Disease prediction with multi-omics and biomarkers empowers case-control genetic discoveries in the UK Biobank.

The emergence of biobank-level datasets offers new opportunities to discover novel biomarkers and develop predictive algorithms for human disease. Here, we present an ensemble machine-learning framework (machine learning with phenotype associations, MILTON) utilizing a range of biomarkers to predict 3,213 diseases in the UK Biobank. Leveraging the UK Biobank's longitudinal health record data, MILTON predicts incident disease cases undiagnosed at time of recruitment, largely outperforming available polygenic risk scores. We further demonstrate the utility of MILTON in augmenting genetic association analyses in a phenome-wide association study of 484,230 genome-sequenced samples, along with 46,327 samples with matched plasma proteomics data. This resulted in improved signals for 88 known (P < 1 × 10-8) gene-disease relationships alongside 182 gene-disease relationships that did not achieve genome-wide significance in the nonaugmented baseline cohorts. We validated these discoveries in the FinnGen biobank alongside two orthogonal machine-learning methods built for gene-disease prioritization. All extracted gene-disease associations and incident disease predictive biomarkers are publicly available ( http://milton.public.cgr.astrazeneca.com ).

γ-aminobutyric acid receptor B signaling drives glioblastoma in females in an immune-dependent manner.

Sex differences in immune responses impact cancer outcomes and treatment response, including in glioblastoma (GBM). However, host factors underlying sex specific immune-cancer interactions are poorly understood. Here, we identify the neurotransmitter γ-aminobutyric acid (GABA) as a driver of GBM-promoting immune response in females. We demonstrated that GABA receptor B (GABBR) signaling enhances L-Arginine metabolism and nitric oxide synthase 2 (NOS2) expression in female granulocytic myeloid-derived suppressor cells (gMDSCs). GABBR agonist and GABA analog promoted GBM growth in females in an immune-dependent manner, while GABBR inhibition reduces gMDSC NOS2 production and extends survival only in females. Furthermore, female GBM patients have enriched GABA transcriptional signatures compared to males, and the use of GABA analogs in GBM patients is associated with worse short-term outcomes only in females. Collectively, these results highlight that GABA modulates anti-tumor immune response in a sex-specific manner, supporting future assessment of GABA pathway inhibitors as part of immunotherapy approaches.

Classifying intervention components used in sleep duration interventions for children: A systematic review and meta-analysis.

The Multiphase Optimization Strategy (MOST) is a three-phase iterative framework that could accelerate the development of behavioral interventions. This systematic review and meta-analysis was conducted within the MOST preparation phase and aimed to classify components included in pediatric sleep duration interventions, using the Behavior Change Technique (BCT) Taxonomy. Across 37 interventions, 46 out of 93 BCTs have been used, with an average of 8 techniques used per study. The most common BCTs used were instruction on how to perform the behavior (N = 29; code 4.1), practical social support (N = 22; code: 3.2), and behavioral practice/rehearsal (N = 22; code: 8.1). A latent class analysis identified two classes of interventions, distinguished by the presence of BCTs falling within the following behavior change groups: shaping knowledge, natural consequences, comparison of behavior, and repetition and substitution. Our meta-analysis revealed that interventions belonging to the latent class with these behavior change groups (N = 15) had a pooled positive intervention effect of 14 min (95 % CI: 8-21) versus 8 min (95 % CI: 1-15) for interventions without these behavior change groups (N = 19). This systematic review and meta-analysis will enhance the development of sleep promotion interventions and guide the selection of candidate intervention components for future optimization and randomized control trials.

Genetic architecture of telomere length in 462,666 UK Biobank whole-genome sequences.

Telomeres protect chromosome ends from damage and their length is linked with human disease and aging. We developed a joint telomere length metric, combining quantitative PCR and whole-genome sequencing measurements from 462,666 UK Biobank participants. This metric increased SNP heritability, suggesting that it better captures genetic regulation of telomere length. Exome-wide rare-variant and gene-level collapsing association studies identified 64 variants and 30 genes significantly associated with telomere length, including allelic series in ACD and RTEL1. Notably, 16% of these genes are known drivers of clonal hematopoiesis-an age-related somatic mosaicism associated with myeloid cancers and several nonmalignant diseases. Somatic variant analyses revealed gene-specific associations with telomere length, including lengthened telomeres in individuals with large SRSF2-mutant clones, compared with shortened telomeres in individuals with clonal expansions driven by other genes. Collectively, our findings demonstrate the impact of rare variants on telomere length, with larger effects observed among genes also associated with clonal hematopoiesis.

The genomic landscape of 2,023 colorectal cancers.

Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.

Associations between Sleep and Physical Activity Behavior Clusters and Epigenetic Age Acceleration in Mexican Adolescents.

INTRODUCTION: Epigenetic aging, a marker of biological aging measured by DNA methylation, may be affected by behaviors, including sleep and physical activity. However, investigations of physical activity and sleep with epigenetic aging among pediatric populations are scant and have not accounted for correlated behaviors. METHODS: The study population included 472 Mexico City adolescents (52% female). Blood collection and 7-day wrist actigraphy (Actigraph GTX-BT) occurred during a follow-up visit when participants were 14.5 (2.09) years. Leukocyte DNA methylation was measured with the Infinium MethylationEPIC array after bisulfite conversion, and 9 epigenetic clocks were calculated. Sleep vs wake time was identified through a pruned dynamic programing algorithm, and physical activity was processed with Chandler cut-offs. Kmeans clustering was used to select actigraphy-assessed physical activity and sleep behavior clusters. Linear regression analyses were used to evaluate adjusted associations between the clusters and epigenetic aging. RESULTS: There were 3 unique clusters: "Short sleep/high sedentary behavior", "Adequate sleep duration and late timing/low moderate or vigorous physical activity (MVPA)", and "Adequate sleep duration/high MVPA". Compared to the "Adequate duration/high MVPA", adolescents with "Adequate duration and late sleep timing/low MVPA" had more accelerated aging for the GrimAge clock (ß = 0.63;95% CI 0.07, 1.19). In pubertal-stratified analyses, more mature adolescents in the "Adequate duration and late sleep timing/low MVPA group" had accelerated epigenetic aging. In contrast, females in the "Short sleep/high sedentary" group had decelerated epigenetic aging for the Wu pediatric clock. CONCLUSIONS: Associations between behavior clusters and epigenetic aging varied by pubertal status and sex. Contrary results in the Wu clock suggest the need for future research on pediatric-specific clocks.

Creating a digital approach for promoting physical activity in pediatric pulmonary hypertension: A framework for future interventions.

Children with pulmonary hypertension (PH) often demonstrate limited exercise capacity. Data support exercise as an effective nonpharmacologic intervention among adults with PH. However, data on exercise training in children and adolescents are limited, and characteristics of the optimal exercise program in pediatric PH have not been identified. Exercise programs may have multiple targets, including muscle deficits which are associated with exercise limitations in both adult and pediatric PH. Wearable accelerometer sensors measure physical activity volume and intensity in the naturalistic setting and can facilitate near continuous data transfer and bidirectional communication between patients and the study team when paired with informatics tools during exercise interventions. To address the knowledge gaps in exercise training in pediatric PH, we designed a prospective, single arm, nonrandomized pilot study to determine feasibility and preliminary estimates of efficacy of a 16-week home exercise intervention, targeting lower extremity muscle mass and enriched by wearable mobile health technology. The exercIse Training in pulmONary hypertEnsion (iTONE) trial includes (1) semistructured exercise prescriptions tailored to the participant's baseline level of activity and access to resources; (2) interval goal setting fostering self-efficacy; (3) real time monitoring of activity via wearable devices; (4) a digital platform enabling communication and feedback between participant and study team; (5) multiple avenues to assess participant safety. This pilot intervention will provide information on the digital infrastructure needed to conduct home-based exercise interventions in PH and will generate important preliminary data on the effect of exercise interventions in youth with chronic cardiorespiratory conditions to power larger studies in the future.

Sleep Duration and Blood Pressure in Youth Referred for Elevated Blood Pressure Evaluation.

