulum may contribute to pathogenesis. Therapeutic advances include inhibitors targeting APOL1 ion channel activity and strategies that block key inflammatory signaling pathways.

SUMMARY

These findings highlight a multifaceted disease process driven by both the intrinsic toxic potential of APOL1 variants and numerous extrinsic triggers. Understanding this complex interplay will be pivotal for risk stratification and the development of precision therapies, potentially improving outcomes for populations disproportionately affected by APOL1-associated kidney disease.

Genetic analysis of elevated levels of creatinine and cystatin C biomarkers reveals novel genetic loci associated with kidney function

The rising prevalence of chronic kidney disease (CKD), affecting an estimated 37 million adults in the United States, presents a significant global health challenge. CKD is typically assessed using estimated Glomerular Filtration Rate (eGFR), which incorporates serum levels of biomarkers such as creatinine and cystatin C. However, these biomarkers do not directly measure kidney function; their elevation in CKD results from diminished glomerular filtration. Genome-wide association studies (GWAS) based on eGFR formulas using creatinine (eGFRcre) or cystatin C (eGFRcys) have identified distinct non-overlapping loci, raising questions about whether these loci govern kidney function or biomarker metabolism. In this study, we show that GWAS on creatinine and cystatin C levels in healthy individuals reveal both nonoverlapping genetic loci impacting their metabolism as well as overlapping genetic loci associated with kidney function; whereas GWAS on elevated levels of these biomarkers uncover novel loci primarily associated with kidney function in CKD patients.

The mediating effect of depressive syndrome on the relationship between adverse childhood experiences and chronic kidney diseases among middle-aged and older adults

Background

Chronic kidney disease (CKD) is projected to rank among the top five causes of mortality by 2050. In addition to established risk factors, adverse childhood experiences (ACEs) have recently emerged as significant contributors to health risks, including CKD and depressive syndrome (DS). However, the mechanisms linking ACEs, DS, and CKD remain unclear. This study aims to explore the role of ACEs in CKD development, with a focus on the mediating effects of DS.

Methods

This retrospective cohort study analyzed data from 10,247 participants in the China Health and Retirement Longitudinal Study (CHARLS). Logistic regression models were applied to assess the associations between ACEs, DS, and incident CKD, adjusting for demographic and lifestyle factors. Mediation analysis was conducted to evaluate the role of DS in the relationship between ACEs and CKD.

Results

Logistic regression analysis indicated that participants with a history of ACEs were at higher risk for both DS and CKD. Mediation analysis demonstrated that DS partially mediated the associations between CKD and seven specific ACEs: physical abuse, household substance abuse, household mental illness, domestic violence, unsafe neighborhood, peer bullying, and parental disability. Notably, DS fully mediated the relationship between CKD and unsafe neighborhood.

Conclusion

ACEs significantly influence CKD risk in middle-aged and older adults, with DS serving as a key mediator. These findings underscore the importance of early mental health interventions and ACE-focused preventive strategies to reduce the burden of CKD.

Family History in the Context of CKD

Background

A family history of health conditions may reflect shared genetic and/or environmental risk. It is not well known to what extent family history affects outcomes among patients with CKD. In this study, we investigated the associations of family history of CKD, diabetes, and other conditions with common comorbidities and kidney disease progression among patients with CKD.

Methods

We performed an observational study of two prospective CKD cohorts, 2573 adults and children from the Cure Glomerulopathy Network and 3939 Chronic Renal Insufficiency Cohort adult participants. Self-reported first-degree family history of CKD, diabetes, and other common diseases was tested for associations with the risk of comorbidities and CKD progression using multivariable models.

Results

Family history of common comorbid conditions was associated with higher risk of these conditions in the context of CKD, including approximately by over three-fold for diabetes (adjusted odds ratio [OR], 3.37; 95% confidence interval [CI], 2.73 to 4.15), 48% for cancer (adjusted OR, 1.48; 95% CI, 1.05 to 2.09), and 69% for cardiovascular disease (adjusted OR, 1.69; 95% CI, 1.36 to 2.10 in combined cohorts). While polygenic risk score (PRS) for CKD was associated with kidney disease progression (adjusted hazards ratio, 1.11; 95% CI, 1.06 to 1.16 in combined cohorts), family history of kidney disease was not an independent risk factor of disease progression in the context of existing CKD. By contrast, family history of diabetes was significantly associated with a higher risk of CKD progression independently of diabetes occurrence or PRS for diabetes (adjusted hazards ratio, 1.19; 95% CI, 1.05 to 1.35 in combined cohorts).

Conclusions

Broad collection of family history in the context of CKD improved clinical risk stratification. Family history of diabetes was consistently associated with a higher risk of CKD progression independently of diabetes status or PRS for diabetes in both cohorts.

Genome-Wide Association Study for Resting Electrocardiogram in the Qatari Population Identifies 6 Novel Genes and Validates Novel Polygenic Risk Scores

BACKGROUND

Electrocardiography is one of the most valuable noninvasive diagnostic tools in determining the presence of many cardiovascular diseases. Genetic factors are important in determining ECG abnormalities and their link to cardiovascular diseases. Genome-wide association studies and polygenic risk scores (PRSs) have been conducted for various ECG traits such as QT interval and QRS duration. However, these studies mainly focused on cohorts of European descent.

METHODS

In this cohort study, genome-wide association studies for 6 ECG traits (RR, PR, corrected QT interval [QTc], QRS, JT, and P wave duration) were conducted in a Middle Eastern cohort from the Qatar Precision Health Institute, comprising 13 827 subjects with whole-genome sequence data. Middle Eastern PRSs were developed using clumping and thresholding, and their performance was compared with 26 published PRSs. Genetic predisposition to long QT syndrome was explored using rare variant analysis.

RESULTS

Seventy-four independent loci were obtained with genome-wide significance across the 6 traits (P<5×10-8). Of the 74 loci, 67 (90.5%) were previously reported, and 7 loci (9.5%) were novel and contained 6 genes: STAC and CSMD1 for PR, ANK1 and NCOA2 for QRS, LSP1 for QTc, and MKLN1 for P wave duration. All 26 published PRSs showed good performance in our cohort. PGS002276 showed the best performance for QTc (R2=0.059, P=4.83×10-185), PGS002166 showed the best performance for QRS (R2=0.024, P=1.53×10-75), and PGS000905 showed the best performance for PR (R2=0.053, P=2.57×10-165). Some of these PRSs were associated with cardiovascular diseases. For example, PGS003500, a QTc PRS, was significantly associated with cardiomyopathy (odds ratio per 1 SD=1.58 [95% CI, 1.23-2.01]; P=2.42×10-4). Middle Eastern PRSs substantially outperformed published PRSs and did not perform well in the UK Biobank data. Ten pathogenic variants, including 3 that are specific to Qatari individuals, were observed in 17 long QT syndrome genes and were carried by 19 individuals. The QTc average was larger for mutation carriers (415.6±23.5 versus 402.3±18.5 in noncarriers). Five-year follow-up data did not show a significant change in ECG patterns, regardless of mutation status and PRS values. Four of 2302 individuals had prolonged QTc intervals over the 2 time points.

