Rethinking clonality using modeling approaches

A combination of experimental procedures, imaging, and probability estimation are typically used as evidence of clonality for the manufacture of a biotherapeutic product. In situations where the totality of evidence is unavailable, establishing a high statistical probability for monoclonality can help strengthen the argument for clonality. In this study, the probability of clonality was re-examined for the limiting dilution method using a combination of experimental and modeling approaches. A limiting dilution experiment was performed using a 50:50 mixed population of GFP-and RFP-expressing cells and the plates were imaged over a span of two weeks. The imaged cells were scored for clonality and double checked with fluorescence imager. Among all wells that had single colony-like growth on day 14 and a single cell-like image on day 0, a fraction of the wells were confirmed to have two colors on day 14 by fluorescence imaging, indicating the singe cell-like day 0 images for these wells were false reads. Considering the possibility of having 2 or more cells with the same color in a particular well, we estimated the worst case total possible number of wells with 2 or more cells on day 0. Moreover, assuming a Poisson distribution for limiting dilution, the recovery rate of any single cell that grew into a visible colony by day 14 was estimated. Our modeling analysis indicated that only a fraction of the wells with \u3e2 cells on day 0 could grow into non-monoclonal colonies. If cells from any of the wells with single colony-like growth on day 14 and single cell-like image on day 0 were chosen as the final clone, the probability of monoclonality was estimated to be \u3e 95% with a 95% upper confidence limit

Case report: Early use of whole exome sequencing unveils HNRNPU-related neurodevelopmental disorder and answers additional clinical questions through reanalysis

This case report chronicles the diagnostic odyssey and resolution of a 27-year-old female with a complex neurodevelopmental disorder (NDD) using Whole Exome Sequencing (WES). The patient presented to a precision medicine clinic with multiple diagnoses including intellectual disability, autism spectrum disorder (ASD), obsessive-compulsive disorder (OCD), tics, seizures, and pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS). Although this patient previously had chromosomal microarray and several single-gene tests, the underlying cause of this patient’s symptoms remained elusive. WES revealed a pathogenic missense mutation in the HNRNPU gene, associated with HNRNPU-related neurodevelopmental disorder (HNRNPU-NDD) and developmental and epileptic encephalopathy-54 (DEE54, OMIM: # 617391). Following this diagnoses, other treating clinicians identified additional indications for genetic testing, however, as the WES data was readily available, the clinical team was able to re-analyze the WES data to address their inquiries without requiring additional tests. This emphasizes the pivotal role of WES in expediting diagnoses, reducing costs, and providing ongoing clinical utility throughout a patient’s life. Accessible WES data in primary care settings can enhance patient care by informing future genetic inquiries, enhancing coordination of care, and facilitating precision medicine interventions, thereby mitigating the burden on families and the healthcare system

LGBT+ History Month 2024 Report

LGBT+ History Month 2024 at the University of Dundee was a great success, bringing together stories and people from across the broad community in our city.It would not have been possible without support and participation from a huge number of people, and we are hugely grateful to everyone who made the Month possible.We’ll also make a note of some key wins, challenges, and lessons from this year, so that everyone can learn from them for future events

Limitations of subcloning as a tool to characterize homogeneity of a cell population