OBJECTIVES: Sleep promotion is not specifically recommended as a target for hypertension management. We examined associations of sleep duration and timing with blood pressure parameters in patients referred to pediatric nephrology clinic for elevated blood pressure evaluation. METHODS: This is a retrospective study of initial ambulatory blood pressure monitoring data and self-report sleep data collected from patients referred to nephrology clinic for the evaluation of elevated blood pressure. Linear and logistic regression modeling determined associations between sleep exposures (duration and timing) and continuous and dichotomous blood pressure outcomes, respectively, adjusted for age, sex, body mass index, and weekday versus weekend status. RESULTS: The study sample included 539 patients with mean age 14.6 years and 56% meeting hypertension criteria. Sleep duration averaged 9.1 hours per night. Average timing of sleep onset and offset were 11:06 pm and 8:18 am, respectively. Longer sleep duration was associated with better daytime blood pressure parameters (eg, every extra hour of sleep duration was associated with a reduced odds of wake hypertension [odds ratio, 0.88; 95% CI, 0.79-0.99]). Later sleep onset was associated with worse daytime blood pressure parameters (eg, each additional hour of later sleep onset was associated with higher wake systolic blood pressure index [mean wake blood pressure/95th percentile]) (ß = 0.07; 95% CI, 0.02-0.13). Associations were consistent across sex, age, body mass index, and weekday status. CONCLUSIONS: Longer sleep duration and earlier sleep onset were associated with lower blood pressure. This suggests that sleep optimization may be an important target for intervention in hypertension management.

Characterising the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases.

The etiology of prostate cancer, the second most common cancer in men globally, has a strong heritable component. While rare coding germline variants in several genes have been identified as risk factors from candidate gene and linkage studies, the exome-wide spectrum of causal rare variants remains to be fully explored. To more comprehensively address their contribution, we analysed data from 37,184 prostate cancer cases and 331,329 male controls from five cohorts with germline exome/genome sequencing and one cohort with imputed array data from a population enriched in low-frequency deleterious variants. Our gene-level collapsing analysis revealed that rare damaging variants in SAMHD1 as well as genes in the DNA damage response pathway (BRCA2, ATM and CHEK2) are associated with the risk of overall prostate cancer. We also found that rare damaging variants in AOX1 and BRCA2 were associated with increased severity of prostate cancer in a case-only analysis of aggressive versus non-aggressive prostate cancer. At the single-variant level, we found rare non-synonymous variants in three genes (HOXB13, CHEK2, BIK) significantly associated with increased risk of overall prostate cancer and in four genes (ANO7, SPDL1, AR, TERT) with decreased risk. Altogether, this study provides deeper insights into the genetic architecture and biological basis of prostate cancer risk and severity.

TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent.

The tree of blobs of a species network shows only the tree-like aspects of relationships of taxa on a network, omitting information on network substructures where hybridization or other types of lateral transfer of genetic information occur. By isolating such regions of a network, inference of the tree of blobs can serve as a starting point for a more detailed investigation, or indicate the limit of what may be inferrable without additional assumptions. Building on our theoretical work on the identifiability of the tree of blobs from gene quartet distributions under the Network Multispecies Coalescent model, we develop an algorithm, TINNiK, for statistically consistent tree of blobs inference. We provide examples of its application to both simulated and empirical datasets, utilizing an implementation in the MSCquartets 2.0 R package.

From little things big things grow: enhancement of an acoustic telemetry network to monitor broad-scale movements of marine species along Australia's east coast.

BACKGROUND: Acoustic telemetry has become a fundamental tool to monitor the movement of aquatic species. Advances in technology, in particular the development of batteries with lives of > 10 years, have increased our ability to track the long-term movement patterns of many species. However, logistics and financial constraints often dictate the locations and deployment duration of acoustic receivers. Consequently, there is often a compromise between optimal array design and affordability. Such constraints can hinder the ability to track marine animals over large spatial and temporal scales. Continental-scale receiver networks have increased the ability to study large-scale movements, but significant gaps in coverage often remain. METHODS: Since 2007, the Integrated Marine Observing System's Animal Tracking Facility (IMOS ATF) has maintained permanent receiver installations on the eastern Australian seaboard. In this study, we present the recent enhancement of the IMOS ATF acoustic tracking infrastructure in Queensland to collect data on large-scale movements of marine species in the northeast extent of the national array. Securing a relatively small initial investment for expanding receiver deployment and tagging activities in Queensland served as a catalyst, bringing together a diverse group of stakeholders (research institutes, universities, government departments, port corporations, industries, Indigenous ranger groups and tourism operators) to create an extensive collaborative network that could sustain the extended receiver coverage into the future. To fill gaps between existing installations and maximise the monitoring footprint, the new initiative has an atypical design, deploying many single receivers spread across 2,100 km of Queensland waters. RESULTS: The approach revealed previously unknown broad-scale movements for some species and highlights that clusters of receivers are not always required to enhance data collection. However, array designs using predominantly single receiver deployments are more vulnerable to data gaps when receivers are lost or fail, and therefore "redundancy" is a critical consideration when designing this type of array. CONCLUSION: Initial results suggest that our array enhancement, if sustained over many years, will uncover a range of previously unknown movements that will assist in addressing ecological, fisheries, and conservation questions for multiple species.

