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Wellcome Open Research

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https://www.readbyqxmd.com/read/29992192/the-quality-sequencing-minimum-qsm-providing-comprehensive-consistent-transparent-next-generation-sequencing-data-quality-assurance
#1
Shazia Mahamdallie, Elise Ruark, Shawn Yost, Márton Münz, Anthony Renwick, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Nazneen Rahman
Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM). The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29946570/detecting-proliferation-of-adult-hemocytes-in-drosophila-by-brdu-incorporation
#2
Saikat Ghosh, Sudip Mandal, Lolitika Mandal
Drosophila and mammalian hematopoiesis share several similarities that ranges from phases to the battery of transcription factors and signaling molecules that execute this process. These resounding similarities along with the rich genetic tools available in fruitfly makes it a popular invertebrate model to study blood cell development both during normal and aberrant conditions. The larval system is the most extensively studied to date. Several studies have shown that these hemocytes just like mammalian counterpart proliferate and get routinely regenerated upon infection...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29911186/detection-and-quantification-of-anopheles-gambiae-sensu-lato-mosquito-larvae-in-experimental-aquatic-habitats-using-environmental-dna-edna
#3
Joel Odero, Bruno Gomes, Ulrike Fillinger, David Weetman
Background: Growing insecticide resistance and changes in biting and resting behavior of malaria vectors threaten efficacy of insecticide treated nets and indoor residual spraying. Larval source management (LSM) is a promising approach that can target mosquitoes irrespective of their behavior as adults. However, the use of traditional monitoring methods for immature stages of Anopheles mosquitoes is a major challenge to LSM due to the variability in their breeding habitats.  We evaluate the use of an environmental DNA (eDNA) analysis technique in monitoring Anopheles gambiae sensu lato larvae in experimental aquatic habitats...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29904730/surveillance-and-epidemiology-of-drug-resistant-infections-consortium-sedric-supporting-the-transition-from-strategy-to-action
#4
Keiji Fukuda, Direk Limmathurotsakul, Iruka N Okeke, Nandini Shetty, Rogier van Doorn, Nicholas A Feasey, Francesca Chiara, Ghada Zoubiane, Tim Jinks, Julian Parkhill, Jean Patel, Stuart W J Reid, Alison H Holmes, Sharon J Peacock
In recognition of the central importance of surveillance and epidemiology in the control of antimicrobial resistance and the need to strengthen surveillance at all levels, Wellcome has brought together a new international expert group SEDRIC (Surveillance and Epidemiology of Drug Resistant Infections Consortium). SEDRIC aims to advance and transform the ways of tracking, sharing and analysing rates of infection and drug resistance, burden of disease, information on antibiotic use, opportunities for preventative measures such as vaccines, and contamination of the environment...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29904729/proteome-wide-analysis-of-protein-abundance-and-turnover-remodelling-during-oncogenic-transformation-of-human-breast-epithelial-cells
#5
Tony Ly, Aki Endo, Alejandro Brenes, Marek Gierlinski, Vackar Afzal, Andrea Pawellek, Angus I Lamond
Background : Viral oncogenes and mutated proto-oncogenes are potent drivers of cancer malignancy. Downstream of the oncogenic trigger are alterations in protein properties that give rise to cellular transformation and the acquisition of malignant cellular phenotypes. Developments in mass spectrometry enable large-scale, multidimensional characterisation of proteomes. Such techniques could provide an unprecedented, unbiased view of how oncogene activation remodels a human cell proteome. Methods : Using quantitative MS-based proteomics and cellular assays, we analysed how transformation induced by activating v-Src kinase remodels the proteome and cellular phenotypes of breast epithelial (MCF10A) cells...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29904728/transcriptomic-profiling-of-human-skin-biopsies-in-the-clinical-trial-setting-a-protocol-for-high-quality-rna-extraction-from-skin-tumours
#6
Marina Danilenko, Robert Stones, Neil Rajan
Transcriptomic profiling of skin disease using next generation sequencing allows for detailed information on aspects of RNA biology including gene expression, non-coding regulatory elements and gene splicing. The application of RNA sequencing to human skin disease and cancer is often hampered by degraded RNA. Here we describe a protocol that allows for consistently intact RNA to be extracted from snap frozen skin biopsy samples, which has been validated in a clinical trial setting. Human skin tumour punch biopsies (n=28) ranging from 4-6mm in diameter were obtained from 14 patients with an inherited skin tumour syndrome (CYLD cutaneous syndrome) and frozen in liquid nitrogen prior to being stored at -80°C...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29900417/the-tatton-brown-rahman-syndrome-a-clinical-study-of-55-individuals-with-de-novo-constitutive-dnmt3a-variants
#7
