Publications
305 results found
Loeser S, Zhang Y, Gregory L, et al., 2014, Novel insights into the <i>in vivo</i> function of <i>Ormdl3</i> - a gene associated with the onset of childhood asthma, IMMUNOLOGY, Vol: 143, Pages: 59-59, ISSN: 0019-2805
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- Citations: 3
Zhang Y, Dean C, Chessum L, et al., 2014, Functional analysis of a novel ENU-induced PHD finger 11 (<i>Phf11)</i> mouse mutant, MAMMALIAN GENOME, Vol: 25, Pages: 573-582, ISSN: 0938-8990
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- Citations: 2
Salter SJ, Cox MJ, Turek EM, et al., 2014, Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biology, Vol: 12, ISSN: 1741-7007
BackgroundThe study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.ResultsIn this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination.ConclusionsThese results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.
Molyneaux PL, Cox MJ, Willis-Owen SAG, et al., 2014, The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis, American Journal of Respiratory and Critical Care Medicine, Vol: 190, Pages: 906-913, ISSN: 1535-4970
Rationale:Idiopathic pulmonaryfibrosis (IPF)isa progressivelung diseaseof unknown cause that leads to respiratory failure and death within 5 yearsof diagnosis. Overt respiratory infection and immunosuppression carrya high morbidity and mortality, and polymorphisms in genes related toepithelial integrity and host defense predispose to IPF.Objectives: To investigate the role of bacteria in the pathogenesisand progression of IPF.Methods: We prospectively enrolled patients diagnosed with IPFaccording to international criteria together with healthy smokers,nonsmokers, and subjectswithmoderate chronic obstructive pulmonarydisease as control subjects. Subjects underwent bronchoalveolarlavage (BAL), from which genomic DNA was isolated. The V3–V5region of the bacterial 16S rRNA gene was amplified, allowingquantification of bacterial load and identification of communities by 16SrRNA quantitative polymerase chain reaction and pyrosequencing. Measurements and Main Results: Sixty-five patients with IPFhad double the burden of bacteria in BAL fluid compared with 44 controlsubjects. Baseline bacterial burden predicted the rate of decline in lungvolume and risk of death and associated independently with thers35705950 polymorphism of the MUC5B mucin gene, a proven hostsusceptibilityfactorfor IPF. Sequencing yielded912,883 high-quality readsfrom all subjects.WeidentifiedHaemophilus, Streptococcus,Neisseria, andVeillonella spp. to be more abundant in cases than control subjects.Regression analyses indicated that these specific operational taxonomicunits as well as bacterial burden associated independently with IPF.Conclusions: IPF is characterized by an increased bacterial burdenin BAL that predicts decline in lung function and death. Trials ofantimicrobial therapy are needed to determine if microbial burdenis pathogenic in the disease.
Dizier M-H, Margaritte-Jeannin P, Madore A-M, et al., 2014, The nuclear factor I/A (<i>NFIA</i>) gene is associated with the asthma plus rhinitis phenotype, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 134, Pages: 576-+, ISSN: 0091-6749
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- Citations: 14
Salter, Susannah Cox, Michael J Turek, et al., 2014, Reagent contamination can critically impact sequence-based microbiome analyses, bioRxiv
