Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

Inhibition of oligodendrocyte precursor motility by oligodendrocyte processes:Implications for transplantation-based approaches to multiple sclerosis

Transplantation of oligodendrocyte precursor cells represents a promising approach to the treatment of the chronic demyelinated lesions of multiple sclerosis. In view of the multi-focal nature of the disease it will be necessary for the transplanted oligodendrocyte precursor cells to migrate through normal white matter between lesions. Work in other systems has shown that differentiated oligodendrocytes within white matter express molecules inhibitory for axon outgrowth. In light of this we have examined the effect of oligodendrocytes on the migration of oligodendrocyte precursors in vitro using time lapse video microscopy. We find that oligodendrocytes induce collapse and loss of motility in oligodendrocyte precursor processes, with this effect being lost as oligodendrocytes undergo programmed cell death. We conclude that the inhibitory factors present on differentiated oligodendrocytes may prevent effective migration between lesion in vivo, and that strategies to overcome this inhibition may be required for successful repair

Intrinsic motivation for physical activity, healthy eating, and self-weighing in association with corresponding behaviors in early pregnancy.

Healthy lifestyle behaviors influence maternal cardiovascular health, but motivation for them in pregnancy is poorly understood. We examined whether intrinsic motivation (assessed on 5-point scales for each behavior) is associated with three lifestyle behaviors in early pregnancy: physical activity, by intensity level; healthy eating, quantified with the Alternate Healthy Eating Index for Pregnancy (AHEI-P); and weight self-monitoring, a standard weight management technique. Participants in the Northern California Pregnancy, Lifestyle and Environment Study (PETALS) population-based cohort completed validated surveys in early pregnancy (2017-18; N = 472; 22 % Asian, 6 % Black, 30 % Hispanic, 13 % multiracial, 30 % White). Cross-sectional data were analyzed in 2021-22. Overall, 40.7 % (n = 192) met United States national physical activity guidelines; the average AHEI-P score was 62.3 out of 130 (SD 11.4); and 36.9 % reported regular self-weighing (≥once/week; n = 174). In models adjusted for participant characteristics, 1-unit increases in intrinsic motivation were associated with increased likelihood of meeting physical activity guidelines (risk ratio [95 % CI]: 1.66 [1.48, 1.86], p < 0.0001); meeting sample-specific 75th percentiles for vigorous physical activity (1.70 [1.44, 1.99], p < 0.0001) and AHEI-P (1.75 [1.33, 2.31], p < 0.0001); and regular self-weighing (2.13 [1.92, 2.37], p < 0.0001). A 1-unit increase in intrinsic motivation lowered the risk of meeting the 75th percentile for sedentary behavior (0.79 [0.67, 0.92], p < 0.003). Intrinsic motivation was not associated with reaching 75th percentiles for total, light, or moderate activity. Intrinsic motivation is associated with physical activity, healthy eating, and self-weighing among diverse individuals in early pregnancy. Results can inform intervention design to promote maternal health via increased enjoyment of lifestyle behaviors

Outreach to diversify clinical trial participation: A randomized recruitment study

Background/aimsRacial and ethnic minorities remain underrepresented in clinical research, yet few recruitment strategies have been rigorously evaluated.MethodsWe experimentally tested whether targeted recruitment letters acknowledging diabetes health disparities and health risks specific to recipients' racial/ethnic group improved two metrics of trial participation: willingness to be screened and enrollment. This experiment was efficiently nested within a randomized clinical trial examining a preventive lifestyle intervention among women at high risk for diabetes. Pregnant women with gestational diabetes or impaired glucose tolerance (N = 445) were randomized to receive a targeted recruitment letter with health risk information specific to their racial/ethnic group (n = 216), or a standard letter with risk information for the general population (n = 229). All letters were bilingual in English and Spanish.ResultsThe targeted as compared to the standard letter did not improve screening or enrollment rates overall or within separate racial/ethnic groups. Among Latina women who preferred Spanish, the targeted letter showed trends for improved screening (66.7% vs 33.3%, p = .06) and enrollment rates (38.9% vs 13.3%, p = .13). In contrast, among Latina women who preferred English, the targeted letter significantly lowered screening (29.6% vs 57.1%, p = .04) and showed trends for lowered enrollment rates (25.9% vs 50.0%, p = .07).ConclusionResults from this randomized study appear to suggest that recruitment letters with diabetes health risk information targeted to recipients' race/ethnicity may improve one metric of clinical trial participation among Latina women who prefer Spanish, but not English. Larger experimental studies, incorporating input from diverse participant stakeholders, are needed to develop evidence-based minority recruitment strategies

