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PubMed2003

UK Biobank: a project in search of a protocol?

Before it has even begun recruiting participants, the UK Biobank project has raised extraordinary passions among scientists. Some scientists are broadly supportive of the project, and feel that it is a scientifically valid, potentially valuable resource, although they still have reservations over the details of the current protocol. Others see it as an ill-conceived, politically motivated project, in which consultations have only been done to give an appearance of legitimacy and in which the scientific case has not been made for its design. There has been resentment over how the protocol has evolved, and the secrecy and legal constraints that surrounded the process for groups bidding to be involved has had the appearance of attempting to stifle debate. For this article even supporters of the project have been unwilling to be quoted on the record. The only point that everyone seems to agree on is that sufficient debate about the project has not taken place.

Aged↗
PubMedDate not supplied

Analogical reasoning in handling emerging technologies: the case of umbilical cord blood biobanking.

How are we individually and as a society to handle new and emerging technologies? This challenging question underlies much of the bioethical debates of modern times. To address this question we need suitable conceptions of the new technology and ways of identifying its proper management and regulation. To establish conceptions and to find ways to handle emerging technologies we tend to use analogies extensively. The aim of this article is to investigate the role that analogies play or may play in the processes of understanding and managing new technology. More precisely we aim to unveil the role of analogies as analytical devices in exploring the "being" of the new technology as well the normative function of analogies in conceptualizing the characteristics and applications of new technology. Umbilical cord blood biobanking will be used as a case to investigate these roles and functions.

Bioethical Issues↗
PubMed2026

ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering.

MOTIVATION: Estimating genetic clusters from sequencing data is a fundamental task in population and medical genetics, enabling demographic inference and adjustment for population structure in association studies. ADMIXTURE, a widely used model-based clustering method, employs an accelerated Expectation-Maximization (EM) algorithm to infer population parameters; however, its computational demands scale poorly, limiting its usefulness for modern biobank-sized datasets. While recent EM acceleration strategies employing second-order quasi-Newton schemes preserve accuracy, they remain computationally intensive. Conversely, EM-free approaches that prioritize speed often compromise solution quality. RESULTS: We introduce ADAMIXTURE, a novel optimization framework that integrates the EM algorithm with Adaptive Moment Estimation (Adam). Unlike traditional acceleration methods, ADAMIXTURE utilizes first-order gradients with adaptive learning rates derived from raw and squared moments to approximate curvature information, bypassing the computational overhead of Hessian approximations. This approach surpasses the convergence efficiency of second-order methods while maintaining the low computational complexity of first-order updates. Across simulated and large-scale empirical datasets, ADAMIXTURE demonstrates substantial reductions in wall-clock runtime and enhanced scalability compared to state-of-the-art methods, while maintaining comparable or improved inference accuracy. Its GPU implementation runs in under 2 h on half a million samples and variants, a two order of magnitude speedup over current state-of-the-art. AVAILABILITY AND IMPLEMENTATION: Source code is available at: https://github.com/AI-sandbox/ADAMIXTURE.

Clustering Algorithms↗
PubMed2006

Snoring and vascular risk factors and disease in a low-risk Chinese population: the Guangzhou Biobank Cohort Study.

STUDY OBJECTIVE: Snoring is a common condition, but data describing the relationship between snoring and vascular disease is very limited in Asian populations. We therefore describe the association between snoring and vascular disease and associated risk factors. DESIGN: Cross-sectional study of baseline data from the Guangzhou Biobank Cohort Study. SETTING: Community-based elderly association from Guangzhou, China. PARTICIPANTS: 10413 Chinese subjects (50-85 years of age). MEASUREMENTS: Self-reported snoring status and frequency and frequency of daytime tiredness were collected by questionnaire, as were demographic and socioeconomic data, disease histories, and potential confounders, such as smoking and alcohol consumption. Anthropometry, blood pressure, and fasting glucose and lipid profile were also measured. RESULTS: Self-reported snoring frequency was identified in 8325 (80.0%) subjects, with 51.6% reporting that they snored, of whom 15.5% were daily snorers. Increasing prevalence of snoring showed a clear positive relationship with cardiovascular risk factors, including age, obesity, blood pressure, and lipid levels (p < .001 for all). The prevalence of self-reported vascular-disease history was low but significantly associated with increasing snoring frequency. Logistic regression showed that snoring frequency was an independent predictor of vascular-disease history (odds ratios [95% confidence intervals] 1.68 [1.32-2.13] for daily snorers compared with the never-snorer reference group), of the metabolic syndrome (2.16 [1.88-2.49]) and each of its components (hypertension [1.37 (1.20-1.56)], and of dyslipidemia [1.22 (1.07-1.40)], central obesity [2.39 (2.08-2.76)], and diabetes [1.30 (1.09-1.56)]) after adjustment for potential confounders. CONCLUSION: Increasing snoring frequency was associated with an increasing prevalence of risk factors and self-reported vascular disease. Snoring may a useful marker for increased risk of vascular disease.

