Scott J Tebbutt

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. ncbi request reprint Genotyping of single nucleotide polymorphisms by arrayed primer extension
    Scott J Tebbutt
    James Hogg iCAPTURE Center for Cardiovascular and Pulmonary Research, University of British Columbia, Vancouver, Canada
    Methods Mol Biol 382:149-61. 2007
  2. ncbi request reprint Combining multiple PCR primer pairs for each amplicon can improve SNP genotyping accuracy by reducing allelic drop-out
    Scott J Tebbutt
    The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, University of British Columbia, St Paul s Hospital, Vancouver, BC, Canada
    Biotechniques 45:637-8, 640, 642 passim. 2008
  3. ncbi request reprint SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia Vancouver, Canada
    Bioinformatics 21:124-7. 2005
  4. ncbi request reprint Microarray genotyping resource to determine population stratification in genetic association studies of complex disease
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, Vancouver, BC, Canada
    Biotechniques 37:977-85. 2004
  5. ncbi request reprint Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, Vancouver, Canada
    Biotechniques 40:331-8. 2006
  6. ncbi request reprint Single-nucleotide polymorphisms and lung disease: clinical implications
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, 1081 Burrard St, Vancouver, BC, Canada
    Chest 131:1216-23. 2007
  7. pmc Gene-metabolite expression in blood can discriminate allergen-induced isolated early from dual asthmatic responses
    Amrit Singh
    James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e67907. 2013
  8. doi request reprint Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge
    Amrit Singh
    James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Vancouver, Canada
    Proteomics Clin Appl 6:476-85. 2012
  9. pmc Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles
    Casey P Shannon
    PROOF Centre of Excellence, Vancouver, BC, Canada
    BMC Genomics 18:43. 2017
  10. pmc SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
    Casey P Shannon
    PROOF Centre of Excellence, Vancouver, BC, Canada
    BMC Bioinformatics 17:460. 2016

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Genotyping of single nucleotide polymorphisms by arrayed primer extension
    Scott J Tebbutt
    James Hogg iCAPTURE Center for Cardiovascular and Pulmonary Research, University of British Columbia, Vancouver, Canada
    Methods Mol Biol 382:149-61. 2007
    ..Utilization of all four dideoxynucleotides, each conjugated to a different fluorophore, allows genotyping by spectral differentiation of the single base extension reaction products...
  2. ncbi request reprint Combining multiple PCR primer pairs for each amplicon can improve SNP genotyping accuracy by reducing allelic drop-out
    Scott J Tebbutt
    The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, University of British Columbia, St Paul s Hospital, Vancouver, BC, Canada
    Biotechniques 45:637-8, 640, 642 passim. 2008
    ..The method has been tested in multiplex using a microarray-based SNP genotyping chip and results in the rescue of previously reported false genotype calls...
  3. ncbi request reprint SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia Vancouver, Canada
    Bioinformatics 21:124-7. 2005
    ..This allows a quick and very effective 'visualization'/'quality control' of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype...
  4. ncbi request reprint Microarray genotyping resource to determine population stratification in genetic association studies of complex disease
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, Vancouver, BC, Canada
    Biotechniques 37:977-85. 2004
    ..Based on 1141 known genotypes from other research groups, our GC SNP chip has an accuracy of 98.5%, including non-calls...
  5. ncbi request reprint Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, Vancouver, Canada
    Biotechniques 40:331-8. 2006
    ....
  6. ncbi request reprint Single-nucleotide polymorphisms and lung disease: clinical implications
    Scott J Tebbutt
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, 1081 Burrard St, Vancouver, BC, Canada
    Chest 131:1216-23. 2007
    ..We conclude with a brief discussion of the future of medicine and how genetic knowledge and application can play an ever-increasing and important role in more effective diagnosis and treatment at a more personalized level...
  7. pmc Gene-metabolite expression in blood can discriminate allergen-induced isolated early from dual asthmatic responses
    Amrit Singh
    James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e67907. 2013
    ..Future studies with larger sample sizes may reveal novel mechanisms and therapeutic targets of the late phase asthmatic response...
  8. doi request reprint Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge
    Amrit Singh
    James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Vancouver, Canada
    Proteomics Clin Appl 6:476-85. 2012
    ..This proteomics study was designed to determine the utility of iTRAQ MALDI-TOF/TOF technology to compare plasma samples from carefully phenotyped mild, atopic asthma subjects undergoing allergen inhalation challenge...
  9. pmc Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles
    Casey P Shannon
    PROOF Centre of Excellence, Vancouver, BC, Canada
    BMC Genomics 18:43. 2017
    ..These profiles are platform-specific, suitable datasets are rare, and generating them is expensive. No such dataset exists on the Affymetrix Gene ST platform...