CONCLUSIONS

In this first genome-wide association study for ECG traits in the Middle East using whole-genome sequence data, 7 novel loci (6 genes) were identified. Published PRSs performed well, but newly developed Middle Eastern-specific PRSs performed the best. Novel variants in long QT syndrome genes were observed for the first time in Qatari individuals. Follow-up data did not show significant changes in ECG patterns.

Donor and Recipient Polygenic Risk Scores Influence Kidney Transplant Function

Kidney transplant outcomes are influenced by donor and recipient age, sex, HLA mismatch, donor type, anti-rejection medication adherence and disease recurrence, but variability in transplant outcomes remains unexplained. We hypothesise that donor and recipient polygenic burden for traits related to kidney function may also influence graft function. We assembled a cohort of 6,060 living and deceased kidney donor-recipient pairs. We calculated polygenic risk scores (PRSs) for kidney function-related traits in both donors and recipients. We investigated the association between these PRSs and recipient eGFR at 1- and 5-year post-transplant as well as graft failure. Donor: hypertension PRS (P < 0.001), eGFR PRS (P < 0.001), and intracranial aneurysm PRS (P = 0.01), along with recipient eGFR PRS (P = 0.001) were associated with eGFR at 1-year post-transplantation. Clinical factors explained 25% of the variation in eGFR at 1-year and 13% at 5-year, with PRSs cumulatively adding 1% in both cases. PRSs were not associated with long-term graft survival. We demonstrate a small, but statistically significant association between donor and recipient PRSs and recipient graft function at 1- and 5-year post-transplant. This effect is, at present, unlikely to have clinical application and further research is required to improve PRS performance.

Polygenic risk scores for eGFR are associated with age at kidney failure

BACKGROUND

The genetic architecture of chronic kidney disease (CKD) is complex, including monogenic and polygenic contributions. CKD progression to kidney failure is influenced by factors including male sex, baseline estimated glomerular filtration rate (eGFR), hypertension, diabetes, proteinuria, and the underlying kidney disease. These traits all have strong genetic components, which can be partially quantified using polygenic risk scores. This paper examines the association between polygenic risk scores for CKD-related traits and age at kidney failure development.

METHODS

Genome-wide genotype data from 10,586 patients with kidney failure were compiled from 12 cohorts. Polygenic risk scores for hypertension, albuminuria, rapid decline in eGFR, decreased total kidney volume, and decreased eGFR were calculated using weights from published independent population-scale genome-wide association studies. The association between each polygenic risk score and age at kidney failure was investigated using logistic regression models. The association between polygenic risk score and age at kidney failure was also investigated separately for each primary kidney disease.

RESULTS

Individuals in the highest 10% of polygenic risk score for decreased eGFR developed kidney failure 2 years earlier than those in the bottom 90% (49.9 years and 47.9 years, P = 5e-5). A standard deviation increase in decreased eGFR polygenic risk score was associated with increased odds of developing kidney failure before the age of 60 years (Odds ratio (OR) = 1.05; 95% CI 1.01-1.10; P = 0.01), as was high decreased eGFR polygenic risk score (OR = 1.26; 95% CI 1.08-1.46; P = 0.003).

CONCLUSIONS

We conclude that decreased eGFR polygenic risk score explains a portion of the variation in age at development of kidney failure.

Emerging role of genetics in kidney transplantation

The advent of more affordable genomic analytical pipelines has facilitated the expansion of genetic studies in kidney transplantation. Advances in genetic sequencing have allowed for a greater understanding of the genetic basis of chronic kidney disease, which has helped to guide transplant management and address issues related to living donation in specific disease settings. Recent efforts have shown significant effects of genetic ancestry and donor APOL1 risk genotypes in determining worse allograft outcomes and increased donation risks. Genetic studies in kidney transplantation outcomes have started to assess the effects of donor and recipient genetics in primary disease recurrence and transplant-related comorbidities, while genome-wide donor-recipient genetic incompatibilities have been shown to represent an important determinant of alloimmunity. Future large-scale comprehensive studies will shed light on the clinical utility of integrative genomics in the kidney transplantation setting.

2025 Heart Disease and Stroke Statistics: A Report of US and Global Data From the American Heart Association

BACKGROUND

The American Heart Association (AHA), in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, nutrition, sleep, and obesity) and health factors (cholesterol, blood pressure, glucose control, and metabolic syndrome) that contribute to cardiovascular health. The AHA Heart Disease and Stroke Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, brain health, complications of pregnancy, kidney disease, congenital heart disease, rhythm disorders, sudden cardiac arrest, subclinical atherosclerosis, coronary heart disease, cardiomyopathy, heart failure, valvular disease, venous thromboembolism, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs).

METHODS

The AHA, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States and globally to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2025 AHA Statistical Update is the product of a full year's worth of effort in 2024 by dedicated volunteer clinicians and scientists, committed government professionals, and AHA staff members. This year's edition includes a continued focus on health equity across several key domains and enhanced global data that reflect improved methods and incorporation of ≈3000 new data sources since last year's Statistical Update.

RESULTS

Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics.

CONCLUSIONS

The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.

Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown) independent loci. Ancestry-specific analysis indicated an attenuation of newly identified signals on common variants in European ancestry populations and the power of population diversity for further discoveries. We defined genotype effects on allele-specific gene expression and regulatory circuitries in more than 700 human kidneys and 237,000 cells. We found 1363 coding variants disrupting 782 genes, with 601 genes also targeted by regulatory variants and convergence in 161 genes. Integrating 32 types of genetic information, we present the "Kidney Disease Genetic Scorecard" for prioritizing potentially causal genes, cell types, and druggable targets for kidney disease.

Prenatal and preimplantation genetic testing for monogenic kidney disorders

In recent years, advances in genetic sequencing techniques and in the analysis of sequencing data have significantly improved our ability to diagnose genetic kidney diseases. Identification of the disease-causing genetic variant(s) is crucial not only for prognostication and personalized management, but also for providing genetic counseling and guiding family planning decisions. It is particularly important that patients desiring children receive advice on their reproductive choices early, ideally before conception. This concise review focuses on the options available for prenatal and preimplantation genetic testing in the context of monogenic kidney diseases, including the latest progress and the legal and ethical issues associated with these reproductive technologies. Although these tests could be performed for all monogenic disorders where the disease-causing variant(s) has (have) been identified in the index patient, invasive prenatal testing is currently primarily performed for severe childhood-onset monogenic kidney disorders. Noninvasive prenatal diagnosis for monogenic disorders is a rapidly developing field that promises to provide an accurate and acceptable alternative to invasive procedures once several technical challenges have been addressed. Preimplantation genetic testing allows for the selection and implantation of embryos free from the disease-causing genetic variants, significantly lowering the risk of affected pregnancies. This option is becoming more popular among individuals with monogenic kidney diseases, particularly those with disorders that manifest later in life, such as autosomal dominant polycystic kidney disease. This review covers the procedure, its outcomes, and the technical, ethical and legal challenges of preimplantation genetic testing for monogenic kidney diseases.

Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues

Non-communicable diseases (NCDs) such as cardiovascular diseases, chronic respiratory diseases, cancers, diabetes, and mental health disorders pose a significant global health challenge, accounting for the majority of fatalities and disability-adjusted life years worldwide. These diseases arise from the complex interactions between genetic, behavioral, and environmental factors, necessitating a thorough understanding of these dynamics to identify effective diagnostic strategies and interventions. Although recent advances in multi-omics technologies have greatly enhanced our ability to explore these interactions, several challenges remain. These challenges include the inherent complexity and heterogeneity of multi-omic datasets, limitations in analytical approaches, and severe underrepresentation of non-European genetic ancestries in most omics datasets, which restricts the generalizability of findings and exacerbates health disparities. This scoping review evaluates the global landscape of multi-omics data related to NCDs from 2000 to 2024, focusing on recent advancements in multi-omics data integration, translational applications, and equity considerations. We highlight the need for standardized protocols, harmonized data-sharing policies, and advanced approaches such as artificial intelligence/machine learning to integrate multi-omics data and study gene-environment interactions. We also explore challenges and opportunities in translating insights from gene-environment (GxE) research into precision medicine strategies. We underscore the potential of global multi-omics research in advancing our understanding of NCDs and enhancing patient outcomes across diverse and underserved populations, emphasizing the need for equity and fairness-centered research and strategic investments to build local capacities in underrepresented populations and regions.

Chronic kidney disease

Chronic kidney disease (CKD) is defined by persistent abnormalities of kidney function or structure that have consequences for the health. A progressive decline of excretory kidney function has effects on body homeostasis. CKD is tightly associated with accelerated cardiovascular disease and severe infections, and with premature death. Kidney failure without access to kidney replacement therapy is fatal - a reality in many regions of the world. CKD can be the consequence of a single cause, but CKD in adults frequently relates rather to sequential injuries accumulating over the life course or to the presence of concomitant risk factors. The shared pathomechanism of CKD progression is the irreversible loss of kidney cells or nephrons together with haemodynamic and metabolic overload of the remaining nephrons, leading to further loss of kidney cells or nephrons. The management of patients with CKD focuses on early detection and on controlling all modifiable risk factors. This approach includes reducing the overload of the remaining nephrons with inhibitors of the renin-angiotensin system and the sodium-glucose transporter 2, as well as disease-specific drug interventions, if available. Hypertension, anaemia, metabolic acidosis and secondary hyperparathyroidism contribute to cardiovascular morbidity and reduced quality of life, and require diagnosis and treatment.

GWAS highlights the neuronal contribution to multiple sclerosis susceptibility

Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative disease affecting the brain and spinal cord. Genetic studies have identified many risk loci, that were thought to primarily impact immune cells and microglia. Here, we performed a multi-ancestry genome-wide association study with 20,831 MS and 729,220 control participants, identifying 236 susceptibility variants outside the Major Histocompatibility Complex, including four novel loci. We derived a polygenic score for MS and, optimized for European ancestry, it is informative for African-American and Latino participants. Integrating single-cell data from blood and brain tissue, we identified 76 genes affected by MS risk variants. Notably, while T cells showed the strongest enrichment, inhibitory neurons emerged as a key cell type. The expression of IL7 and STAT3 are affected only in inhibitory neurons, highlighting the importance of neuronal and glial dysfunction in MS susceptibility.

Frequency of adding salt is a stronger predictor of chronic kidney disease in individuals with genetic risk

The incidence of chronic kidney disease (CKD) is increasing worldwide, but there is no specific treatment available. Therefore, understanding and controlling the risk factors for CKD are essential for preventing disease occurrence. Salt intake raises blood pressure by increasing fluid volume and contributes to the deterioration of kidney function by enhancing the renin-angiotensin system and sympathetic tone. Thus, a low-salt diet is important to reduce blood pressure and prevent kidney diseases. With recent advancements in genetic research, our understanding of the etiology and genetic background of CKD has deepened, enabling the identification of populations with a high genetic predisposition to CKD. It is thought that the impact of lifestyle or environmental factors on disease occurrence or prevention may vary based on genetic factors. This study aims to investigate whether frequency of adding salt has different effects depending on genetic risk for CKD. CKD polygenic risk scores (PRS) were generated using CKDGen Consortium GWAS (N= 765,348) summary statics. Then we applied the CKD PRS to UK Biobank subjects. A total of 331,318 European individuals aged 40-69 without CKD were enrolled in the study between 2006-2010. The average age at enrollment of the participants in this study was 56.69, and 46% were male. Over an average follow-up period of 8 years, 12,279 CKD cases were identified. The group that developed CKD had a higher percentage of individuals who added salt (46.37% vs. 43.04%) and higher CKD high-risk PRS values compared to the group that did not develop CKD (23.53% vs. 19.86%). We classified the individuals into four groups based on PRS: low (0-19%), intermediate (20-79%), high (80-94%), very high (≥ 95%). Incidence of CKD increased incrementally according to CKD PRS even after adjusting for age, sex, race, Townsend deprivation index, body mass index, estimated glomerular filtration rate, smoking, alcohol, physical activity, diabetes mellitus, dyslipidemia, hypertension, coronary artery diseases, cerebrovascular diseases at baseline. Compared to the "never/rarely" frequency of adding salt group, "always" frequency of adding salt group had an increasing incidence of CKD proportionate to the degree of frequency of adding salt. However, the significant association of "always" group on incident CKD disappeared in the low PRS group. This study validated the signal from PRSs for CKD across a large cohort and confirmed that frequency of adding salt contributes to the occurrence of CKD. Additionally, it confirmed that the effect of frequency of "always" adding salt on CKD incidence is greater in those with more than intermediate CKD-PRS. This study suggests that increased salt intake is particularly concerning for individuals with genetic risk factors for CKD, underscoring the clinical importance of reducing salt intake for these individuals.

Polygenic scores and their applications in kidney disease

Genome-wide association studies (GWAS) have uncovered thousands of risk variants that individually have small effects on the risk of human diseases, including chronic kidney disease, type 2 diabetes, heart diseases and inflammatory disorders, but cumulatively explain a substantial fraction of disease risk, underscoring the complexity and pervasive polygenicity of common disorders. This complexity poses unique challenges to the clinical translation of GWAS findings. Polygenic scores combine small effects of individual GWAS risk variants across the genome to improve personalized risk prediction. Several polygenic scores have now been developed that exhibit sufficiently large effects to be considered clinically actionable. However, their clinical use is limited by their partial transferability across ancestries and a lack of validated models that combine polygenic, monogenic, family history and clinical risk factors. Moreover, prospective studies are still needed to demonstrate the clinical utility and cost-effectiveness of polygenic scores in clinical practice. Here, we discuss evolving methods for developing polygenic scores, best practices for validating and reporting their performance, and the study designs that will empower their clinical implementation. We specifically focus on the polygenic scores relevant to nephrology and other chronic, complex diseases and review their key limitations, necessary refinements and potential clinical applications.

Perioperative Acute Kidney Injury: Diagnosis, Prediction, Prevention, and Treatment

In this review, the authors define acute kidney injury in the perioperative setting, describe the epidemiologic burden, discuss procedure-specific risk factors, detail principles of management, and highlight areas of ongoing controversy and research.