Aged↗
PubMed2023

Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank.

Exome-sequencing association studies have successfully linked rare protein-coding variation to risk of thousands of diseases. However, the relationship between rare deleterious compound heterozygous (CH) variation and their phenotypic impact has not been fully investigated. Here, we leverage advances in statistical phasing to accurately phase rare variants (MAF ~ 0.001%) in exome sequencing data from 175,587 UK Biobank (UKBB) participants, which we then systematically annotate to identify putatively deleterious CH coding variation. We show that 6.5% of individuals carry such damaging variants in the CH state, with 90% of variants occurring at MAF < 0.34%. Using a logistic mixed model framework, systematically accounting for relatedness, polygenic risk, nearby common variants, and rare variant burden, we investigate recessive effects in common complex diseases. We find six exome-wide significant () and 17 nominally significant () gene-trait associations. Among these, only four would have been identified without accounting for CH variation in the gene. We further incorporate age-at-diagnosis information from primary care electronic health records, to show that genetic phase influences lifetime risk of disease across 20 gene-trait combinations (FDR < 5%). Using a permutation approach, we find evidence for genetic phase contributing to disease susceptibility for a collection of gene-trait pairs, including FLG-asthma () and USH2A-visual impairment (). Taken together, we demonstrate the utility of phasing large-scale genetic sequencing cohorts for robust identification of the phenome-wide consequences of compound heterozygosity.

Preprint↗
PubMed2025

Genetic liability to meniscus degeneration and its comorbidity patterns: a phenome-wide association study in the UK Biobank.

Meniscus degeneration is a common knee pathology causing pain, disability, and osteoarthritis. While mechanical factors are established, the contribution of inherited genetic liability to its systemic disease patterns remains unclear. We applied a polygenic risk score (PRS) for meniscus degeneration, derived from FinnGen genome-wide association study (GWAS) results to 323,999 UK Biobank participants and conducted a phenome-wide association study (PRS-PheWAS) across 962 clinical phenotypes. The PRS-PheWAS revealed significant associations beyond musculoskeletal traits, extending to metabolic, cardiovascular, psychiatric, and gastrointestinal domains, indicating broad shared genetic architecture. To support these findings, linkage disequilibrium score regression confirmed strong genetic correlations with osteoarthritis and related arthropathies, and genotype-tissue expression (GTEx) analysis highlighted tissue-specific expression of lead genes (e.g., GDF5, SOX5, BMP6) in connective and metabolic tissues. The results demonstrate that genetic liability to meniscus degeneration extends beyond the knee, sharing pathways with systemic conditions. This systemic genetic architecture underscores the need for integrative management approaches that combine orthopedic care with metabolic and lifestyle interventions.

Journal Article↗
PubMed2006

Parity and the metabolic syndrome in older Chinese women: the Guangzhou Biobank Cohort Study.

OBJECTIVE: To examine whether parity or gravidity contributes to the development of the metabolic syndrome (MS). METHODS: The first phase of the Guangzhou Biobank Cohort Study recruited 7352 women and 3065 men aged 50-93 years in 2003-4. Data on the number of live births and pregnancies, other reproduction-associated factors and socioeconomic and lifestyles factors were collected by standardized interview. The MS components were determined through physical examination and measurement of fasting blood samples. MS was identified if waist circumference was >or= 90 cm for men or >or= 80 cm for women, plus any two of: (a) raised triglyceride (TG) level (1.7 mmol/l) or specific treatment for this lipid abnormality; (b) reduced high density lipoprotein (HDL)-cholesterol (< 1.03 mmol/l in males or < 1.29 mmol/l in females) or specific treatment for this lipid abnormality; (c) raised blood pressure (BP, systolic BP >or= 130 mmHg or diastolic BP >or= 85 mmHg) or hypertension therapy; and (d) raised fasting glucose (>or= 5.6 mmol/l) or previously diagnosed type 2 diabetes. RESULTS: Before adjustment for potential confounders, we found associations between the number of births and lifestyle and socioeconomic factors in both sexes. However, in women, but not in men, body mass index (BMI), waist-hip ratio, triglyceride and glucose were positively associated with the number of birth after adjusting for a range of potential confounders. The age-adjusted prevalence of the MS increased with the number of births and pregnancies in women, but the gradient for birth was steeper than that for pregnancies [odds ratio change per birth 1.16, 95% confidence interval (CI) 1.11-1.22, P < 0.001; odds ratio change per pregnancy 1.11, 95% CI 1.06-1.16, P < 0.001], although attenuating the association adjustment did not affect the significance of these findings. There was no association in men with regard to the number of their partners' live births given the same analysis and similar shared living background with the women. CONCLUSION: Higher parity or gravidity was associated with a consistent increase in the risk of MS in Chinese women. As the association persisted after adjustment for lifestyle factors and there was no association between the risk of MS and the number of births associated with the partners of the males, the association in women may represent a biological response to pregnancy.

