Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.

In vivo selection of anti-HIV-1 gene-modified human hematopoietic stem/progenitor cells to enhance engraftment and HIV-1 inhibition

Hematopoietic stem/progenitor cell (HSPC)-based anti-HIV-1 gene therapy holds great promise to eradicate HIV-1 or to provide long-term remission through a continuous supply of anti-HIV-1 gene-modified cells without ongoing antiretroviral therapy. However, achieving sufficient engraftment levels of anti-HIV gene-modified HSPC to provide therapeutic efficacy has been a major limitation. Here, we report an in vivo selection strategy for anti-HIV-1 gene-modified HSPC by introducing 6-thioguanine (6TG) chemoresistance through knocking down hypoxanthine-guanine phosphoribosyl transferase (HPRT) expression using RNA interference (RNAi). We developed a lentiviral vector capable of co-expressing short hairpin RNA (shRNA) against HPRT alongside two anti-HIV-1 genes: shRNA targeting HIV-1 co-receptor CCR5 and a membrane-anchored HIV-1 fusion inhibitor, C46, for efficient in vivo selection of anti-HIV-1 gene-modified human HSPC. 6TG-mediated preconditioning and in vivo selection significantly enhanced engraftment of HPRT-knockdown anti-HIV-1 gene-modified cells (>2-fold, p < 0.0001) in humanized bone marrow/liver/thymus (huBLT) mice. Viral load was significantly reduced (>1 log fold, p < 0.001) in 6TG-treated HIV-1-infected huBLT mice compared to 6TG-untreated mice. We demonstrated that 6TG-mediated preconditioning and in vivo selection considerably improved engraftment of HPRT-knockdown anti-HIV-1 gene-modified HSPC and repopulation of anti-HIV-1 gene-modified hematopoietic cells in huBLT mice, allowing for efficient HIV-1 inhibition.

Stress perceived by pregnant and decision-making factors of maternal caesarean section request

Background

Pregnancy is a time of psychological vulnerability which can generate intense stress. This represents a maternal and child public health problem. Prenatal stress has harmful impacts on the foetus, the newborn and can cause an increased maternal request for caesareans sections, with nonmedical grounds. The perceived level of prenatal stress factors was assessed in women, as well as mothers’ incentives and decision-making factors for a caesarean section on maternal request.

Methods

A descriptive study on 203 pregnant women, then a comparative study between primiparas (n = 72) and multiparas (n = 131) were carried out with the Antenatal perceived stress inventory. Incentives and decision-making factors for a caesarean on the mother’s demand were studied by in-depth interviews with primiparas mothers (n = 16) who had made this choice.

Results

The perception of stress level during pregnancy is higher at the first quarter regarding the foetus’ health, medical and obstetric risks and reverses with the perception of projections linked to giving birth at the last quarter. Primiparas are significantly (p &lt; 0.001) more stressed. All the elements of the three assessed factors are very significantly (p &lt; 0.001) correlated for the whole population. Among them, 75% choose a caesarean section on maternal request during the first quarter. This choice is confirmed at the end of the second quarter or during the third one for 50% of them, with a one-month time to think for 58.3% of them. The main incentives are tokophobia (66.7%) and preserving the baby’s health (50%).

Conclusions

Pregnancy causes important stress, which is pronounced in primiparas. In France, these results speak in favour of screening tokophobia and an earlier start of birth and parenthood preparation classes in order to handle stress from the first quarter of pregnancy, when medical and prenatal exams are initiated. Birth preparation should be taken on at the last quarter.

Key messages

Investigate stress perceived and identification incentives and decision-making factors of maternal caesarean section request it’s a solution to building bridge for solidarity with tokophobic women. The relation enter stress perceived by pregnant women and decision-making factors of maternal caesarean section request, represents a maternal and child public health problem.

Homotaurine Treatment Enhances CD4+ and CD8+ Regulatory T Cell Responses and Synergizes with Low-Dose Anti-CD3 to Enhance Diabetes Remission in Type 1 Diabetic Mice

Immune cells express γ-aminobutyric acid receptors (GABA-R), and GABA administration can inhibit effector T cell responses in models of autoimmune disease. The pharmacokinetic properties of GABA, however, may be suboptimal for clinical applications. The amino acid homotaurine is a type A GABA-R (GABA_A-R) agonist with good pharmacokinetics and appears safe for human consumption. In this study, we show that homotaurine inhibits in vitro T cell proliferation to a similar degree as GABA but at lower concentrations. In vivo, oral homotaurine treatment had a modest ability to reverse hyperglycemia in newly hyperglycemic NOD mice but was ineffective after the onset of severe hyperglycemia. In severely diabetic NOD mice, the combination of homotaurine and low-dose anti-CD3 treatment significantly increased 1) disease remission, 2) the percentages of splenic CD4⁺ and CD8⁺ regulatory T cells compared with anti-CD3 alone, and 3) the frequencies of CD4⁺ and CD8⁺ regulatory T cells in the pancreatic lymph nodes compared with homotaurine monotherapy. Histological examination of their pancreata provided no evidence of the large-scale GABA_A-R agonist–mediated replenishment of islet β-cells that has been reported by others. However, we did observe a few functional islets in mice that received combined therapy. Thus, GABA_A-R activation enhanced CD4⁺ and CD8⁺ regulatory T cell responses following the depletion of effector T cells, which was associated with the preservation of some functional islets. Finally, we observed that homotaurine treatment enhanced β-cell replication and survival in a human islet xenograft model. Hence, GABA_A-R agonists, such as homotaurine, are attractive candidates for testing in combination with other therapeutic agents in type 1 diabetes clinical trials.

[Medical simulation as a tool in the training of perinatal professionals]

Though technology plays an increasingly important role in modern health systems, human performance remains a major determinant of safety, effectiveness and efficiency of patient care. This is especially true in the delivery room. Thus, the training of professionals must aim not only for the acquisition of theory and practical skills on an individual basis, but also for the learning of teamwork systematically. Training health professionals with simulation enhances their theoretical knowledge and meets formal requirements in literacy, technical skills and communication. Therefore, we intend to explore how, in perinatal care, training with simulation is actually a key teaching tool in initial education and in perpetuation of knowledge. We will approach three main aspects: individual, collective (team) and the impact of simulation in medical practice. The choice of this educational strategy improves the clinical skills that are required for optimal performance in complex, unpredictable and high-stake environments such as the delivery room. Nonetheless, the long term clinical impact of simulation and whether it's modalities, technical or not, are beneficial to the mother and the newborn are areas still to be explored.