Exome-wide genetic risk score (ExGRS) to predict high myopia across multi-ancestry populations

BACKGROUND

High myopia (HM), characterized by a severe myopic refractive error, stands as a leading cause of visual impairment and blindness globally. HM is a multifactorial ocular disease that presents high genetic heterogeneity. Employing a genetic risk score (GRS) is useful for capturing genetic susceptibility to HM.

METHODS

This study assesses the effectiveness of these strategies via incorporating rare variations into the GRS assessment. This study enrolled two independent cohorts: 12,600 unrelated individuals of Han Chinese ancestry from Myopia Associated Genetics and Intervention Consortium (MAGIC) and 8682 individuals of European ancestry from UK Biobank (UKB).

RESULTS

Here, we first estimate the heritability of HM resulting in 0.53 (standard error, 0.06) in the MAGIC cohort and 0.21 (standard error, 0.10) in the UKB cohort by using whole-exome sequencing (WES) data. We generate, optimize, and validate an exome-wide genetic risk score (ExGRS) for HM prediction by combining rare risk genotypes with common variant GRS (cvGRS). ExGRS improved the AUC from 0.819 (cvGRS) to 0.856 for 1219 Han Chinese individuals of an independent testing dataset. Individuals with a top 5% ExGRS confer a 15.57-times (95% CI, 5.70-59.48) higher risk for developing HM compared to the remaining 95% of individuals in MAGIC cohort.

CONCLUSIONS

Our study suggests that rare variants are a major source of the missing heritability of HM and that ExGRS provides enhanced accuracy for HM prediction in Han Chinese ancestry, shedding new light on research and clinical practice.

Novel Aspects of Immunogenetics and Post-Transplant Events in Kidney Transplantation

HLA typing and matching have been crucial in kidney transplantation, but methods for assessing tissue histocompatibility have advanced significantly. While serological-level HLA typing remains common, it captures only a small fraction of true HLA variation, and molecular matching is already replacing traditional HLA matching. Recent studies have expanded our understanding of genetic tissue compatibility beyond HLA loci. Candidate gene analyses and genome-wide association studies (GWAS) have identified genetic factors linked to post-transplant complications, though replication of these findings is challenging. An alternative approach involves genome-wide matching of genes or genetic variations. This method has shown promise in hematopoietic stem cell and kidney transplantation. For instance, homozygous gene deletions in LIMS1 or complement factor H (CFH) genes have been associated with acute rejection risk. This may be due to alloimmune responses against proteins absent in the patient but present in the graft, or due to the missing protein's function. Genetic studies in clinical medicine face challenges due to the interplay of genetic and environmental factors, necessitating large datasets for meaningful associations. International collaboration and large consortia, like iGeneTRAin, are essential for validating findings and advancing the field. This review highlights recent advancements in immunogenetics and tissue histocompatibility, emphasizing future research directions.

GWAS highlights the neuronal contribution to multiple sclerosis susceptibility

Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative disease affecting the brain and spinal cord. Genetic studies have identified many risk loci, that were thought to primarily impact immune cells and microglia. Here, we performed a multi-ancestry genome-wide association study with 20,831 MS and 729,220 control participants, identifying 236 susceptibility variants outside the Major Histocompatibility Complex, including four novel loci. We derived a polygenic score for MS and, optimized for European ancestry, it is informative for African-American and Latino participants. Integrating single-cell data from blood and brain tissue, we identified 76 genes affected by MS risk variants. Notably, while T cells showed the strongest enrichment, inhibitory neurons emerged as a key cell type, highlighting the importance of neuronal and glial dysfunction in MS susceptibility.

Advancing Genetic Testing in Kidney Diseases: Report From a National Kidney Foundation Working Group

About 37 million people in the United States have chronic kidney disease, a disease that encompasses multiple causes. About 10% or more of kidney diseases in adults and as many as 70% of selected chronic kidney diseases in children are expected to be explained by genetic causes. Despite the advances in genetic testing and an increasing understanding of the genetic bases of certain kidney diseases, genetic testing in nephrology lags behind other medical fields. More understanding of the benefits and logistics of genetic testing is needed to advance the implementation of genetic testing in chronic kidney diseases. Accordingly, the National Kidney Foundation convened a Working Group of experts with diverse expertise in genetics, nephrology, and allied fields to develop recommendations for genetic testing for monogenic disorders and to identify genetic risk factors for oligogenic and polygenic causes of kidney diseases. Algorithms for clinical decision making on genetic testing and a road map for advancing genetic testing in kidney diseases were generated. An important aspect of this initiative was the use of a modified Delphi process to reach group consensus on the recommendations. The recommendations and resources described herein provide support to nephrologists and allied health professionals to advance the use of genetic testing for diagnosis and screening of kidney diseases.

Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits

Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and somatic traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and somatic traits were calculated in European-ancestry (EUR; n = 5691) participants and, when discovery datasets were available, for African-ancestry (AFR; n = 4918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGSMDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGSBMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and somatic traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.

Estimating the Number of Polygenic Diseases Among Six Mutually Exclusive Entities of Non-Tumors and Cancer

In the era of precision medicine with increasing amounts of sequenced cancer and non-cancer genomes of different ancestries, we here enumerate the resulting polygenic disease entities. Based on the cell number status, we first identified six fundamental types of polygenic illnesses, five of which are non-cancerous. Like complex, non-tumor disorders, neoplasms normally carry alterations in multiple genes, including in 'Drivers' and 'Passengers'. However, tumors also lack certain genetic alterations/epigenetic changes, recently named 'Goners', which are toxic for the neoplasm and potentially constitute therapeutic targets. Drivers are considered essential for malignant transformation, whereas environmental influences vary considerably among both types of polygenic diseases. For each form, hyper-rare disorders, defined as affecting <1/108 individuals, likely represent the largest number of disease entities. Loss of redundant tumor-suppressor genes exemplifies such a profoundly rare mutational event. For non-tumor, polygenic diseases, pathway-centered taxonomies seem preferable. This classification is not readily feasible in cancer, but the inclusion of Drivers and possibly also of epigenetic changes to the existing nomenclature might serve as initial steps in this direction. Based on the detailed genetic alterations, the number of polygenic diseases is essentially countless, but different forms of nosologies may be used to restrict the number.

Single-Ancestry versus Multi-Ancestry Polygenic Risk Scores for CKD in Black American Populations

Key Points

The predictive performance of an African ancestry–specific polygenic risk score (PRS) was comparable to a European ancestry–derived PRS for kidney traits. However, multi-ancestry PRSs outperform single-ancestry PRSs in Black American populations. Predictive accuracy of PRSs for CKD was improved with the use of race-free eGFR.

Background

CKD is a risk factor of cardiovascular disease and early death. Recently, polygenic risk scores (PRSs) have been developed to quantify risk for CKD. However, African ancestry populations are underrepresented in both CKD genetic studies and PRS development overall. Moreover, European ancestry–derived PRSs demonstrate diminished predictive performance in African ancestry populations.