Randomised controlled trial of the impact of haemodiafiltration on uraemic neuropathy: FINESSE study protocol

Introduction: The majority of patients undergoing haemodialysis (HD) show evidence of uraemic neuropathy, a condition with no known disease-modifying treatments. The pathogenesis of uraemic neuropathy is poorly understood, but may be related to cumulative exposure to middle molecules or other solutes such as potassium. It is not known whether haemodiafiltration (HDF) reduces the progression of uraemic neuropathy. Methods and analysis: Filtration In the Neuropathy of End-Stage kidney disease Symptom Evolution (FINESSE) is a multicentre, randomised, open-label, blinded endpoint assessment, controlled trial designed to assess the impact of HDF versus HD on uraemic neuropathy. Maintenance HD patients will be randomised in a 1:1 ratio to receive HDF or HD with high-flux membranes for 4 years. The primary endpoint is the difference in the mean change in Total Neuropathy Score (TNS) - a measure of peripheral neuropathy combining symptoms, signs and nerve conduction velocity - over the study period. Secondary outcomes include change at annual timepoints in the TNS and the Neuropathy Symptom Score; and in morbidity, mortality and safety events. Ethics and dissemination: The FINESSE trial has been approved by the Ethics Review Committee of the Sydney South West Area Health Service (HREC/09/RPAH/268) and of Adventist HealthCare Limited (2012-027). When published in a peer-reviewed journal, it will be the largest and longest reported randomised trial aimed at reducing the incidence and severity of uraemic neuropathy. It will advance the understanding of the natural history of uraemic neuropathy and the influence of convective therapies on both neurophysiological and clinical outcomes. It will also allow refinement of current hypotheses surrounding the pathogenesis of uraemic neuropathy and, most importantly, may lead to improvements in the lives of the many patients affected by this debilitating condition

Outreach to diversify clinical trial participation: A randomized recruitment study

BACKGROUND/AIMS: Racial and ethnic minorities remain underrepresented in clinical research, yet few recruitment strategies have been rigorously evaluated. METHODS: We experimentally tested whether targeted recruitment letters acknowledging diabetes health disparities and health risks specific to recipients’ racial/ethnic group improved two metrics of trial participation: willingness to be screened and enrollment. This experiment was efficiently nested within a randomized clinical trial examining a preventive lifestyle intervention among women at high risk for diabetes. Pregnant women with gestational diabetes or impaired glucose tolerance (N = 445) were randomized to receive a targeted recruitment letter with health risk information specific to their racial/ethnic group (n = 216), or a standard letter with risk information for the general population (n = 229). All letters were bilingual in English and Spanish. RESULTS: The targeted as compared to the standard letter did not improve screening or enrollment rates overall or within separate racial/ethnic groups. Among Latina women who preferred Spanish, the targeted letter showed trends for improved screening (66.7% vs. 33.3%, p = .06) and enrollment rates (38.9% vs. 13.3%, p = .13). In contrast, among Latina women who preferred English, the targeted letter significantly lowered screening (29.6% vs. 57.1%, p = .04) and showed trends for lowered enrollment rates (25.9% vs. 50.0%, p = .07). CONCLUSIONS: Results from this randomized study appear to suggest that recruitment letters with diabetes health risk information targeted to recipients’ race/ethnicity may improve one metric of clinical trial participation among Latina women who prefer Spanish, but not English. Larger experimental studies, incorporating input from diverse participant stakeholders, are needed to develop evidence-based minority recruitment strategies