Impact of the inaccessible genome on genotype imputation and genome-wide association studies.

Genotype imputation is widely used in genome-wide association studies (GWAS). However, both the genotyping chips and imputation reference panels are dependent on next-generation sequencing (NGS). Due to the nature of NGS, some regions of the genome are inaccessible to sequencing. To date, there has been no complete evaluation of these regions and their impact on the identification of associations in GWAS remains unclear. In this study, we systematically assess the extent to which variants in inaccessible regions are underrepresented on genotyping chips and imputation reference panels, in GWAS results and in variant databases. We also determine the proportion of genes located in inaccessible regions and compare the results across variant masks defined by the 1000 Genomes Project and the TOPMed program. Overall, fewer variants were observed in inaccessible regions in all categories analyzed. Depending on the mask used and normalized for region size, only 4%-17% of the genotyped variants are located in inaccessible regions and 52 to 581 genes were almost completely inaccessible. From the Cooperative Health Research in South Tyrol (CHRIS) study, we present a case study of an association located in an inaccessible region that is driven by genotyped variants and cannot be reproduced by imputation in GRCh37. We conclude that genotyping, NGS, genotype imputation and downstream analyses such as GWAS and fine mapping are systematically biased in inaccessible regions, due to missed variants and spurious associations. To help researchers assess gene and variant accessibility, we provide an online application (https://gab.gm.eurac.edu).

Indications and outcomes of transjugular intrahepatic portosystemic shunt insertion in two regional Australian hepatology centres.

BACKGROUND: Transjugular intrahepatic portosystemic shunt (TIPS) is an important therapy for complications of portal hypertension but remains underutilised in regional settings. AIMS: The aim of this study is to explore the demographics, indications, outcomes and complications in patients undergoing TIPS in two regional hepatology centres. METHODS: Retrospective analysis was undertaken of all patients undergoing TIPS at two regional centres between January 2017 and March 2023. The primary outcome measures were efficacy and complications of TIPS. Patient demographics (such as age, baseline liver severity scores and aetiology of liver disease) and indications for TIPS are detailed. RESULTS: Forty-eight patients underwent TIPS. Median age was 56 years (interquartile range (IQR): 46-65). The most common indications for TIPS were refractory ascites (n = 17) and failure of secondary prophylaxis of variceal bleeding (n = 13). Cumulative survival at 3 months and 1 year was 93% and 77% respectively. There was no significant difference in outcomes based on TIPS indication. The median number of paracenteses in patients undergoing TIPS for refractory ascites 1 year pre- and post-TIPS were 10 (IQR: 4.5-16) and 2 (IQR: 0-4) respectively (P < 0.001). There were no procedure-related deaths. Inpatient management of liver disease complications had a mean cost of $32 874.67 (SEM: 7779) in 1 year pre-TIPS compared with $12 304.70 (SEM: 3531.1) in 1 year post-TIPS (P < 0.001). CONCLUSIONS: TIPS is a safe and effective treatment to reduce complications of portal hypertension and can be performed successfully in the regional setting.

Gamification to Promote Physical Activity in Youth and Mothers With Obesity.

PURPOSE: Physical inactivity and sugar-sweetened beverage (SSB) consumption are associated with obesity. Gamification and self-monitoring to promote physical activity in youth is unknown, but evidence of effectiveness is present in adults. This study examined the effects of a gamification intervention on increased steps per day among parent-adolescent dyads with obesity compared with digital self-monitoring and if self-monitored SSB intake differed between these arms. METHODS: Youth ages 10-16 years and their mothers (N = 39 pairs), both with obesity, were randomized to a self-monitoring (N = 18) or a self-monitoring plus gamification arm (N = 21) for 9 weeks. The step goal was set and incrementally increased each week and was measured with Fitbit devices. Mixed effects linear regression examined changes in steps and SSB consumption per day, per week by study arm. RESULTS: During run-in, mothers averaged 8317 and youth 7508 steps per day. Compared with self-monitoring alone, gamification did not increase daily steps in mothers or youth beyond baseline levels. On average, SSB intake decreased in mothers by approximately 0.5 servings per day; occurred in both arms and persisted throughout the intervention. CONCLUSION: Gamification did not promote physical activity levels in mother-youth dyads with obesity. SSB intake declined in mothers with obesity in both study arms.