Methods

This study aimed to develop a PRS for CKD in Black American populations. We obtained score weights from a meta-analysis of genome-wide association studies for eGFR in the Million Veteran Program and Reasons for Geographic and Racial Differences in Stroke Study to develop an eGFR PRS. We optimized the PRS risk model in a cohort of participants from the Hypertension Genetic Epidemiology Network. Validation was performed in subsets of Black participants of the Trans-Omics in Precision Medicine Consortium and Genetics of Hypertension Associated Treatment Study.

Results

The prevalence of CKD—defined as stage 3 or higher—was associated with the PRS as a continuous predictor (odds ratio [95% confidence interval]: 1.35 [1.08 to 1.68]) and in a threshold-dependent manner. Furthermore, including APOL1 risk status—a putative variant for CKD with higher prevalence among those of sub-Saharan African descent—improved the score's accuracy. PRS associations were robust to sensitivity analyses accounting for traditional CKD risk factors, as well as CKD classification based on prior eGFR equations. Compared with previously published PRS, the predictive performance of our PRS was comparable with a European ancestry–derived PRS for kidney traits. However, single-ancestry PRSs were less predictive than multi-ancestry–derived PRSs.

Conclusions

In this study, we developed a PRS that was significantly associated with CKD with improved predictive accuracy when including APOL1 risk status. However, PRS generated from multi-ancestry populations outperformed single-ancestry PRS in our study.

Projection of the clinical and economic burden of chronic kidney disease between 2022 and 2027 in Spain: Results of the Inside CKD project

BACKGROUND AND OBJECTIVE

Chronic kidney disease (CKD) is a growing health problem affecting between 10% and 15% of the Spanish population. The lack of updated projections of the evolution of the disease burden hinders the development of evidence-based health policies and interventions to optimise the management of the disease and prevent its progression. The aim of this study is to project the evolution of the clinical and economic burden of CKD in Spain between 2022 and 2027.

MATERIALS AND METHODS

Inside CKD uses a validated microsimulation approach to project the burden of CKD. The projection is based on a virtual population according to Spanish demographics, literature, national data registries and clinical expert opinion. Costs associated with CKD management, renal replacement therapy (RRT), cardiovascular complications and arterial comorbidities were included.

RESULTS

In Spain, an absolute increase in the prevalence of CKD of 1% (from 10.7% to 11.7%) is expected between 2022 and 2027, corresponding to an increase from 5.14 million to 5.68 million patients in 2027. However, only one third of CKD patients would be diagnosed. Of these diagnosed patients, 3.9% will require RRT in 2027, an increase of 14.7% from 2022. A total of 654,281 accumulated deaths are expected in patients with CKD diagnosed between 2022 and 2027. The economic burden of diagnosed CKD is expected to increase by 13.8% to 4.89 billion euros in 2027, representing 5.56% of total Spanish public health expenditure in 2027 (compared to 4.88% in 2022), of which 42.5% will be allocated to RRT (2.4% of public health expenditure).

CONCLUSIONS

The Inside CKD project highlights the growing clinical, economic and social burden of CKD in Spain expected by 2027. Progression to more advanced stages with the need for RRT and associated complications represent a small proportion of the total CKD population, but contribute significantly to overall costs.

Discovery and prioritization of genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan

Current genome-wide association studies (GWAS) for kidney function lack ancestral diversity, limiting the applicability to broader populations. The East-Asian population is especially under-represented, despite having the highest global burden of end-stage kidney disease. We conducted a meta-analysis of multiple GWASs (n = 244,952) on estimated glomerular filtration rate and a replication dataset (n = 27,058) from Taiwan and Japan. This study identified 111 lead SNPs in 97 genomic risk loci. Functional enrichment analyses revealed that variants associated with F12 gene and a missense mutation in ABCG2 may contribute to chronic kidney disease (CKD) through influencing inflammation, coagulation, and urate metabolism pathways. In independent cohorts from Taiwan (n = 25,345) and the United Kingdom (n = 260,245), polygenic risk scores (PRSs) for CKD significantly stratified the risk of CKD (p < 0.0001). Further research is required to evaluate the clinical effectiveness of PRSCKD in the early prevention of kidney disease.

Population Performance and Individual Agreement of Coronary Artery Disease Polygenic Risk Scores

Importance

Polygenic risk scores (PRSs) for coronary artery disease (CAD) are a growing clinical and commercial reality. Whether existing scores provide similar individual-level assessments of disease liability is a critical consideration for clinical implementation that remains uncharacterized.

Objective

Characterize the reliability of CAD PRSs that perform equivalently at the population level at predicting individual-level risk.

Design

Cross-sectional Study.

Setting

All of Us Research Program (AOU), Penn Medicine Biobank (PMBB), and UCLA ATLAS Precision Health Biobank.

Participants

Volunteers of diverse genetic backgrounds enrolled in AOU, PMBB, and UCLA with available electronic health record and genotyping data.

Exposures

Polygenic risk for CAD from previously published PRSs and new PRSs developed separately from the testing cohorts.

Main Outcomes and Measures

Sets of CAD PRSs that perform population prediction equivalently were identified by comparing calibration and discrimination (Brier score and AUROC) of generalized linear models of prevalent CAD using Bayesian analysis of variance. Among equivalently performing scores, individual-level agreement between risk estimates was tested with intraclass correlation (ICC) and Light's Kappa, measures of inter-rater reliability.

Results

50 PRSs were calculated for 171,095 AOU participants. When included in a model of prevalent CAD, 48 scores had practically equivalent Brier scores and AUROCs (region of practical equivalence = 0.02). Across these scores, 84% of participants had at least one score in both the top and bottom risk quintile. Continuous agreement of individual risk predictions from the 48 scores was poor, with an ICC of 0.351 (95% CI; 0.349, 0.352). Agreement between two statistically equivalent scores was moderate, with an ICC of 0.649 (95% CI; 0.646, 0.652). Light's Kappa, used to evaluate consistency of assignment to high-risk thresholds, did not exceed 0.56 (interpreted as 'fair') across statistically and practically equivalent scores. Repeating the analysis among 41,193 PMBB and 50,748 UCLA participants yielded different sets of statistically and practically equivalent scores which also lacked strong individual agreement.

Conclusions and Relevance

Across three diverse biobanks, CAD PRSs that performed equivalently at the population level produced unreliable individual risk estimates. Approaches to clinical implementation of CAD PRSs must consider the potential for discordant individual risk estimates from otherwise indistinguishable scores.