Cloning, or the derivation of a cell line from a single cell is a critical step in the generation of a manufacturing cell line. The expectation is that the process of cloning will result in a uniform and homogeneous cell line that will ensure robust product quality over the lifetime of the product. Regulatory guidelines require the sponsors provide assurance of clonality of the production cell line and when such evidence is not available, additional studies are required to further ensure consistent long-term manufacturing of the product. One approach to characterize homogeneity of a cell line is subclone analysis where clones are generated from the original cell line and an evaluation of their similarity is performed lines. To study the suitability of subclone analysis to provide additional assurance that a production cell line is clonally derived, an antibody producing CHO Master Cell Bank (MCB), which was cloned by a validated FACS method and with a clear documented day 0 image was characterized. Specifically, this MCB was subcloned and imaged to assure each of the subclones were derived from a single cell. A total of 46 subclones were analyzed for growth, productivity, product quality, as well as copy number and integration site analysis. Despite demonstration of clonality for both the MCB and the subclones, significant diversity in cell growth, protein productivity, and product quality attributes was observed between the 46 subclones. The diversity in protein productivity and quality were reproduced across bioreactor scales, suggesting that albeit different, the subclones were stable populations that varied from the parental clonal cell line. Additionally, while ~2-fold shifts in copy number were seen, no significant integration site changes were observed. Our data suggest subcloning induces changes (genetic or epigenetic) outside the region of the transgene which result in the subclones exhibiting a wide diversity in cell growth protein productivity, and product quality. Transcriptomic and genomic characterization studies are underway to further characterize the differences between subclones and the MCB. Importantly, the subclones do keep their individual characteristics as they mature and stabilize, suggesting that the resulting population that grows out of a single cell is stable but with unique properties. Overall, this work adds to the growing body of work on CHO cell plasticity and suggests that subcloning is not an effective approach to demonstrate homogeneity of a cell bank

LGBT+ History Month 2024 Report

LGBT+ History Month 2024 at the University of Dundee was a great success, bringing together stories and people from across the broad community in our city.It would not have been possible without support and participation from a huge number of people, and we are hugely grateful to everyone who made the Month possible.We’ll also make a note of some key wins, challenges, and lessons from this year, so that everyone can learn from them for future events

What are we missing? Risk behaviors among Arabâ American adolescents and emerging adults

Background and purposeResearch on Arabâ Americans as a distinct ethnic group is limited, especially when considering the health of Arabâ American youth. This study describes health risk (substance use, violence); health promotive behaviors (hope, spirituality); and sexual activity (oral, vaginal, anal sex) of Arabâ American adolescents and emerging adults (aged 15â 23) within their life context, as well as the association between these behaviors.MethodsA secondary analysis of data on a subset of Arabâ American participants obtained from a randomizedâ control trial was utilized to conduct mixed methods analyses. Qualitative analyses completed on the openâ ended questions used the constant comparative method for a subsample (n = 24) of participants. Descriptive quantitative analyses of survey data utilized bivariate analyses and stepwise logistic regression to explore the relation between risk behaviors and sexual activity among the full sample (n = 57).ConclusionsQualitative analyses revealed two groups of participants: (a) multiple risk behaviors and negative lifeâ events, and (b) minimal risk behaviors and positive lifeâ events. Quantitative analyses indicated older youth, smokers, and those with higher hope pathways were more likely to report vaginal sex.Implications for practiceThe unique cultural and social contexts of Arabâ American youth provide a framework for recommendations for the prevention of risk behaviors.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134166/1/jaan12352.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134166/2/jaan12352_am.pd

Evaluation of a health promoting schools program in a school board in Nova Scotia, Canada.

A Health promoting schools (HPS) approach aims to make schools a healthy place through a holistic approach that promotes a supportive 'school ethos' and emphasizes improvements in physical, social, and emotional well-being and educational outcomes. A HPS initiative in rural Nova Scotia (Canada) provided an opportunity for a population-level natural experiment. This study investigated student well-being and health behaviours between schools with and without HPS implementation and schools with high and low school ethos scores. Student well-being, nutrition, and physical activity were examined in a cross-sectional survey of elementary students in Nova Scotia, Canada in 2014. Multiple regression was used to assess the relationship with student well-being using the Quality of Life in School (QoLS) instrument and health behaviours. The main exposure was attending one of the 10 HPS schools; secondary exposure was the school ethos score. The overall QoLS score and its subdomain scores in the adjusted models were higher in students attending HPS schools compared to those in non-HPS schools, but the differences were not statistically significant and the effect sizes were small. Students in schools that scored high on school ethos score had higher scores for the QoLS and its subdomains, but the difference was only significant for the teacher-student relationship domain. Although this study did not find significant differences between HPS and non-HPS schools, our results highlight the complexity of evaluating HPS effects in the real world. The findings suggest a potential role of a supportive school ethos for student well-being in school