  10. pmc SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
    Casey P Shannon
    PROOF Centre of Excellence, Vancouver, BC, Canada
    BMC Bioinformatics 17:460. 2016
    ....
  11. pmc Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge
    Masatsugu Yamamoto
    UBC James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Room 166, Burrard Building, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
    BMC Genomics 13:655. 2012
    ..We aimed to evaluate changes in the microRNA profiles in the peripheral blood of asthmatic subjects undergoing allergen inhalation challenge...
  12. pmc Dynamic variable selection in SNP genotype autocalling from APEX microarray data
    Mohua Podder
    Department of Statistics, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 7:521. 2006
    ..Using this microarray platform, our current genotype calling system (known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias...
  13. pmc Dual organism transcriptomics of airway epithelial cells interacting with conidia of Aspergillus fumigatus
    Jean L Oosthuizen
    UBC James Hogg Research Centre, Institute for Heart Lung Health, Providence Health Care, Vancouver, British Columbia, Canada
    PLoS ONE 6:e20527. 2011
    ..In the present study, we profiled simultaneously the transcriptional response of both A. fumigatus and human airway epithelial cells (AECs)...
  14. pmc The Effect of Different Case Definitions of Current Smoking on the Discovery of Smoking-Related Blood Gene Expression Signatures in Chronic Obstructive Pulmonary Disease
    Ma en Obeidat
    University of British Columbia Centre for Heart Lung Innovation, St Paul s Hospital, Vancouver, BC, Canada
    Nicotine Tob Res 18:1903-9. 2016
    ..In this study, we determined the impact of different case definitions of current cigarette smoking on gene expression in peripheral blood of patients with COPD...
  15. pmc Novel multivariate methods for integration of genomics and proteomics data: applications in a kidney transplant rejection study
    Oliver P Günther
    1 NCE CECR Prevention of Organ Failure PROOF Centre of Excellence, Vancouver, British Columbia, Canada
    OMICS 18:682-95. 2014
    ..In all, this article offers candidate biomarkers for future detection and monitoring of acute kidney transplant rejection, as well as ways forward for methodological advances to better harness multi-omics data sets...
  16. ncbi request reprint DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs
    Young C Song
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
    Bioinformatics 23:780-2. 2007
    ..AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml...
  17. ncbi request reprint MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data
    David C Walley
    James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul s Hospital, University of British Columbia Vancouver, V6Z 1Y6, Canada
    Bioinformatics 22:1147-9. 2006
    ..Calling accuracy by MACGT exceeds 98% when applied to genotyping data from APEX microarrays, and can be increased to >99.5% by applying thresholds to the confidence measures...
  18. pmc The Effect of Statins on Blood Gene Expression in COPD
    Ma en Obeidat
    The University of British Columbia Centre for Heart Lung Innovation, St Paul s Hospital, Vancouver, BC, Canada
    PLoS ONE 10:e0140022. 2015
    ..Observational studies have shown that statins may have a beneficial role in COPD. The impact of statins on blood gene expression from COPD patients is largely unknown...
  19. pmc Two-stage, in silico deconvolution of the lymphocyte compartment of the peripheral whole blood transcriptome in the context of acute kidney allograft rejection
    Casey P Shannon
    PROOF Centre of Excellence, Vancouver, BC, Canada UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada
    PLoS ONE 9:e95224. 2014
    ..Finally, we demonstrate that the strategy described here can be used to derive useful hypotheses by validating a cell type-specific ratio in an independent cohort using the nanoString nCounter assay. ..
  20. pmc MicroRNA expression in response to controlled exposure to diesel exhaust: attenuation by the antioxidant N-acetylcysteine in a randomized crossover study
    Masatsugu Yamamoto
    Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    Environ Health Perspect 121:670-5. 2013
    ..MicroRNAs (miRNAs) regulate gene expression post-transcriptionally and may respond to exposures such as DE...
  21. pmc A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
    Oliver P Günther
    NCE CECR Prevention of Organ Failure PROOF Centre of Excellence, Vancouver, BC, V6Z 1Y6, Canada
    BMC Bioinformatics 13:326. 2012
    ..of acute renal allograft rejection as a case study, we address the following question in this paper: Can acute rejection classification performance be improved by combining individual genomic and proteomic classifiers in an ensemble?..
  22. doi request reprint Peripheral blood gene expression changes during allergen inhalation challenge in atopic asthmatic individuals
    Sarah H Y Kam
    James Hogg Research Centre, St Paul s Hospital, University of British Columbia, Vancouver, BC, Canada
    J Asthma 49:219-26. 2012
    ....