The association between patterns of exposure to adverse life events and the risk of chronic kidney disease: a prospective cohort study of 140,997 individuals

Exposure to adverse life events is linked to somatic disorders. The study aims to evaluate the association between adverse events at varying life stages and the risk of chronic kidney disease (CKD), a condition affecting about 10% population worldwide. This prospective cohort study included 140,997 participants from the UK Biobank. Using survey items related to childhood maltreatment, adulthood adversity and catastrophic trauma, we performed latent class analysis to summarize five distinct patterns of exposure to adverse life events, namely "low-level exposure", "childhood exposure", "adulthood exposure", "sexual abuse" and "child-to-adulthood exposure". We used Cox proportional hazard regression to evaluate the association of patterns of exposure to adverse life events with CKD, regression-based mediation analysis to decompose the total effect, and gene-environment-wide interaction study (GEWIS) to identify interactions between genetic loci and adverse life events. During a median follow-up of 5.98 years, 2734 cases of incident CKD were identified. Compared with the "low-level exposure" pattern, "child-to-adulthood exposure" was associated with increased risk of CKD (hazard ratio 1.37, 95% CI 1.14 to 1.65). BMI, smoking and hypertension mediated 11.45%, 9.79%, and 4.50% of this total effect, respectively. Other patterns did not show significant results. GEWIS and subsequent analyses indicated that the magnitude of the association between adverse life events and CKD differed according to genetic polymorphisms, and identified potential underlying pathways (e.g., interleukin 1 receptor activity). These findings underscore the importance of incorporating an individual's psychological encounters and genetic profiles into the precision prevention of CKD.

Identification of GTF2I Polymorphisms as Potential Biomarkers for CKD in the Han Chinese Population : Multicentric Collaborative Cross-Sectional Cohort Study

Key Points

Genetic factors are key players in CKD, with two linked single-nucleotide polymorphisms in the GTF2I gene, associated with CKD susceptibility in the Taiwanese population. Individuals with specific GTF2I genotypes (CT/TT for rs117026326 and CT/CC for rs73366469) show higher CKD prevalence and earlier onset. Men with the specific genotypes of rs117026326 and rs73366469 face a heightened CKD risk compared with women, particularly at lower eGFR.

Background

CKD poses a global health challenge, but its molecular mechanisms are poorly understood. Genetic factors play a critical role, and phenome-wide association studies and genome-wide association studies shed light on CKD's genetic architecture, shared variants, and biological pathways.

Methods

Using data from the multicenter collaborative precision medicine cohort, we conducted a retrospective prospectively maintained cross-sectional study. Participants with comprehensive information and genotyping data were selected, and genome-wide association study and phenome-wide association study analyses were performed using the curated Taiwan Biobank version 2 array to identify CKD-associated genetic variants and explore their phenotypic associations.

Results

Among 58,091 volunteers, 8420 participants were enrolled. Individuals with CKD exhibited higher prevalence of metabolic, cardiovascular, autoimmune, and nephritic disorders. Genetic analysis unveiled two closely linked single-nucleotide polymorphisms, rs117026326 and rs73366469, both associated with GTF2I and CKD (r 2 = 0.64). Further examination revealed significant associations between these single-nucleotide polymorphisms and various kidney-related diseases. The CKD group showed a higher proportion of individuals with specific genotypes (CT/TT for rs117026326 and CT/CC for rs73366469), suggesting potential associations with CKD susceptibility (P < 0.001). Furthermore, individuals with these genotypes developed CKD at an earlier age. Multiple logistic regression confirmed the independent association of these genetic variants with CKD. Subgroup analysis based on eGFR demonstrated an increased risk of CKD among carriers of the rs117026326 CT/TT genotypes (odds ratio [OR], 1.15; 95% confidence interval [CI], 1.07 to 1.24; P < 0.001; OR, 1.32, 95% CI, 1.04 to 1.66; P = 0.02, respectively) and carriers of the rs73366469 CT/CC genotypes (OR, 1.13; 95% CI, 1.05 to 1.21; P < 0.001; OR, 1.31; 95% CI, 1.08 to 1.58; P = 0.0049, respectively). In addition, men had a higher CKD risk than women at lower eGFR levels (OR, 1.35; 95% CI, 1.13 to 1.61; P < 0.001).

Conclusions

Our study reveals important links between genetic variants GTF2I and susceptibility to CKD, advancing our understanding of CKD development in the Taiwanese population and suggesting potential for personalized prevention and management strategies. More research is needed to validate and explore these variants in diverse populations.

Disease trend analysis platform accurately predicts the occurrence of cervical cancer under mixed diseases

Cervical cancer (CC) is one of the most common gynecological malignancies. Cytological screening, while being the most common and accurate method for detecting cervical cancer, is both time-consuming and costly. Predicting CC based on bioinformatics can assist in the rapid early screening of CC in clinical practice. Most recent CC prediction methods require a large amount of detection data or sequencing data and are not ideal for CC detection in complex disease samples. We developed the Disease trend analysis platform (Dtap), which can quickly predict the occurrence of diseases using only blood routine data. Blood routine data was collected from 1,292 cervical cancer patients, 4,860 patients with complex diseases, and 4,980 healthy individuals from various sources. The results show that the Dtap-based trend model maintained good and stable performance in the prediction task of multiple datasets as well as complex disease samples. Finally, we built DTAPCC (http://bioinfor.imu.edu.cn/dtapcc), a Dtap-based CC disease prediction platform, to help users quickly predict CC and visualize trend features.

Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations

BACKGROUND

The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing.

OBJECTIVE AND RATIONALE

This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom.

SEARCH METHODS

We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant.

OUTCOMES

The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling.

WIDER IMPLICATIONS

The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.

Identifying and characterizing disease subpopulations that most benefit from polygenic risk scores

Polygenic risk scores (PRSs) hold promise in their potential translation into clinical settings to improve disease risk prediction. An important consideration in integrating PRSs into clinical settings is to gain an understanding of how to identify which subpopulations of individuals most benefit from PRSs for risk prediction. In this study, using the UK Biobank dataset, we trained logistic regression models to predict the 10 year incident risk of myocardial infarction, breast cancer, and schizophrenia using either just clinical features or clinical features combined with PRSs. For each disease, we identified the top 10% subgroup with the greatest magnitude of improvement in risk prediction accuracy attributed to PRSs in the multi-modal model. Using up to ~ 3.6 k demographic, lifestyle, diagnostic, lab, and physical measurement features from the UK Biobank dataset of ~ 500 k individuals, we characterized these subgroups based on various clinical, lifestyle, and demographic characteristics. The incident cases in the top 10% subgroup for each disease represent distinct phenotypes that differ from other cases and that are strongly correlated with genetic predisposition. Our findings provide insights into disease subtypes and can encourage future studies aimed at classifying these individuals to enhance the targeting of polygenic risk scoring in practice.

The impact of population ageing on the burden of chronic kidney disease

The burden of chronic kidney disease (CKD) and its risk factors are projected to rise in parallel with the rapidly ageing global population. By 2050, the prevalence of CKD category G3-G5 may exceed 10% in some regions, resulting in substantial health and economic burdens that will disproportionately affect lower-income countries. The extent to which the CKD epidemic can be mitigated depends largely on the uptake of prevention efforts to address modifiable risk factors, the implementation of cost-effective screening programmes for early detection of CKD in high-risk individuals and widespread access and affordability of new-generation kidney-protective drugs to prevent the development and delay the progression of CKD. Older patients require a multidisciplinary integrated approach to manage their multimorbidity, polypharmacy, high rates of adverse outcomes, mental health, fatigue and other age-related symptoms. In those who progress to kidney failure, comprehensive conservative management should be offered as a viable option during the shared decision-making process to collaboratively determine a treatment approach that respects the values and wishes of the patient. Interventions that maintain or improve quality of life, including pain management and palliative care services when appropriate, should also be made available.

