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).

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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.

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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.

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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.

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Annotation of plasmid genes.

Plasmid

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.

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Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction.

Cell 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.

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An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes.

PLoS 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.

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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.

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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.

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

Proc 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

Article Synopsis
  • * A comprehensive genomic analysis of over 300 K. pneumoniae isolates has led to the identification of three distinct species and revealed over 150 lineages within K. pneumoniae (KpI) that are linked to human infections.
  • * The study highlights a large accessory genome with numerous virulence genes associated with invasive disease, raising concerns about the potential emergence of untreatable K. pneumoniae infections due to the integration of resistance and virulence traits.
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Natural selection and infectious disease in human populations.

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.

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A transcriptional switch underlies commitment to sexual development in malaria parasites.

Nature

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.

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Ensembl Genomes 2013: scaling up access to genome-wide data.

Nucleic 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.

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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.

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Royal Society discussion meeting: utilising the genome sequence of parasitic protozoa.

Comp 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.

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A re-annotation of the Saccharomyces cerevisiae genome.

Comp 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.

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RNA-mediated interference as a tool for identifying drug targets.

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.

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MaxBench: evaluation of sequence and structure comparison methods.

Bioinformatics

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.

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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.

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Genome acrobatics: understanding complex genomes.

Drug 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

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The human major histocompatability complex: lessons from the DNA sequence.

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.

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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.

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Parasites are GO.

Trends Parasitol

October 2001

The Sanger Centre, Wellcome Trust, Genome Campus, Hinxton, Cambridge, UK.

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