Susannah Salter1,7 (sb18{at}sanger.ac.uk), Michael J Cox2 (michael.cox1{at}imperial.ac.uk), Elena M Turek2 (elena.turek11{at}imperial.ac.uk), Szymon T Calus3 (s.t.calus{at}bham.ac.uk), William O Cookson2 (w.cookson{at}imperial.ac.uk), Miriam F Moffatt2 (m.moffatt{at}imperial.ac.uk), Paul Turner4 (pault{at}tropmedres.ac), Julian Parkhill5 (parkhill{at}sanger.ac.uk), Nick Loman3 (n.j.loman{at}bham.ac.uk) and Alan W Walker6 (alan.walker{at}abdn.ac.uk) 1 Wellcome Trust Sanger Institute; 2 Molecular Genetics and Genomics, National Heart and Lung Institute, Imperial College London; 3 Institute of Microbiology and Infection, University of Birmingham; 4 Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford; 5 Pathogen Genomics, Wellcome Trust Sanger Institute; 6 Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen ↵* Corresponding author; email: sb18{at}sanger.ac.uk AbstractThe study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples i
van der Valk RJP, Duijts L, Timpson NJ, et al., 2014, Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 134, Pages: 46-55, ISSN: 0091-6749
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- Citations: 30
Ma B, Wilker EH, Willis-Owen SAG, et al., 2014, Predicting DNA methylation level across human tissues, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 3515-3528, ISSN: 0305-1048
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- Citations: 72
Scholtens S, Postma DS, Moffatt MF, et al., 2014, Novel childhood asthma genes interact with <i>in utero</i> and early-life tobacco smoke exposure, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 133, Pages: 885-888, ISSN: 0091-6749
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- Citations: 36
Weidinger S, Willis-Owen SA, Kamatani Y, et al., 2014, A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis, 41st Annual Meeting of the Arbeitsgemeinschaft-Dermatologische-Forschung (ADF), Publisher: WILEY, Pages: E21-E21, ISSN: 0906-6705
Portelli MA, Siedlinski M, Stewart CE, et al., 2014, Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels, FASEB JOURNAL, Vol: 28, Pages: 923-934, ISSN: 0892-6638
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- Citations: 31
Peljto A, Selman M, Kim DS, et al., 2014, Genetic Variants Associated With Pulmonary Fibrosis In Asian And Hispanic Populations, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
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- Citations: 1
Weidinger S, Willis-Owen SAG, Kamatani Y, et al., 2013, A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis, Human Molecular Genetics, Vol: 22, Pages: 4841-4856, ISSN: 0964-6906
Atopic dermatitis (AD) is the most common dermatological disease of childhood. Many children with AD have asthma and AD shares regions of genetic linkage with psoriasis, another chronic inflammatory skin disease. We present here a genome-wide association study (GWAS) of childhood-onset AD in 1563 European cases with known asthma status and 4054 European controls. Using Illumina genotyping followed by imputation, we generated 268 034 consensus genotypes and in excess of 2 million single nucleotide polymorphisms (SNPs) for analysis. Association signals were assessed for replication in a second panel of 2286 European cases and 3160 European controls. Four loci achieved genome-wide significance for AD and replicated consistently across all cohorts. These included the epidermal differentiation complex (EDC) on chromosome 1, the genomic region proximal to LRRC32 on chromosome 11, the RAD50/IL13 locus on chromosome 5 and the major histocompatibility complex (MHC) on chromosome 6; reflecting action of classical HLA alleles. We observed variation in the contribution towards co-morbid asthma for these regions of association. We further explored the genetic relationship between AD, asthma and psoriasis by examining previously identified susceptibility SNPs for these diseases. We found considerable overlap between AD and psoriasis together with variable coincidence between allergic rhinitis (AR) and asthma. Our results indicate that the pathogenesis of AD incorporates immune and epidermal barrier defects with combinations of specific and overlapping effects at individual loci.