Genetic determinants of renal scarring in children with febrile UTI

BACKGROUND

Febrile urinary tract infections (UTIs) are among the most severe bacterial infections in infants, in which a subset of patients develops complications. Identifying infants at risk of recurrent infections or kidney damage based on clinical signs is challenging. Previous observations suggest that genetic factors influence UTI outcomes and could serve as predictors of disease severity. In this study, we conducted a nationwide survey of infant genotypes to develop a strategy for infection management based on individual genetic risk. Our aims were to identify genetic susceptibility variants for renal scarring (RS) and genetic host factors predisposing to dilating vesicoureteral reflux (VUR) and recurrent UTIs.

METHODS

To assess genetic susceptibility, we collected and analyzed DNA from blood using exome genotyping. Disease-associated genetic variants were identified through bioinformatics analysis, including allelic frequency tests and odds ratio calculations. Kidney involvement was defined using dimercaptosuccinic acid (DMSA) scintigraphy.

RESULTS

In this investigation, a cohort comprising 1087 infants presenting with their first episode of febrile UTI was included. Among this cohort, a subset of 137 infants who underwent DMSA scanning was subjected to gene association analysis. Remarkable genetic distinctions were observed between patients with RS and those exhibiting resolved kidney involvement. Notably, the genetic signature indicative of renal scarring prominently featured mitochondrial genes.

CONCLUSIONS

In this nationwide study of genetic susceptibility to RS after febrile UTIs in infancy, we identified a profile dominated by mitochondrial polymorphisms. This profile can serve as a predictor of future complications, including RS and recurrent UTIs.

A methylation risk score for chronic kidney disease: a HyperGEN study

Chronic kidney disease (CKD) impacts about 1 in 7 adults in the United States, but African Americans (AAs) carry a disproportionately higher burden of disease. Epigenetic modifications, such as DNA methylation at cytosine-phosphate-guanine (CpG) sites, have been linked to kidney function and may have clinical utility in predicting the risk of CKD. Given the dynamic relationship between the epigenome, environment, and disease, AAs may be especially sensitive to environment-driven methylation alterations. Moreover, risk models incorporating CpG methylation have been shown to predict disease across multiple racial groups. In this study, we developed a methylation risk score (MRS) for CKD in cohorts of AAs. We selected nine CpG sites that were previously reported to be associated with estimated glomerular filtration rate (eGFR) in epigenome-wide association studies to construct a MRS in the Hypertension Genetic Epidemiology Network (HyperGEN). In logistic mixed models, the MRS was significantly associated with prevalent CKD and was robust to multiple sensitivity analyses, including CKD risk factors. There was modest replication in validation cohorts. In summary, we demonstrated that an eGFR-based CpG score is an independent predictor of prevalent CKD, suggesting that MRS should be further investigated for clinical utility in evaluating CKD risk and progression.

The Role of Genetic Testing in Adult CKD

Mounting evidence indicates that monogenic disorders are the underlying cause in a significant proportion of patients with CKD. In recent years, the diagnostic yield of genetic testing in these patients has increased significantly as a result of revolutionary developments in genetic sequencing techniques and sequencing data analysis. Identification of disease-causing genetic variant(s) in patients with CKD may facilitate prognostication and personalized management, including nephroprotection and decisions around kidney transplantation, and is crucial for genetic counseling and reproductive family planning. A genetic diagnosis in a patient with CKD allows for screening of at-risk family members, which is also important for determining their eligibility as kidney transplant donors. Despite evidence for clinical utility, increased availability, and data supporting the cost-effectiveness of genetic testing in CKD, especially when applied early in the diagnostic process, many nephrologists do not use genetic testing to its full potential because of multiple perceived barriers. Our aim in this article was to empower nephrologists to (further) implement genetic testing as a diagnostic means in their clinical practice, on the basis of the most recent insights and exemplified by patient vignettes. We stress why genetic testing is of significant clinical benefit to many patients with CKD, provide recommendations for which patients to test and which test(s) to order, give guidance about interpretation of genetic testing results, and highlight the necessity for and essential components of pretest and post-test genetic counseling.

Systems Biology and Novel Biomarkers for the Early Detection of Diabetic Kidney Disease

Diabetic kidney disease is the most common driver of chronic kidney disease (CKD)-associated mortality and kidney replacement therapy. Despite recent therapeutic advances (sodium glucose co-transporter 2 [SGLT2] inhibitors, finerenone), the residual kidney and mortality risk remains high for patients already diagnosed of having CKD (i.e., estimated glomerular filtration rate <60 mL/min/1.73 m2 or urinary albumin:creatinine ratio >30 mg/g). The challenge for the near future is to identify patients at higher risk of developing CKD to initiate therapy before CKD develops (primary prevention of CKD) and to identify patients with CKD and high risk of progression or death, in order to intensify therapy. We now discuss recent advances in biomarkers that may contribute to the identification of such high-risk individuals for clinical trials of novel primary prevention or treatment approaches for CKD. The most advanced biomarker from a clinical development point of view is the urinary peptidomics classifier CKD273, that integrates prognostic information from 273 urinary peptides and identifies high-risk individuals before CKD develops.

Genetic and Phenotypic Features of Schizophrenia in the UK Biobank

Importance

Large-scale biobanks provide important opportunities for mental health research, but selection biases raise questions regarding the comparability of individuals with those in clinical research settings.

Objective

To compare the genetic liability to psychiatric disorders in individuals with schizophrenia in the UK Biobank with individuals in the Psychiatric Genomics Consortium (PGC) and to compare genetic liability and phenotypic features with participants recruited from clinical settings.

Design, Setting, and Participants

This cross-sectional study included participants from the population-based UK Biobank and schizophrenia samples recruited from clinical settings (CLOZUK, CardiffCOGS, Cardiff F-Series, and Cardiff Affected Sib-Pairs). Data were collected between January 1993 and July 2021. Data analysis was conducted between July 2021 and June 2023.

Main Outcomes and Measures

A genome-wide association study of UK Biobank schizophrenia case-control status was conducted, and the results were compared with those from the PGC via genetic correlations. To test for differences with the clinical samples, polygenic risk scores (PRS) were calculated for schizophrenia, bipolar disorder, depression, and intelligence using PRS-CS. PRS and phenotypic comparisons were conducted using pairwise logistic regressions. The proportions of individuals with copy number variants associated with schizophrenia were compared using Firth logistic regression.

Results

The sample of 517 375 participants included 1438 UK Biobank participants with schizophrenia (550 [38.2%] female; mean [SD] age, 54.7 [8.3] years), 499 475 UK Biobank controls (271 884 [54.4%] female; mean [SD] age, 56.5 [8.1] years), and 4 schizophrenia research samples (4758 [28.9%] female; mean [SD] age, 38.2 [21.0] years). Liability to schizophrenia in UK Biobank was highly correlated with the latest genome-wide association study from the PGC (genetic correlation, 0.98; SE, 0.18) and showed the expected patterns of correlations with other psychiatric disorders. The schizophrenia PRS explained 6.8% of the variance in liability for schizophrenia case status in UK Biobank. UK Biobank participants with schizophrenia had significantly lower schizophrenia PRS than 3 of the clinically ascertained samples and significantly lower rates of schizophrenia-associated copy number variants than the CLOZUK sample. UK Biobank participants with schizophrenia had higher educational attainment and employment rates than the clinically ascertained schizophrenia samples, lower rates of smoking, and a later age of onset of psychosis.