OR30-1 Safety and Efficacy of Recombinant Human Parathyroid Hormone 1-84 for the Treatment of Adults with Chronic Hypoparathyroidism: Six-Year Results of the RACE Study

RACE is an open-label study that assessed the long-term safety and efficacy of recombinant human parathyroid hormone 1-84 (rhPTH[1-84]) for the treatment of hypoparathyroidism in adults (ClinicalTrials.gov identifier NCT01297309). Patients initially received 25 or 50 µg/day of rhPTH(1-84) subcutaneously, once daily, with stepwise dose adjustments of 25 µg (up or down) to a maximum of 100 µg/day. rhPTH(1-84) could be titrated and oral calcium (Ca) and calcitriol doses adjusted at any time during the study to maintain albumin-corrected serum Ca levels in the target range of 8.0-9.0 mg/dL. A composite efficacy endpoint was the proportion of patients who achieved at least a 50% reduction from baseline (BL) in oral Ca dose (or Ca ≤500 mg/day) and at least a 50% reduction from BL in calcitriol dose (or calcitriol ≤0.25 µg/day), while normalizing or maintaining albumin-corrected serum Ca compared with BL value and not exceeding the upper limit of normal for the central laboratory. Here, we present 6-year safety and efficacy data with descriptive summary statistics (mean ± SD). The study cohort consisted of 49 patients enrolled at 12 US centers (mean age, 48.1±9.78 years; 81.6% female); data from 34 patients (69.4%) who completed 72 months (M72) of treatment with rhPTH(1-84) as of July 17, 2018 are presented here. Oral Ca and calcitriol doses were reduced by 40.4% and 72.2% at M72, respectively, and albumin-corrected serum Ca levels were maintained within the target range (BL, 8.4±0.70 mg/dL; M72, 8.4±0.68 mg/dL). At M72, 22 of 34 patients (64.7%) achieved the composite efficacy endpoint. Urinary Ca excretion declined from above-normal at BL to within the normal range (BL, 356.7±200.37 mg/24 h; M72, 213.2±128.82 mg/24 h). Mean serum creatinine levels remained stable (BL, 1.0±0.21 mg/dL; M72, 0.9±0.21 mg/dL), as did estimated glomerular filtration rate (eGFR; BL, 77.7±17.67 mL/min/1.73 m2; M72, 79.4±18.39 mL/min/1.73 m2). Serum phosphorus levels declined from above-normal at BL to within normal range (BL, 4.8±0.58 mg/dL; M72, 4.0±0.62 mg/dL); calcium-phosphorus product levels also declined (BL, 42.1±6.35 mg2/dL2; M72, 33.7±5.01 mg2/dL2). Treatment-emergent adverse events and treatment-emergent serious adverse events were reported in 98.0% and 26.5% of patients, respectively; no new safety concerns were identified. Continuous use of rhPTH(1-84) over 6 years resulted in a favorable safety profile, was effective, and improved key measurements of mineral homeostasis, notably normalization of urinary calcium. Disclosures: All of the authors disclose a relationship with Shire: advisory board member, JPB, MAL, MM, DMS, TJV; consultant, JPB, BLC, MAL, MM, DMS, TJV; grant recipient, JPB, DD, MM, MP, DMS, MLW; employee, H-ML, NS; research investigator, JPB, HB, JR, DMS, TJV, MLW, NBW; speaker, JPB, HB, MLW, NBW. Funding: Shir

Dialogue on the Impact of Coronavirus on Research and Publishing: Monday 22nd June 2020

This roundtable took place via Microsoft Teams on Monday 22nd June 2020 to discuss the impact of COVID-19 on Research and Publishing in the U

The Human Disease Ontology 2022 update.

The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO\u27s 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and genomic resources around the world. This update reports on the addition of 1,793 new disease terms, a 14% increase of textual definitions and the integration of 22 137 new SubClassOf axioms defining disease to disease connections representing the DO\u27s complex disease classification. The DO\u27s updated website provides multifaceted etiology searching, enhanced documentation and educational resources