Abortion, Spontaneous↗
PubMed2006

Biobanks, bioethics and concepts of donated blood in the UK.

In recent years international bioethics bodies have made prominent declarations about the uses of donated tissue and related information in genetic research(1). Following the 'legislative' mode of bioethics(2), these organisations have put forward a number of general principles with a view to promoting the fair and equitable use of donated tissue in such research. However, government policies in this field are shaped differently in different national regimes. In this paper, I use recent debates in the UK about a national genetic 'biobank' to illustrate how the shape and texture of policy discussions surrounding the use of donated blood for genetic research have been built upon a prior national consensus that regarded blood as a public good.

Bioethics↗
PubMed2005

Building on relationships of trust in biobank research.

Trust among current and future patients is essential for the success of biobank research. The submission of an informed consent is an act of trust by a patient or a research subject, but a strict application of the rule of informed consent may not be sensitive to the multiplicity of patient interests at stake, and could thus be detrimental to trust. According to a recently proposed law on "genetic integrity" in Sweden, third parties will be prohibited from requesting or seeking genetic information about an individual. Cumbersome restrictions on research may be lifted, thus creating a more favourable climate for medical research.

Biological Specimen Banks↗
PubMed2003

How could primary care meet the informatics needs of UK Biobank? A Scottish proposal.

UK Biobank is an ambitious post-genomic project involving the recruitment and follow-up of 500 000 volunteers aged 45 to 69 years. Many primary care teams will be involved in the study directly or indirectly. The programme of research will use at least five data sources: paper-based questionnaires, blood samples, genotype information derived from the bloods, clinical/prescribing data from the medical records, and data on deaths. We describe three of the key challenges to primary care informatics posed by this project: patient recruitment, confidentiality, and data management. We then describe solutions proposed in Scotland, based on existing technologies. Some of these may be applicable elsewhere in the other Regional Collaborating Centres and other large-scale collaborative projects which rely on primary care informatics.

Aged↗
PubMed2005

UK Biobank: from concept to reality.

The UK Biobank is a major UK collaborative research project to recruit and follow longitudinally the health of 500,000 volunteers aged between 40-69 years. It will provide important biological samples and environmental exposure data. As such, it will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental and lifestyle factors on human morbidity, mortality and health.

Adult↗
PubMed2026

Polygenic score for sleep duration in relation to the risk of Alzheimer's disease: results from the UK biobank.

Studies have suggested that sleep duration may be associated with Alzheimer's disease risk; however, findings based on self-reported sleep duration are likely to be influenced by reverse causation and residual confounding bias. We derived weights for genetic variants associated with wearable-derived sleep duration using the LDpred2-auto method in 77,770 white British participants from the UK Biobank, following the generation of new genome-wide association summary statistics. We then used these weights to generate polygenic scores (PGSs) for the remaining 264,746 white British participants for the association analysis, independent of the sample used to develop PGS weights. We assessed the association of fifths between genetically predicted sleep duration and the risk of Alzheimer's disease (1,451 cases/264,746 individuals over a median 12.5&#x202f;years of follow-up). The PGS explained approximately 2% of the variation in device-measured sleep duration. Compared with individuals in the middle fifth of PGSs, those in the highest fifth (indicating approximately 15&#x202f;min/day longer sleep) had a lower risk of Alzheimer's disease (hazard ratio (HR)&#x202f;=&#x202f;0.79[95%CI, 0.67-0.94]). Our results indicate that genetic predisposition to relatively long sleep duration is associated with a lower Alzheimer's disease risk.

Alzheimer&#x2019;s disease↗
PubMed2025

Integration of Genetic Information to Improve Brain Age Gap Estimation Models in the UK Biobank.

Neurodegeneration occurs when the body's central nervous system becomes impaired as a person ages, which can happen at an accelerated pace. Neurodegeneration impairs quality of life, affecting essential functions, including memory and the ability to self-care. Genetics play an important role in neurodegeneration and longevity. Brain age gap estimation (BrainAGE) is a biomarker that quantifies the difference between a machine learning model-predicted biological age of the brain and the true chronological age for healthy subjects; however, a large portion of the variance remains unaccounted for in these models, attributed to individual differences. This study focuses on predicting the BrainAGE more accurately, aided by genetic information associated with neurodegeneration. To achieve this, a BrainAGE model was developed based on MRI measures, and then the associated genes were determined with a Genome-Wide Association Study. Subsequently, genetic information was incorporated into the models. The incorporation of genetic information yielded improvements in the model performances by 7% to 12%, showing that the incorporation of genetic information can notably reduce unexplained variance. This work helps to define new ways of determining persons susceptible to neurological aging decline and reveals genes for targeted precision medicine therapies.