  23. doi request reprint Controlled diesel exhaust and allergen coexposure modulates microRNA and gene expression in humans: Effects on inflammatory lung markers
    Christopher F Rider
    Chan Yeung Centre for Occupational and Environmental Respiratory Disease COERD, University of British Columbia, Vancouver, British Columbia, Canada Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    J Allergy Clin Immunol 138:1690-1700. 2016
    ..Air pollution's association with asthma may be due to its augmentation of allergenic effects, but the role of microRNA (miRNA) and gene expression in this synergy is unknown...
  24. pmc COPD Exacerbation Biomarkers Validated Using Multiple Reaction Monitoring Mass Spectrometry
    Janice M Leung
    Centre for Heart Lung Innovation, St Paul s Hospital, Vancouver, British Columbia, Canada
    PLoS ONE 11:e0161129. 2016
    ..Acute exacerbations of chronic obstructive pulmonary disease (AECOPD) result in considerable morbidity and mortality. However, there are no objective biomarkers to diagnose AECOPD...
  25. pmc Robust SNP genotyping by multiplex PCR and arrayed primer extension
    Mohua Podder
    The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St, Paul s Hospital, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada
    BMC Med Genomics 1:5. 2008
    ..Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project...
  26. doi request reprint Discovery of novel plasma protein biomarkers to predict imminent cystic fibrosis pulmonary exacerbations using multiple reaction monitoring mass spectrometry
    Bradley S Quon
    Centre for Heart Lung Innovation, University of British Columbia and St Paul s Hospital, Vancouver, British Columbia, Canada Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    Thorax 71:216-22. 2016
    ..Despite the significant morbidity and mortality related to pulmonary exacerbations in cystic fibrosis (CF), there remains no reliable predictor of imminent exacerbation...
  27. doi request reprint Serum proteomics in multiple sclerosis disease progression
    Helen Tremlett
    Faculty of Medicine, Department of Medicine, Division of Neurology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
    J Proteomics 118:2-11. 2015
    ..Validated biomarkers may result in the development of a minimally-invasive tool to monitor MS progression and complement current clinical practices...
  28. doi request reprint Combined polymorphisms in oxidative stress genes predict coronary artery disease and oxidative stress in coronary angiography patients
    Claire L Heslop
    The James Hogg Research Centre, St Paul s Hospital, University of British Columbia and Institute for HEART LUNG Health, Vancouver, BC, Canada
    Ann Hum Genet 76:435-47. 2012
    ..Genetic markers that represent lifetime oxidative stress burden may implicate specific oxidative stress pathways in the pathogenesis of atherosclerosis, and offer therapeutic opportunities...
  29. pmc Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion
    Heesun Shin
    NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada UBC Department of Medicine Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada UBC James Hogg Research Centre and Institute for HEART LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 9:e91041. 2014
    ..In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples...
  30. doi request reprint Proteomic biomarkers of recovered heart function
    Zsuzsanna Hollander
    PROOF Centre of Excellence, Vancouver, Canada
    Eur J Heart Fail 16:551-9. 2014
    ..The purpose of this study was to discover novel blood proteomic biomarker signatures of recovered heart function that could lead to more effective heart failure patient management by both primary care and specialty physicians...
  31. pmc Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus
    Pol Gomez
    UBC James Hogg Research Centre, Providence Heart Lung Institute, St, Paul s Hospital, Vancouver, BC, Canada
    BMC Genomics 11:358. 2010
    ..fumigatus conidia expressing green fluorescent protein from cells without spores. Total RNA was then isolated and the transcriptome of 16HBE14o- cells was evaluated using Agilent Whole Human Genome microarrays...
  32. pmc Interactions of Aspergillus fumigatus Conidia with Airway Epithelial Cells: A Critical Review
    Carys A Croft
    Centre for Heart Lung Innovation, St Paul s Hospital, University of British Columbia, Vancouver BC, Canada
    Front Microbiol 7:472. 2016
    ..A clear understanding of the mechanisms involved in the early establishment of infection by A. fumigatus could point to novel targets for therapy and prophylaxis. ..
  33. doi request reprint A Regulatory T-Cell Gene Signature Is a Specific and Sensitive Biomarker to Identify Children With New-Onset Type 1 Diabetes
    Anne M Pesenacker
    Department of Surgery, The University of British Columbia, and Child and Family Research Institute, Vancouver, British Columbia, Canada
    Diabetes 65:1031-9. 2016
    ..These findings provide new insight into the mechanisms underlying the failure to control autoimmunity in T1D and might lead to a biomarker test to monitor Tregs throughout disease progression. ..
  34. ncbi request reprint Evaluation of gene targeting by homologous recombination in ovine somatic cells
    Sarah H Williams
    Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom
    Mol Reprod Dev 66:115-25. 2003
    ..These data stress the importance of donor cell choice in somatic cell cloning and suggest that culture time be kept to a minimum prior to nuclear transfer in order to maximize cell viability...