Katrina Tatton-Brown, Anna Zachariou, Chey Loveday, Anthony Renwick, Shazia Mahamdallie, Lise Aksglaede, Diana Baralle, Daniela Barge-Schaapveld, Moira Blyth, Mieke Bouma, Jeroen Breckpot, Beau Crabb, Tabib Dabir, Valerie Cormier-Daire, Christine Fauth, Richard Fisher, Blanca Gener, David Goudie, Tessa Homfray, Matthew Hunter, Agnete Jorgensen, Sarina G Kant, Cathy Kirally-Borri, David Koolen, Ajith Kumar, Anatalia Labilloy, Melissa Lees, Carlo Marcelis, Catherine Mercer, Cyril Mignot, Kathryn Miller, Katherine Neas, Ruth Newbury-Ecob, Daniela T Pilz, Renata Posmyk, Carlos Prada, Keri Ramsey, Linda M Randolph, Angelo Selicorni, Deborah Shears, Mohnish Suri, I Karen Temple, Peter Turnpenny, Lionel Val Maldergem, Vinod Varghese, Hermine E Veenstra-Knol, Naomi Yachelevich, Laura Yates, Nazneen Rahman
Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as the DNMT3A-overgrowth syndrome, is an overgrowth intellectual disability syndrome first described in 2014 with a report of 13 individuals with constitutive heterozygous DNMT3A variants. Here we have undertaken a detailed clinical study of 55 individuals with de novo DNMT3A variants, including the 13 previously reported individuals. An intellectual disability and overgrowth were reported in >80% of individuals with TBRS and were designated major clinical associations...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29900416/mir-155-induction-is-a-marker-of-murine-norovirus-infection-but-does-not-contribute-to-control-of-replication-in-vivo
#8
Lucy Thorne, Jia Lu, Yasmin Chaudhry, Ian Goodfellow
Background: Due to their role in fine-tuning cellular protein expression, microRNAs both promote viral replication and contribute to antiviral responses, for a range of viruses. The interactions between norovirus and the microRNA machinery have not yet been studied. Here, we investigated the changes that occur in microRNA expression during murine norovirus (MNV) infection. Methods: Using RT-qPCR-based arrays, we analysed changes in miRNA expression during infection with the acute strain MNV-1 in two permissive cell lines, a murine macrophage cell line, RAW264...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29881786/coverview-a-sequence-quality-evaluation-tool-for-next-generation-sequencing-data
#9
Márton Münz, Shazia Mahamdallie, Shawn Yost, Andrew Rimmer, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Elise Ruark, Nazneen Rahman
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29881785/the-liverpool-care-pathway-for-the-dying-patient-a-critical-analysis-of-its-rise-demise-and-legacy-in-england
#10
Jane Seymour, David Clark
Background : The Liverpool Care Pathway for the Dying Patient ('the LCP') was an integrated care pathway (ICP) recommended by successive governments in England and Wales to improve end-of-life care, using insights from hospice and palliative care. It was discontinued in 2014 following mounting criticism and a national review.  The ensuing debate among clinicians polarised between 'blaming' of the LCP and regret at its removal. Employing the concept of 'boundary objects', we aimed to address three questions: 1) why and how did the LCP come to prominence as a vehicle of policy and practice 2) what factors contributed to its demise? 3) what immediate implications and lessons resulted from its withdrawal? Methods : We use primary and secondary sources in the public domain to assemble a critical and historical review...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29862326/long-read-assemblies-of-geographically-dispersed-plasmodium-falciparum-isolates-reveal-highly-structured-subtelomeres
#11
Thomas D Otto, Ulrike Böhme, Mandy Sanders, Adam Reid, Ellen I Bruske, Craig W Duffy, Pete C Bull, Richard D Pearson, Abdirahman Abdi, Sandra Dimonte, Lindsay B Stewart, Susana Campino, Mihir Kekre, William L Hamilton, Antoine Claessens, Sarah K Volkman, Daouda Ndiaye, Alfred Amambua-Ngwa, Mahamadou Diakite, Rick M Fairhurst, David J Conway, Matthias Franck, Chris I Newbold, Matt Berriman
Background : Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods : Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29862325/distinct-behavior-of-myelomonocytic-cells-and-cd8-t-cells-underlies-the-hepatic-response-to-listeria-monocytogenes
#12
Peter Velázquez, Cassandra Williams, Ingrid Leiner, Eric G Pamer, Michael L Dustin
Background : The immune response to Listeria monocytogenes (LM) is characterized by formation of leukocyte rich foci of infection in liver and spleen.  Although much has been gained in our understanding of immune response through the study of LM, little is known about spatio-temporal regulation of immune response to Listeria in liver. Methods: We utilize a combination of molecular, genetic and intravital microscopic approaches to gain insight into the dynamics of foci and leukocyte behavior during hepatic Listeriosis...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29806039/operational-challenges-in-conducting-a-community-based-technology-enabled-mental-health-services-delivery-model-for-rural-india-experiences-from-the-smart-mental-health-project
#13
Pallab K Maulik, Sudha Kallakuri, Siddhardha Devarapalli
Background: There are large gaps in the delivery of mental health care in low- and middle-income countries such as India, and the problems are even more acute in rural settings due to lack of resources, remoteness, and lack of infrastructure, amongst other factors. The Systematic Medical Appraisal Referral and Treatment (SMART) Mental Health Project was conceived as a mental health services delivery model using technology-based solutions for rural India. This paper reports on the operational strategies used to facilitate the implementation of the intervention...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29806038/ethical-considerations-in-controlled-human-malaria-infection-studies-in-low-resource-settings-experiences-and-perceptions-of-study-participants-in-a-malaria-challenge-study-in-kenya
#14
Maureen Njue, Patricia Njuguna, Melissa C Kapulu, Gladys Sanga, Philip Bejon, Vicki Marsh, Sassy Molyneux, Dorcas Kamuya
Background: The range and amount of volunteer infection studies, known as Controlled Human Infection Model (CHMI) studies, in Low-Middle Income Countries (LMICs) is increasing with rapid technological advancement, world-class laboratory facilities and increasing capacity development initiatives. However, the ethical issues these studies present in LMICs have not been empirically studied. We present findings of a descriptive social science study nested within a malaria volunteer infection study, on-going at the time of writing, at the KEMRI-Wellcome Trust Research Programme (KWTRP) on the Kenyan Coast...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29806037/age-23-years-oral-health-questionnaire-in-avon-longitudinal-study-of-parents-and-children
#15
Tom Dudding, Simon Haworth, Jonathan Sandy, Nicholas J Timpson
Oral health data in large longitudinal cohort studies is rarely collected at multiple time-points. This type of data is important for assessing oral health trajectories and their determinants. This data resource includes self-report questionnaire data on up to 4,222 young adults at approximately 23 years of age from the Avon Longitudinal Study of Parents and Children (ALSPAC). The resource includes questions on dental attendance, tooth restorations and extractions, third molars (wisdom teeth) and mouth ulcers...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29780892/understanding-barriers-to-the-introduction-of-precision-medicines-in-non-small-cell-lung-cancer-a-qualitative-interview-protocol
#16
Stuart Wright, Gavin Daker-White, William Newman, Katherine Payne
Background: While precision medicines targeting genetic mutations and alterations in non-small cell lung cancer (NSCLC) have been available since 2010, their adoption into clinical practice has been slow. Evidence suggests that a number of barriers, such as insufficient clinician knowledge, a need for training of test providers, or a lack of specific clinical guidelines, may slow the implementation of precision in general. However, little attention has been given to the barriers to providing precision medicines in NSCLC...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#17
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29774244/classification-and-characterisation-of-brain-network-changes-in-chronic-back-pain-a-multicenter-study
#18
Hiroaki Mano, Gopal Kotecha, Kenji Leibnitz, Takashi Matsubara, Aya Nakae, Nicholas Shenker, Masahiko Shibata, Valerie Voon, Wako Yoshida, Michael Lee, Toshio Yanagida, Mitsuo Kawato, Maria Joao Rosa, Ben Seymour
Background. Chronic pain is a common, often disabling condition thought to involve a combination of peripheral and central neurobiological factors. However, the extent and nature of changes in the brain is poorly understood. Methods. We investigated brain network architecture using resting-state fMRI data in chronic back pain patients in the UK and Japan (41 patients, 56 controls), as well as open data from USA. We applied machine learning and deep learning (conditional variational autoencoder architecture) methods to explore classification of patients/controls based on network connectivity...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29744390/stage-1-registered-report-variation-in-neurodevelopmental-outcomes-in-children-with-sex-chromosome-trisomies-protocol-for-a-test-of-the-double-hit-hypothesis
#19
Dianne F Newbury, Nuala H Simpson, Paul A Thompson, Dorothy V M Bishop
Background : The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. Group averages, however, obscure a wide range of outcomes. Hypothesis: The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. Neuroligin-4 genes are expressed from X and Y chromosomes; they play an important role in synaptic development and have been implicated in neurodevelopment...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29721551/investigating-the-role-of-rts1-in-dna-replication-initiation
#20
Ana B A Wallis, Conrad A Nieduszynski
Background: Understanding DNA replication initiation is essential to understand the mis-regulation of replication seen in cancer and other human disorders. DNA replication initiates from DNA replication origins. In eukaryotes, replication is dependent on cell cycle kinases which function during S phase. Dbf4-dependent kinase (DDK) and cyclin-dependent kinase (CDK) act to phosphorylate the DNA helicase (composed of mini chromosome maintenance proteins: Mcm2-7) and firing factors to activate replication origins...
2018: Wellcome Open Research
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