Humans↗
PubMed2006

Association of vascular risk factors with increasing glycemia even in normoglycemic subjects in an older Chinese population: the Guangzhou Biobank Cohort Study.

Hyperglycemia increases cardiovascular disease risk, but the association between increasing glycemia and cardiovascular risk factors, angina, and coronary heart disease in normoglycemic subjects is less clear, particularly in Chinese. We report on possible associations in a large group of Mainland Chinese subjects. A total of 10,400 older subjects (> or = 50 years) were recruited, and vascular risk factors were measured, including anthropometry, blood pressure, and fasting plasma biochemical factors including glucose, lipid profile, and C-reactive protein (CRP). Subjects were categorized by glycemic status, and the relationship between glycemia and cardiovascular risk factors was investigated using analysis of variance and multiple linear regression analyses. Tertiles of fasting glucose levels showed a clear positive relationship with cardiovascular risk factors including age, obesity, blood pressure, lipid levels, and CRP (P < .001 for all). The overall prevalence of self-reported vascular disease was low, but significantly associated with increasing glycemia. Multiple regression showed that waist circumference (standardized regression coefficient beta = .10, P < .001), triglycerides (beta = 0.16, P < .001), CRP (beta = 0.06, P < .001), female sex (beta = .03, P = .007), high-density lipoprotein cholesterol (beta = -.02, P = .016), and mean arterial pressure (beta = .06, P < .001) were independently associated with fasting glucose levels. Among the normoglycemic subjects (n = 5190), increasing glycemia was still associated with increasing obesity indices, systolic blood pressure, triglyceride, and CRP levels (all P < .05). Increasing glycemia, even in the reference range, is associated with increasing prevalence of vascular risk factors. Control of these risk factors, particularly obesity, the most important avoidable independent determinant of glycemia in normoglycemic subjects, is critical to reduce the risk of the associated vascular disease.

Age Factors↗
PubMed2006

c-Reactive protein and the metabolic syndrome in older Chinese: Guangzhou Biobank Cohort Study.

OBJECTIVE: To examine the association between serum c-reactive protein (CRP) concentration and the metabolic syndrome (MS) using the International Diabetes Federation Metabolic Syndrome Guidelines (April, 2005) definition in an older Chinese population. METHODS: Three thousand and fourteen men and 7275 women aged 50-85 years were recruited and received a full medical check-up including measurement of blood pressure, obesity indices, fasting total, LDL-, HDL-cholesterol, triglycerides, glucose and c-reactive protein. Data describing socioeconomic and lifestyle factors was also collected. RESULTS: Vascular risk factors including waist circumference, weight gain and waist gain since the age of 18, body mass index, waist-hip-ratio, triglyceride, HDL-cholesterol, and systolic and diastolic blood pressures were positively associated with CRP in both men and women (p from <0.001 to 0.016). Compared to those without MS components, adjusted odds ratios for having elevated CRP increased in those with the MS or its components compared those without MS or components (all p<0.001), except for the low HDL-cholesterol in both genders and raised fasting glucose in men. Similarly, the risk of elevated CRP increased with escalating MS components even after adjustment of a range of potential confounders. CONCLUSIONS: There is a strong relationship between CRP and the constellation of MS components and associated vascular risk in this older Chinese population.

Aged↗
PubMed2025

A pancreatic cancer organoid biobank links multi-omics signatures to therapeutic response and clinical evaluation of statin combination therapy.

Chemotherapy remains the primary treatment for pancreatic ductal adenocarcinoma (PDAC), but most patients ultimately develop resistance. Here, we established 260 pancreatic cancer organoid lines, followed by extensive multi-omics profiling and therapeutic sensitivity assessments. Integrated analyses uncovered 6 novel coding and 35 noncoding driver candidates. We discovered 2,794 multi-omics features associated with drug sensitivity and 322 features linked to radiation sensitivity. Pharmacogenomic analyses revealed that chemoresistant organoids exhibited enrichment in protein glycosylation and cholesterol metabolism pathways. Notably, statins effectively targeted chemoresistant PDAC organoids. Statin treatment attenuated protein glycosylation, cholesterol levels, and the epithelial-to-mesenchymal transition (EMT) signature in PDAC organoids. We conducted a single-center, single-arm, phase 2 clinical trial (NCT06241352) combining atorvastatin with chemotherapy in patients with advanced pancreatic cancer. Among 37 patients, 26 (70.3%) demonstrated a response, with tumor markers decreasing by more than 20%, suggesting durable responses and potential clinical benefits in this challenging patient population.

Humans↗