Publications
305 results found
Cardenas PA, Cooper PJ, Cox MJ, et al., 2012, Upper Airways Microbiota in Antibiotic-Naive Wheezing and Healthy Infants from the Tropics of Rural Ecuador, PLOS ONE, Vol: 7, ISSN: 1932-6203
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- Citations: 73
Jiang W, Johnson C, Jayaraman J, et al., 2012, Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors, Genome Res
Wan YI, Shrine NRG, Artigas MS, et al., 2012, Genome-wide association study to identify genetic determinants of severe asthma, THORAX, Vol: 67, Pages: 762-768, ISSN: 0040-6376
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- Citations: 130
Dizier M-H, Margaritte-Jeannin P, Madore A-M, et al., 2012, The <i>ANO3</i>/<i>MUC15</i> locus is associated with eczema in families ascertained through asthma, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 129, Pages: 1547-+, ISSN: 0091-6749
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- Citations: 16
Imboden M, Bouzigon E, Curjuric I, et al., 2012, Genome-wide association study of lung function decline in adults with and without asthma, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 129, Pages: 1218-1228, ISSN: 0091-6749
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- Citations: 82
Zhang M, Liang L, Morar N, et al., 2012, Integrating pathway analysis and genetics of gene expression for genome-wide association study of basal cell carcinoma, HUMAN GENETICS, Vol: 131, Pages: 615-623, ISSN: 0340-6717
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- Citations: 24
Sim K, Cox MJ, Wopereis H, et al., 2012, Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing, PLoS One, Vol: 7, Pages: e32543-e32543
The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, 'bifidobacteria-optimised' universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence in situ hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria.
Freidin MB, Bhudia N, Lim E, et al., 2012, Impact of Collection and Storage of Lung Tumor Tissue on Whole Genome Expression Profiling, JOURNAL OF MOLECULAR DIAGNOSTICS, Vol: 14, Pages: 140-148, ISSN: 1525-1578
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- Citations: 35
Sarnowski C, Malerba G, Laprise C, et al., 2012, Taking Into Account Imprinting And Maternal Genotype Effects Facilitates Detection Of New Genes, 20th Annual Meeting of the International-Genetic-Epidemiology-Society (IGES), Publisher: WILEY-BLACKWELL, Pages: 122-123, ISSN: 0741-0395
Zhang Y, Moffatt MF, Cookson WOC, 2012, Genetic and genomic approaches to asthma: new insights for the origins, Current Opinion in Pulmonary Medicine, Vol: 18, Pages: 6-13, ISSN: 1070-5287
Purpose of review: The aim is to update current understanding of the genes identified by the recent genome-wide association studies (GWASs) of asthma and its associated traits. The review also discusses how to dissect the functional roles of novel genes in future research.Recent findings: More than 10 GWAS aimed at identifying the genes underlying asthma and relevant traits have been published in the past 3 years. The largest of these was from the GABRIEL consortium, which discovered that the IL18R1, IL33, SMAD3, ORMDL3, HLA-DQ and IL2RB loci were all significantly associated with asthma. Many novel asthma genes, including those previously identified by positional cloning, are expressed within the respiratory epithelium, emphasizing the importance of epithelial barriers in causing asthma . The genes controlling IgE levels have surprisingly little overlap with the genes mediating asthma susceptibility, suggesting that atopy is secondary to asthma rather than a primary driver of the disease. The next challenge will be the systematic analysis of the precise functions of these genes in the pathogenesis of asthma.Summary: GWAS have uncovered many novel genes underlying asthma and detailed functional dissection of their roles in asthma will point the way to new therapies for the disease.