Molyneaux PL, Cox MJ, Mallia P, et al., 2013, THE ROLE OF THE RESPIRATORY MICROBIOME IN IDIOPATHIC PULMONARY FIBROSIS, Winter Meeting of the British-Thoracic-Society, Publisher: BMJ PUBLISHING GROUP, Pages: A22-A22, ISSN: 0040-6376
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- Citations: 2
Molyneaux PL, Mallia P, Cox MJ, et al., 2013, Outgrowth of the Bacterial Airway Microbiome after Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease, AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, Vol: 188, Pages: 1224-1231, ISSN: 1073-449X
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- Citations: 262
Fingerlin TE, Murphy E, Zhang W, et al., 2013, Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis., Nat Genet, Vol: 45
Fingerlin TE, Murphy E, Zhang W, et al., 2013, Corrigendum: Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis (vol 45, pg 613, 2013), NATURE GENETICS, Vol: 45, Pages: 1409-1409, ISSN: 1061-4036
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- Citations: 2
Cox MJ, Cookson WOCM, Moffatt MF, 2013, Sequencing the human microbiome in health and disease, HUMAN MOLECULAR GENETICS, Vol: 22, Pages: R88-R94, ISSN: 0964-6906
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- Citations: 89
Cardenas P, Cooper P, Moffatt M, et al., 2013, The development of the upper respiratory microbiome on infancy and the dysbiosis related with wheezing syndrome and health on children from the rural tropics of Ecuador, EUROPEAN RESPIRATORY JOURNAL, Vol: 42, ISSN: 0903-1936
Esparza-Gordillo J, Schaarschmidt H, Liang L, et al., 2013, A functional IL-6 receptor (<i>IL6R</i>) variant is a risk factor for persistent atopic dermatitis, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 132, Pages: 371-377, ISSN: 0091-6749
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- Citations: 66
Binia A, Van Stiphout N, Liang L, et al., 2013, A Polymorphism Affecting MYB Binding within the Promoter of the <i>PDCD4</i> Gene is Associated with Severe Asthma in Children, HUMAN MUTATION, Vol: 34, Pages: 1131-1139, ISSN: 1059-7794
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- Citations: 14
Cookson WOC, Moffatt MF, 2013, Bedside to Gene and Back in Idiopathic Pulmonary Fibrosis, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 368, Pages: 2228-2230, ISSN: 0028-4793
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- Citations: 6
Fingerlin TE, Murphy E, Zhang W, et al., 2013, Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis, Nature Genetics, Vol: 45, Pages: 613-624, ISSN: 1061-4036
We performed a genome-wide association study of non-Hispanic, white individuals with fibrotic idiopathic interstitial pneumonias (IIPs; n = 1,616) and controls (n = 4,683), with follow-up replication analyses in 876 cases and 1,890 controls. We confirmed association with TERT at 5p15, MUC5B at 11p15 and the 3q26 region near TERC, and we identified seven newly associated loci (Pmeta = 2.4 × 10−8 to 1.1 × 10−19), including FAM13A (4q22), DSP (6p24), OBFC1 (10q24), ATP11A (13q34), DPP9 (19p13) and chromosomal regions 7q22 and 15q14-15. Our results suggest that genes involved in host defense, cell-cell adhesion and DNA repair contribute to risk of fibrotic IIPs.
Berndt SI, Gustafsson S, Maegi R, et al., 2013, Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture, NATURE GENETICS, Vol: 45, Pages: 501-U69, ISSN: 1061-4036
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- Citations: 443
Duff RM, Simmonds NJ, Davies JC, et al., 2013, A molecular comparison of microbial communities in bronchiectasis and cystic fibrosis, EUROPEAN RESPIRATORY JOURNAL, Vol: 41, Pages: 991-993, ISSN: 0903-1936
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- Citations: 10
Melen E, Granell R, Kogevinas M, et al., 2013, Genome-wide association study of body mass index in 23000 individuals with and without asthma, CLINICAL AND EXPERIMENTAL ALLERGY, Vol: 43, Pages: 463-474, ISSN: 0954-7894
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- Citations: 61
Liang L, Morar N, Dixon AL, et al., 2013, A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines, GENOME RESEARCH, Vol: 23, Pages: 716-726, ISSN: 1088-9051
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- Citations: 111
Miller S, Obeidat M, Portelli MA, et al., 2013, Snp Rs2070600 Is Associated With Lung Function And The Level Of Serum Soluble Rage In Uk Smokers, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
Fingerlin TE, Murphy E, Zhang W, et al., 2013, Novel Genetic Risk Loci For Pulmonary Fibrosis, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
van der Harst P, Zhang W, Leach IM, et al., 2012, Seventy-five genetic loci influencing the human red blood cell, NATURE, Vol: 492, Pages: 369-+, ISSN: 0028-0836
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- Citations: 242
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