The informatics challenges facing biobanks:a perspective from a United Kingdom biobanking network

The challenges facing biobanks are changing from simple collections of materials to quality-assured fit-for-purpose clinically annotated samples. As a result, informatics awareness and capabilities of a biobank are now intrinsically related to quality. A biobank may be considered a data repository, in the form of raw data (the unprocessed samples), data surrounding the samples (processing and storage conditions), supplementary data (such as clinical annotations), and an increasing ethical requirement for biobanks to have a mechanism for researchers to return their data. The informatics capabilities of a biobank are no longer simply knowing sample locations; instead the capabilities will become a distinguishing factor in the ability of a biobank to provide appropriate samples. There is an increasing requirement for biobanking systems (whether in-house or com-mercially sourced) to ensure the informatics systems stay apace with the changes being experienced by the biobanking community. In turn, there is a requirement for the biobanks to have a clear informatics policy and directive that is embedded into the wider decision making process. As an example, the Breast Cancer Campaign Tissue Bank in the UK was a collaboration between four individual and diverse biobanks in the UK, and an informatics platform has been developed to address the challenges of running a distributed network. From developing such a system there are key observations about what can or cannot be achieved by informatics in isolation. This article will highlight some of the lessons learned during this development process

Hierarchically coupled ultradian oscillators generating robust circadian rhythms

Ensembles of mutually coupled ultradian cellular oscillators have been proposed by a number of authors to explain the generation of circadian rhythms in mammals. Most mathematical models using many coupled oscillators predict that the output period should vary as the square root of the number of participating units, thus being inconsistent with the well-established experimental result that ablation of substantial parts of the suprachiasmatic nuclei (SCN), the main circadian pacemaker in mammals, does not eliminate the overt circadian functions, which show no changes in the phases or periods of the rhythms. From these observations, we have developed a theoretical model that exhibits the robustness of the circadian clock to changes in the number of cells in the SCN, and that is readily adaptable to include the successful features of other known models of circadian regulation, such as the phase response curves and light resetting of the phase

Fat dads must not be blamed for their children's health problems

The relationship between the parental genomes in terms of the future growth and development of their offspring is not critical. For the majority of the genome the tissue-specific gene expression and epigenetic status is shared between the parents equally, with both alleles contributing without parental bias. For a very small number of genes the rules change and control of expression is restricted to a specific, parentally derived allele, a phenomenon known as genomic imprinting. The insulin-like growth factor 2 (Igf2/IGF2) is a robustly imprinted gene, important for fetal growth in both mice and humans. In utero IGF2 exhibits paternal expression, which is controlled by several mechanisms, including the maternally expressing untranslated H19 gene. In the study by Soubry et al., a correlation is drawn between the IGF2 methylation status in fetal cord blood leucocytes, and the obesity status of the father from whom the active IGF2 allele is derived through his sperm. These data imply that paternal obesity affects the normal IGF2 methylation in the sperm and this in turn alters the expression of IGF2 in the baby

Larger females have more calves: influence of maternal body length on fecundity in North Atlantic right whales

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stewart, J., Durban, J., Europe, H., Fearnbach, H., Hamilton, P., Knowlton, A., Lynn, M., Miller, C., Perryman, W., Tao, B., & Moore, M. Larger females have more calves: influence of maternal body length on fecundity in North Atlantic right whales. Marine Ecology Progress Series, 689, (2022): 179–189, https://doi.org/10.3354/meps14040.North Atlantic right whales (NARW) are critically endangered and have been declining in abundance since 2011. In the past decade, human-caused mortalities from vessel strikes and entanglements have been increasing, while birth rates in the population are at a 40 yr low. In addition to declining abundance, recent studies have shown that NARW length-at-age is decreasing due to the energetic impacts of sub-lethal entanglements, and that the body condition of the population is poorer than closely related southern right whales. We examined whether shorter body lengths are associated with reduced fecundity in female NARW. We compared age-corrected, modeled metrics of body length with 3 metrics of fecundity: age at first reproduction, average inter-birth interval, and the number of calves produced per potential reproductive year. We found that body length is significantly related to birth interval and calves produced per reproductive year, but not age at first reproduction. Larger whales had shorter inter-birth intervals and produced more calves per potential reproductive year. Larger whales also had higher lifetime calf production, but this was a result of larger whales having longer potential reproductive spans, as body lengths have generally been declining over the past 40 yr. Declining body sizes are a potential contributor to low birth rates over the past decade. Efforts to reduce entanglements and vessel strikes could help maintain population viability by increasing fecundity and improving resiliency of the population to other anthropogenic and climate impacts.Funding to the New England Aquarium for curation of the photo-identification catalog is provided by NOAA Contract 1305M2- 18-P-NFFM-0108

DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children.