Freidin M, Nicholson A, Popat S, et al., 2012, Distribution profile of baseline gene expression to standardise tumour expression: a pilot study of cisplatin resistant genes in lung cancer, Publisher: ELSEVIER IRELAND LTD, Pages: S2-S3, ISSN: 0169-5002
Tulah AS, Parker SG, Moffatt MF, et al., 2011, The role of <i>ALOX5AP</i>, <i>LTA4H</i> and <i>LTB4R</i> polymorphisms in determining baseline lung function and COPD susceptibility in UK smokers, BMC MEDICAL GENETICS, Vol: 12
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- Citations: 11
Cox MJ, Jones AL, Loebinger MR, et al., 2011, MUCOIDY AND THE MICROBIOME: COMMUNITY COMPOSITION IN RELATION TO THE PRESENCE OF CULTURABLE, MUCOID <i>PSEUDOMONAS AERUGINOSA</i>, Winter Meeting of the British-Thoracic-Society, Publisher: B M J PUBLISHING GROUP, Pages: A24-A24, ISSN: 0040-6376
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- Citations: 2
Zhang Q, Liang Z, Gibeon D, et al., 2011, PRESENCE OF BACTERIA FROM ASTHMATIC AIRWAYS: RELATIONSHIP TO SEVERITY, RESPIROLOGY, Vol: 16, Pages: 220-221, ISSN: 1323-7799
Chambers JC, Zhang W, Sehmi J, et al., 2011, Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma, NATURE GENETICS, Vol: 43, Pages: 1131-1138, ISSN: 1061-4036
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- Citations: 409
Heid IM, Jackson AU, Randall JC, et al., 2011, Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution, NATURE GENETICS, Vol: 43, Pages: 1164-1164, ISSN: 1061-4036
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- Citations: 9
Cookson W, Moffatt M, Strachan DP, 2011, Genetic risks and childhood-onset asthma, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 128, Pages: 266-272, ISSN: 0091-6749
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- Citations: 27
Freidin MB, Bhudia N, Lim E, et al., 2011, SAMPLE HANDLING AND PROCESSING ARE CRITICAL FACTORS INFLUENCING THE RESULTS OF WHOLE GENOME GENE EXPRESSION PROFILING IN LUNG CANCER TISSUES, Publisher: LIPPINCOTT WILLIAMS & WILKINS, Pages: S373-S374, ISSN: 1556-0864
Freidin MB, Nicholson AG, Lim E, et al., 2011, GLOBAL GENE EXPRESSION PROFILING TO IDENTIFY COMMON NETWORKS UNDERLYING LUNG CANCER AND SPECIFIC MARKERS OF DIFFERENT LUNG CANCER HISTOLOGICAL TYPES, Publisher: LIPPINCOTT WILLIAMS & WILKINS, Pages: S455-S455, ISSN: 1556-0864
Cookson WOC, Moffatt MF, 2011, Genetics of complex airway disease., Proc Am Thorac Soc, Vol: 8, Pages: 149-153
The past 3 years have seen highly significant genetic effects identified for a wide variety of common complex diseases, including the airway disorders of asthma and chronic obstructive pulmonary disease. It appears that only a portion of the genetically mediated susceptibility to complex diseases has been identified, and there is much left to be discovered. This review briefly describes the results of the genome-wide association studies of asthma and gives an overview of the parallel and increasingly large-scale studies that are taking place with chronic obstructive pulmonary disease. The future impact is discussed of technological advances that allow increasingly large-scale gene expression studies, next-generation sequencing, and genome-wide testing for epigenetic effects. The use of genetic technology to examine the airway microbiota that interact with the mucosa in health and disease is described.
Zhang M, Liang L, Morar N, et al., 2011, Integrating pathway analysis and genetics of gene expression for genome-wide association study on basal cell carcinoma, CANCER RESEARCH, Vol: 71, ISSN: 0008-5472
Holt RJ, Zhang Y, Binia A, et al., 2011, Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)., Journal of Allergy and Clinical Immunology, Vol: 127, Pages: 1054-1062.e2, ISSN: 0091-6749
Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.ObjectiveHere we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels—rs3765526, rs9526569, and rs1046295—for a role in transcription factor binding.MethodsWe used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.ResultsElectrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10−16), preferential expression of the A allele consistent with a functional role for rs1046295.ConclusionThese results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.
Ege MJ, Strachan DP, Cookson WOCM, et al., 2011, Gene-environment interaction for childhood asthma and exposure to farming in Central Europe, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 127, Pages: 138-U226, ISSN: 0091-6749
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- Citations: 113
Thompson AR, Natanek SA, Willis-Owen SA, et al., 2011, Gene Expression Profiling Of Quadriceps Femoris Muscle In COPD, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
Wan YI, Soler-Artigas M, Shrine NRG, et al., 2011, Genome-Wide Association Study To Identify Genetic Determinants Of Severe Asthma (AUGOSA), Publisher: AMER THORACIC SOC, ISSN: 1073-449X
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- Citations: 1
Molyneaux PL, Mallia P, Duff RM, et al., 2011, Investigating The Role Of Rhinovirus Infection In Precipitating Bacterial Infections In COPD Using Culture Independent Molecular Microbiology, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
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- Citations: 1
Cox MJ, Duff RM, Simmonds NJ, et al., 2011, Comparison Of The Microbiomes Of Two Chronic Airway Diseases Using High-Throughput Sequencing, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
Wan YI, Shrine NRG, Soler-Artigas M, et al., 2011, Comprehensive Evaluation Of Mild-To-Moderate Asthma Genes In Severe Asthma (AUGOSA), Publisher: AMER THORACIC SOC, ISSN: 1073-449X
Heid IM, Jackson AU, Randall JC, et al., 2010, Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution, NATURE GENETICS, Vol: 42, Pages: 949-U160, ISSN: 1061-4036
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- Citations: 690
Altshuler D, Durbin RM, Abecasis GR, et al., 2010, A map of human genome variation from population-scale sequencing, NATURE, Vol: 467, Pages: 1061-1073, ISSN: 0028-0836
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- Citations: 4415
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