Conclusions and Relevance

Individuals with schizophrenia in the UK Biobank, and likely other volunteer-based biobanks, represent those less severely affected. Their inclusion in wider studies should enhance the representation of the full spectrum of illness severity.

Influence of Polygenic Background on the Clinical Presentation of Familial Hypercholesterolemia

BACKGROUND

Heterozygous familial hypercholesterolemia (FH) is among the most common genetic conditions worldwide that affects ≈ 1 in 300 individuals. FH is characterized by increased levels of low-density lipoprotein cholesterol (LDL-C) and increased risk of coronary artery disease (CAD), but there is a wide spectrum of severity within the FH population. This variability in expression is incompletely explained by known risk factors. We hypothesized that genome-wide genetic influences, as represented by polygenic risk scores (PRSs) for cardiometabolic traits, would influence the phenotypic severity of FH.

METHODS

We studied individuals with clinically diagnosed FH (n=1123) from the FH Canada National Registry, as well as individuals with genetically identified FH from the UK Biobank (n=723). For all individuals, we used genome-wide gene array data to calculate PRSs for CAD, LDL-C, lipoprotein(a), and other cardiometabolic traits. We compared the distribution of PRSs in individuals with clinically diagnosed FH, genetically diagnosed FH, and non-FH controls and examined the association of the PRSs with the risk of atherosclerotic cardiovascular disease.

RESULTS

Individuals with clinically diagnosed FH had higher levels of LDL-C, and the incidence of atherosclerotic cardiovascular disease was higher in individuals with clinically diagnosed compared with genetically identified FH. Individuals with clinically diagnosed FH displayed enrichment for higher PRSs for CAD, LDL-C, and lipoprotein(a) but not for other cardiometabolic risk factors. The CAD PRS was associated with a risk of atherosclerotic cardiovascular disease among individuals with an FH-causing genetic variant.

CONCLUSIONS

Genetic background, as expressed by genome-wide PRSs for CAD, LDL-C, and lipoprotein(a), influences the phenotypic severity of FH, expanding our understanding of the determinants that contribute to the variable expressivity of FH. A PRS for CAD may aid in risk prediction among individuals with FH.

A new era in the science and care of kidney diseases

Notable progress in basic, translational and clinical nephrology research has been made over the past five decades. Nonetheless, many challenges remain, including obstacles to the early detection of kidney disease, disparities in access to care and variability in responses to existing and emerging therapies. Innovations in drug development, research technologies, tissue engineering and regenerative medicine have the potential to improve patient outcomes. Exciting prospects include the availability of new drugs to slow or halt the progression of chronic kidney disease, the development of bioartificial kidneys that mimic healthy kidney functions, and tissue engineering techniques that could enable transplantable kidneys to be created from the cells of the recipient, removing the risk of rejection. Cell and gene therapies have the potential to be applied for kidney tissue regeneration and repair. In addition, about 30% of kidney disease cases are monogenic and could potentially be treated using these genetic medicine approaches. Systemic diseases that involve the kidney, such as diabetes mellitus and hypertension, might also be amenable to these treatments. Continued investment, communication, collaboration and translation of innovations are crucial to realize their full potential. In addition, increasing sophistication in exploring large datasets, implementation science, and qualitative methodologies will improve the ability to deliver transformational kidney health strategies.

Shared genetic effect of kidney function on bipolar and major depressive disorders: a large-scale genome-wide cross-trait analysis

BACKGROUND

Epidemiological studies have revealed a significant association between impaired kidney function and certain mental disorders, particularly bipolar disorder (BIP) and major depressive disorder (MDD). However, the evidence regarding shared genetics and causality is limited due to residual confounding and reverse causation.

METHODS

In this study, we conducted a large-scale genome-wide cross-trait association study to investigate the genetic overlap between 5 kidney function biomarkers (eGFRcrea, eGFRcys, blood urea nitrogen (BUN), serum urate, and UACR) and 2 mental disorders (MDD, BIP). Summary-level data of European ancestry were extracted from UK Biobank, Chronic Kidney Disease Genetics Consortium, and Psychiatric Genomics Consortium.

RESULTS

Using LD score regression, we found moderate but significant genetic correlations between kidney function biomarker traits on BIP and MDD. Cross-trait meta-analysis identified 1 to 19 independent significant loci that were found shared among 10 pairs of 5 kidney function biomarkers traits and 2 mental disorders. Among them, 3 novel genes: SUFU, IBSP, and PTPRJ, were also identified in transcriptome-wide association study analysis (TWAS), most of which were observed in the nervous and digestive systems (FDR < 0.05). Pathway analysis showed the immune system could play a role between kidney function biomarkers and mental disorders. Bidirectional mendelian randomization analysis suggested a potential causal relationship of kidney function biomarkers on BIP and MDD.

CONCLUSIONS

In conclusion, the study demonstrated that both BIP and MDD shared genetic architecture with kidney function biomarkers, providing new insights into their genetic architectures and suggesting that larger GWASs are warranted.

Diet quality in relation to kidney function and its potential interaction with genetic risk of kidney disease among Dutch post-myocardial infarction patients

PURPOSE

We examined the relation between diet quality, its components and kidney function decline in post-myocardial infarction (MI) patients, and we explored differences by genetic risk of chronic kidney disease (CKD).

METHODS

We analysed 2169 patients from the Alpha Omega Cohort (aged 60-80 years, 81% male). Dietary intake was assessed at baseline (2002-2006) using a validated food-frequency questionnaire and diet quality was defined using the Dutch Healthy Diet Cardiovascular Disease (DHD-CVD) index. We calculated 40-months change in estimated glomerular filtration rate (eGFR, mL/min per 1.73m2). We constructed a weighted genetic risk score (GRS) for CKD using 88 single nucleotide polymorphisms previously linked to CKD. Betas with 95%-confidence intervals (CIs) were obtained using multivariable linear regression models for the association between DHD-CVD index and its components and eGFR change, by GRS.

RESULTS

The average DHD-CVD index was 79 (SD 15) points and annual eGFR decline was 1.71 (SD 3.86) mL/min per 1.73 m2. The DHD-CVD index was not associated with annual eGFR change (per 1-SD increment in adherence score: -0.09 [95% CI -0.26,0.08]). Results for adherence to guidelines for red meat showed less annual eGFR decline (per 1-SD: 0.21 [0.04,0.38]), whereas more annual eGFR decline was found for legumes and dairy (per 1-SD: -0.20legumes [-0.37,-0.04] and - 0.18dairy [-0.34,-0.01]). Generally similar results were obtained in strata of GRS.

CONCLUSION

The DHD-CVD index for overall adherence to Dutch dietary guidelines for CVD patients was not associated with kidney function decline after MI, irrespective of genetic CKD risk. The preferred dietary pattern for CKD prevention in CVD patients warrants further research.