PanCake: A Data Structure for Pangenomes

We present a pangenome data structure ("PanCake") for sets of related genomes, based on bundling similar sequence regions into shared features, which are derived from genome-wide pairwise sequence alignments. We discuss the design of the data structure, basic operations on it and methods to predict core genomes and singleton regions. In contrast to many other pangenome analysis tools, like EDGAR or PGAT, PanCake is independent of gene annotations. Nevertheless, comparison of identified core and singleton regions shows good agreements. The PanCake data structure requires significantly less space than the sum of individual sequence files

Political objects : Prescriptions, injustices and promises of material agents

The journal uses a Creative Commons License CC BY 3.0

Political objects : Prescriptions, injustices and promises of material agents

The journal uses a Creative Commons License CC BY 3.0

Polygenic risk scores indicate extreme ages at onset of breast cancer in female BRCA1/2 pathogenic variant carriers

BACKGROUND: Clinical management of women carrying a germline pathogenic variant (PV) in the BRCA1/2 genes demands for accurate age-dependent estimators of breast cancer (BC) risks, which were found to be affected by a variety of intrinsic and extrinsic factors. Here we assess the contribution of polygenic risk scores (PRSs) to the occurrence of extreme phenotypes with respect to age at onset, namely, primary BC diagnosis before the age of 35 years (early diagnosis, ED) and cancer-free survival until the age of 60 years (late/no diagnosis, LD) in female BRCA1/2 PV carriers. METHODS: Overall, estrogen receptor (ER)-positive, and ER-negative BC PRSs as developed by Kuchenbaecker et al. for BC risk discrimination in female BRCA1/2 PV carriers were employed for PRS computation in a curated sample of 295 women of European descent carrying PVs in the BRCA1 (n=183) or the BRCA2 gene (n=112), and did either fulfill the ED criteria (n=162, mean age at diagnosis: 28.3 years, range: 20 to 34 years) or the LD criteria (n=133). Binomial logistic regression was applied to assess the association of standardized PRSs with either ED or LD under adjustment for patient recruitment criteria for germline testing and localization of BRCA1/2 PVs in the corresponding BC or ovarian cancer (OC) cluster regions. RESULTS: For BRCA1 PV carriers, the standardized overall BC PRS displayed the strongest association with ED (odds ratio (OR) = 1.62; 95% confidence interval (CI): 1.16–2.31, p<0.01). Additionally, statistically significant associations of selection for the patient recruitment criteria for germline testing and localization of pathogenic PVs outside the BRCA1 OC cluster region with ED were observed. For BRCA2 PV carriers, the standardized PRS for ER-negative BC displayed the strongest association (OR = 2.27, 95% CI: 1.45–3.78, p<0.001). CONCLUSIONS: PRSs contribute to the development of extreme phenotypes of female BRCA1/2 PV carriers with respect to age at primary BC diagnosis. Construction of optimized PRS SNP sets for BC risk stratification in BRCA1/2 PV carriers should be the task of future studies with larger, well-defined study samples. Furthermore, our results provide further evidence, that localization of PVs in BC/OC cluster regions might be considered in BC risk calculations for unaffected BRCA1/2 PV carriers

Fair and equitable AI in biomedical research and healthcare:Social science perspectives

Artificial intelligence (AI) offers opportunities but also challenges for biomedical research and healthcare. This position paper shares the results of the international conference “Fair medicine and AI” (online 3–5 March 2021). Scholars from science and technology studies (STS), gender studies, and ethics of science and technology formulated opportunities, challenges, and research and development desiderata for AI in healthcare. AI systems and solutions, which are being rapidly developed and applied, may have undesirable and unintended consequences including the risk of perpetuating health inequalities for marginalized groups. Socially robust development and implications of AI in healthcare require urgent investigation. There is a particular dearth of studies in human-AI interaction and how this may best be configured to dependably deliver safe, effective and equitable healthcare. To address these challenges, we need to establish diverse and interdisciplinary teams equipped to develop and apply medical AI in a fair, accountable and transparent manner. We formulate the importance of including social science perspectives in the development of intersectionally beneficent and equitable AI for biomedical research and healthcare, in part by strengthening AI health evaluation

Increasing risk of breakthrough COVID-19 in outbreaks with high attack rates in European long-term care facilities, July to October 2021

We collected data from 10 EU/EEA countries on 240 COVID-19 outbreaks occurring from July-October 2021 in long-term care facilities with high vaccination coverage. Among 17,268 residents, 3,832 (22.2%) COVID-19 cases were reported. Median attack rate was 18.9% (country range: 2.8-52.4%), 17.4% of cases were hospitalised, 10.2% died. In fully vaccinated residents, adjusted relative risk for COVID-19 increased with outbreak attack rate. Findings highlight the importance of early outbreak detection and rapid containment through effective infection prevention and control measures.S

Use of complementary alternative medicine for low back pain consulting in general practice: a cohort study

<p>Abstract</p> <p>Background</p> <p>Although back pain is considered one of the most frequent reasons why patients seek complementary and alternative medical (CAM) therapies little is known on the extent patients are actually using CAM for back pain.</p> <p>Methods</p> <p>This is a post hoc analysis of a longitudinal prospective cohort study embedded in a RCT. General practitioners (GPs) recruited consecutively adult patients presenting with LBP. Data on physical function, on subjective mood, and on utilization of health services was collected at the first consultation and at follow-up telephone interviews for a period of twelve months</p> <p>Results</p> <p>A total of 691 (51%) respectively 928 (69%) out of 1,342 patients received one form of CAM depending on the definition. Local heat, massage, and spinal manipulation were the forms of CAM most commonly offered. Using CAM was associated with specialist care, chronic LBP and treatment in a rehabilitation facility. Receiving spinal manipulation, acupuncture or TENS was associated with consulting a GP providing these services. Apart from chronicity disease related factors like functional capacity or pain only showed weak or no association with receiving CAM.</p> <p>Conclusion</p> <p>The frequent use of CAM for LBP demonstrates that CAM is popular in patients and doctors alike. The observed association with a treatment in a rehabilitation facility or with specialist consultations rather reflects professional preferences of the physicians than a clear medical indication. The observed dependence on providers and provider related services, as well as a significant proportion receiving CAM that did not meet the so far established selection criteria suggests some arbitrary use of CAM.</p

Computational pan-genomics: status, promises and challenges

International audienceMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains