156 results match your criteria: "Sanger Centre[Affiliation]"
IKZF1 deletions (ΔIKZF1) are commonly detected in B-precursor acute lymphoblastic leukemia (ALL; B-ALL) and are widely assumed to have a significant impact on outcome. We compared the ability of multiplex ligand-dependent probe amplification (MLPA) and polymerase chain reaction (PCR) to detect ΔIKZF1 and to determine the impact on event-free survival of patients with precursor B-ALL aged 23 to 65 years recruited to the completed trial UKALL14 (ISRCTN 66541317). From 655 recruits with BCR-ABL1+ and BCR-ABL1- B-ALL, all available diagnostic DNA samples (76% of the recruited population) were screened by multiplex end point PCR covering 4 deletions: dominant-negative (DN) Δ4-7 or the loss of function Δ2-7, Δ4-8, and Δ2-8 (n = 498), MLPA (n = 436), or by both (n = 420).
View Article and Find Full Text PDFSci Transl Med
June 2018
Section of Paediatrics, Imperial College, London W2 1PG, UK.
The pathogenesis of infectious diseases depends on the interaction of host and pathogen. In malaria, host and parasite processes can be assessed by dual RNA sequencing of blood from infected patients. We performed dual transcriptome analyses on samples from 46 malaria-infected Gambian children to reveal mechanisms driving the systemic pathophysiology of severe malaria.
View Article and Find Full Text PDFCleft Palate Craniofac J
March 2018
1 University of Manchester, Faculty of Biology, Medicine and Health, Manchester, United Kingdom.
Objective: Point mutations and deletions within the SOX11 gene have recently been described in individuals with a rare variant of Coffin-Siris syndrome, OMIM 615866, an intellectual disability syndrome with associated features of nail hypoplasia, microcephaly, and characteristic facial features including a wide mouth and prominent lips.
Participant: We describe a further patient with a mutation in SOX11 and phenotype resembling mild Coffin-Siris syndrome.
Results: This boy had a cleft palate, a feature not previously seen in other patients with SOX11 mutations.
Clin Infect Dis
March 2018
Wellcome Trust Sanger Centre, Cambridge, United Kingdom.
Background: Yaws-like chronic ulcers can be caused by Treponema pallidum subspecies pertenue, Haemophilus ducreyi, or other, still-undefined bacteria. To permit accurate evaluation of yaws elimination efforts, programmatic use of molecular diagnostics is required. The accuracy and sensitivity of current tools remain unclear because our understanding of T.
View Article and Find Full Text PDFPlasmid
May 2017
Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
Good annotation of plasmid genomes is essential to maximise the value of the rapidly increasing volume of plasmid sequences. This short review highlights some of the current issues and suggests some ways forward. Where a well-studied related plasmid system exists we recommend that new annotation adheres to the convention already established for that system, so long as it is based on sound principles and solid experimental evidence, even if some of the new genes are more similar to homologues in different systems.
View Article and Find Full Text PDFCell Host Microbe
October 2016
Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK. Electronic address:
Interferon-induced transmembrane proteins (IFITMs) restrict the entry of diverse enveloped viruses through incompletely understood mechanisms. While IFITMs are reported to inhibit HIV-1, their in vivo relevance is unclear. We show that IFITM sensitivity of HIV-1 strains is determined by the co-receptor usage of the viral envelope glycoproteins as well as IFITM subcellular localization within the target cell.
View Article and Find Full Text PDFPLoS Genet
April 2016
Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
Metastasis remains the primary cause of patient morbidity and mortality in solid tumors and is due to the action of a large number of tumor-autonomous and non-autonomous factors. Here we report the results of a genome-wide integrated strategy to identify novel metastasis susceptibility candidate genes and molecular pathways in breast cancer metastasis. This analysis implicates a number of transcriptional regulators and suggests cell-mediated immunity is an important determinant.
View Article and Find Full Text PDFNat Commun
September 2015
School of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork T12 Y337, Ireland.
Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria.
View Article and Find Full Text PDFElife
August 2015
Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom.
Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
July 2015
Pathogen Genomics, Wellcome Trust Sanger Centre, CB10 1SA Cambridge, United Kingdom; Department of Pathogen Molecular Biology, The London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdom
Nat Rev Genet
June 2014
1] Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA. [3] Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders.
View Article and Find Full Text PDFNature
March 2014
1] Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA [2] Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA [3] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA (B.F.C.K.); Department of Molecular Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, State College, Pennsylvania 16802, USA (V.M.C., M.L.).
The life cycles of many parasites involve transitions between disparate host species, requiring these parasites to go through multiple developmental stages adapted to each of these specialized niches. Transmission of malaria parasites (Plasmodium spp.) from humans to the mosquito vector requires differentiation from asexual stages replicating within red blood cells into non-dividing male and female gametocytes.
View Article and Find Full Text PDFNucleic Acids Res
January 2014
The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA and USDA-ARS, Cornell University, Ithaca, NY, 14853, USA.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species.
View Article and Find Full Text PDFNat Rev Cancer
January 2010
The Wellcome Trust Sanger Centre, Wellcome Trust Genome Campus Hinxton, Cambridge, UK.
Integrated genome-wide screens of DNA copy number and gene expression in human cancers have accelerated the rate of discovery of amplified and overexpressed genes. However, the biological importance of most of the genes identified in such studies remains unclear. In this Analysis, we propose a weight-of-evidence based classification system for identifying individual genes in amplified regions that are selected for during tumour development.
View Article and Find Full Text PDFComp Funct Genomics
June 2010
The Sanger Centre, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Protozoan parasites cause some of the world's most important diseases. Genome sequencing information is rapidly being acquired and combined with new developments in functional genome analysis to transform our understanding of parasites, and to enable new approaches to combating the diseases they cause.
View Article and Find Full Text PDFComp Funct Genomics
June 2010
The Sanger Centre, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK.
Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described.
View Article and Find Full Text PDFBiosci Rep
May 2004
The Sanger Centre, Cambridge, United Kingdom.
Methods Mol Biol
July 2003
Sanger Centre, Hinxton, United Kingdom.
Am J Pharmacogenomics
September 2002
Sanger Centre, Wellcome Trust Genome Campus, Hinxton, England.
The nematode Caenorhabditis elegans is the first multicellular organism with a fully sequenced genome. As a model organism, C. elegans is playing a special role in functional genomic analyses because it is experimentally tractable on many levels.
View Article and Find Full Text PDFBioinformatics
March 2002
Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
Summary: MaxBench is a web-based system available for evaluating the results of sequence and structure comparison methods, based on the SCOP protein domain classification. The system makes it easy for developers to both compare the overall performance of their methods to standard algorithms and investigate the results of individual comparisons.
Availability: http://www.
DNA Seq
December 2001
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
Obtaining the complete DNA sequence of a genome is often not straightforward. After standard shotgun sequencing strategies have been employed there are often gaps remaining and these can be the most intractable regions, frequently containing repeat sequences, "uncloneable" sequences and/or regions of potential secondary structure or differential base composition. In genomes with a high A/T content, such as Plasmodium falciparum and Dictyostelium discoideum, solving these gaps is a particularly difficult problem as the sequences concerned are "fragile" and easily denatured, commonly uncloneable and have a paucity of good oligonucleotide priming sites.
View Article and Find Full Text PDFDrug Discov Today
December 2001
Head of Human Sequencing, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, tel: +44 1223 494952; fax: +44 1223 494919, Cambridge, UK
Annu Rev Genomics Hum Genet
February 2002
The Sanger Centre, Wellcome Trust Genome Campus, University of Cambridge, Cambridge CB10 1SA United Kindgom.
The entire 3.6-MbpDNA sequence of a human major histocompatibility complex derived from a composite of DNA clones from different haplotypes, was completed in 1999, primarily through the work of four main groups. At that time, it was the longest contiguous human DNA sequence to have been determined.
View Article and Find Full Text PDFNature
October 2001
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S.
View Article and Find Full Text PDFTrends Parasitol
October 2001
The Sanger Centre, Wellcome Trust, Genome Campus, Hinxton, Cambridge, UK.