Ethical considerations in using sensors to remotely assess pediatric health behaviors.

Sensors, including accelerometer-based and electronic adherence monitoring devices, have transformed health data collection. Sensors allow for unobtrusive, real-time sampling of health behaviors that relate to psychological health, including sleep, physical activity, and medication-taking. These technical strengths have captured scholarly attention, with far less discussion about the level of human touch involved in implementing sensors. Researchers face several subjective decision points when collecting health data via sensors, with these decisions posing ethical concerns for users and the public at large. Using examples from pediatric sleep, physical activity, and medication adherence research, we pose critical ethical questions, practical dilemmas, and guidance for implementing health-based sensors. We focus on youth given that they are often deemed the ideal population for digital health approaches but have unique technology-related vulnerabilities and preferences. Ethical considerations are organized according to Belmont principles of respect for persons (e.g., when sensor-based data are valued above the subjective lived experiences of youth and their families), beneficence (e.g., with sensor data management and sharing), and justice (e.g., with sensor access and acceptability among minoritized pediatric populations). Recommendations include the need to increase transparency about the extent of subjective decision making with sensor data management. Without greater attention to the human factors involved in sensor research, ethical risks could outweigh the scientific promise of sensors, thereby negating their potential role in improving child health and care. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Clinical application of tumour-in-normal contamination assessment from whole genome sequencing.

The unexpected contamination of normal samples with tumour cells reduces variant detection sensitivity, compromising downstream analyses in canonical tumour-normal analyses. Leveraging whole-genome sequencing data available at Genomics England, we develop a tool for normal sample contamination assessment, which we validate in silico and against minimal residual disease testing. From a systematic review of [Formula: see text] patients with haematological malignancies and sarcomas, we find contamination across a range of cancer clinical indications and DNA sources, with highest prevalence in saliva samples from acute myeloid leukaemia patients, and sorted CD3+ T-cells from myeloproliferative neoplasms. Further exploration reveals 108 hotspot mutations in genes associated with haematological cancers at risk of being subtracted by standard variant calling pipelines. Our work highlights the importance of contamination assessment for accurate somatic variants detection in research and clinical settings, especially with large-scale sequencing projects being utilised to deliver accurate data from which to make clinical decisions for patient care.

Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme.

The Cancer Programme of the 100,000 Genomes Project was an initiative to provide whole-genome sequencing (WGS) for patients with cancer, evaluating opportunities for precision cancer care within the UK National Healthcare System (NHS). Genomics England, alongside NHS England, analyzed WGS data from 13,880 solid tumors spanning 33 cancer types, integrating genomic data with real-world treatment and outcome data, within a secure Research Environment. Incidence of somatic mutations in genes recommended for standard-of-care testing varied across cancer types. For instance, in glioblastoma multiforme, small variants were present in 94% of cases and copy number aberrations in at least one gene in 58% of cases, while sarcoma demonstrated the highest occurrence of actionable structural variants (13%). Homologous recombination deficiency was identified in 40% of high-grade serous ovarian cancer cases with 30% linked to pathogenic germline variants, highlighting the value of combined somatic and germline analysis. The linkage of WGS and longitudinal life course clinical data allowed the assessment of treatment outcomes for patients stratified according to pangenomic markers. Our findings demonstrate the utility of linking genomic and real-world clinical data to enable survival analysis to identify cancer genes that affect prognosis and advance our understanding of how cancer genomics impacts patient outcomes.

Enhancing patient safety: A national standard for cyber resiliency in healthcare.

With support from Public Safety Canada's Cyber Security Cooperation Program, HealthCareCAN and the Digital Governance Council developed a new standard to support cyber resiliency in Canada's healthcare system. With a clear framework and enhanced cybersecurity capabilities, healthcare organizations will be better protected from cybercrime, allowing them to respond more effectively to evolving threats and defend critical infrastructure. Health and information technology leaders can derive practical guidance and next steps from this three-year national project to enhance cyber resilience and improve safety within their organizations.

The missing link? LGMN connects hypoxia and immunosuppression in glioblastoma.

In this issue, Pang and colleagues1 identify the protease legumain as a potential immunotherapy target in glioblastoma that drives tumor-associated macrophages in response to hypoxia.

Rare variant associations with plasma protein levels in the UK Biobank.

Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.