Funder: Wellcome TrustPAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease

Molecular profiling of signet ring cell colorectal cancer provides a strong rationale for genomic targeted and immune checkpoint inhibitor therapies

We would like to thank all patients whose samples were used in this study. We are also thankful to the Northern Ireland Biobank and Grampian Biorepository for providing us with tissue blocks and patient data; and Dr HG Coleman (Queen’s University Belfast) for her advice on statistical analyses. This work has been carried out with financial support from Cancer Research UK (grant: C11512/A18067), Experimental Cancer Medicine Centre Network (grant: C36697/A15590 from Cancer Research UK and the NI Health and Social Care Research and Development Division), the Sean Crummey Memorial Fund and the Tom Simms Memorial Fund. The Northern Ireland Biobank is funded by HSC Research and Development Division of the Public Health Agency in Northern Ireland and Cancer Research UK through the Belfast CRUK Centre and the Northern Ireland Experimental Cancer Medicine Centre; additional support was received from Friends of the Cancer Centre. The Northern Ireland Molecular Pathology Laboratory which is responsible for creating resources for the Northern Ireland Biobank has received funding from Cancer Research UK, Friends of the Cancer Centre and Sean Crummey Foundation.Peer reviewedPublisher PD

The SWELLS Survey. I. A large spectroscopically selected sample of edge-on late-type lens galaxies

The relative contribution of baryons and dark matter to the inner regions of spiral galaxies provides critical clues to their formation and evolution, but it is generally difficult to determine. For spiral galaxies that are strong gravitational lenses, however, the combination of lensing and kinematic observations can be used to break the disk-halo degeneracy. In turn, such data constrain fundamental parameters such as i) the mass density profile slope and axis ratio of the dark matter halo, and by comparison with dark matter-only numerical simulations the modifications imposed by baryons; ii) the mass in stars and therefore the overall star formation efficiency, and the amount of feedback; iii) by comparison with stellar population synthesis models, the normalization of the stellar initial mass function. In this first paper of a series, we present a sample of 16 secure, 1 probable, and 6 possible strong lensing spiral galaxies, for which multi-band high-resolution images and rotation curves were obtained using the Hubble Space Telescope and Keck-II Telescope as part of the Sloan WFC Edge-on Late-type Lens Survey (SWELLS). The sample includes 8 newly discovered secure systems. [abridged] We find that the SWELLS sample of secure lenses spans a broad range of morphologies (from lenticular to late-type spiral), spectral types (quantified by Halpha emission), and bulge to total stellar mass ratio (0.22-0.85), while being limited to M_*>10^{10.5} M_sun. The SWELLS sample is thus well-suited for exploring the relationship between dark and luminous matter in a broad range of galaxies. We find that the deflector galaxies obey the same size-mass relation as that of a comparison sample of elongated non-lens galaxies selected from the SDSS survey. We conclude that the SWELLS sample is consistent with being representative of the overall population of high-mass high-inclination disky galaxies.Comment: 21 pages, 6 figures, MNRAS, in pres

Cardiac resynchronization therapy: mechanisms of action and scope for further improvement in cardiac function.

Aims: Cardiac resynchronization therapy (CRT) may exert its beneficial haemodynamic effect by improving ventricular synchrony and improving atrioventricular (AV) timing. The aim of this study was to establish the relative importance of the mechanisms through which CRT improves cardiac function and explore the potential for additional improvements with improved ventricular resynchronization. Methods and Results: We performed simulations using the CircAdapt haemodynamic model and performed haemodynamic measurements while adjusting AV delay, at low and high heart rates, in 87 patients with CRT devices. We assessed QRS duration, presence of fusion, and haemodynamic response. The simulations suggest that intrinsic PR interval and the magnitude of reduction in ventricular activation determine the relative importance of the mechanisms of benefit. For example, if PR interval is 201 ms and LV activation time is reduced by 25 ms (typical for current CRT methods), then AV delay optimization is responsible for 69% of overall improvement. Reducing LV activation time by an additional 25 ms produced an additional 2.6 mmHg increase in blood pressure (30% of effect size observed with current CRT). In the clinical population, ventricular fusion significantly shortened QRS duration (Δ-27 ± 23 ms, P < 0.001) and improved systolic blood pressure (mean 2.5 mmHg increase). Ventricular fusion was present in 69% of patients, yet in 40% of patients with fusion, shortening AV delay (to a delay where fusion was not present) produced the optimal haemodynamic response. Conclusions: Improving LV preloading by shortening AV delay is an important mechanism through which cardiac function is improved with CRT. There is substantial scope for further improvement if methods for delivering more efficient ventricular resynchronization can be developed. Clinical Trial Registration: Our clinical data were obtained from a subpopulation of the British Randomised Controlled Trial of AV and VV Optimisation (BRAVO), which is a registered clinical trial with unique identifier: NCT01258829, https://clinicaltrials.gov

Understanding Dwarf Galaxies in order to Understand Dark Matter

Much progress has been made in recent years by the galaxy simulation community in making realistic galaxies, mostly by more accurately capturing the effects of baryons on the structural evolution of dark matter halos at high resolutions. This progress has altered theoretical expectations for galaxy evolution within a Cold Dark Matter (CDM) model, reconciling many earlier discrepancies between theory and observations. Despite this reconciliation, CDM may not be an accurate model for our Universe. Much more work must be done to understand the predictions for galaxy formation within alternative dark matter models.Comment: Refereed contribution to the Proceedings of the Simons Symposium on Illuminating Dark Matter, to be published by Springe