A P Morris

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Meta-analysis of sex-specific genome-wide association studies
    Reedik Magi
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 34:846-53. 2010
  2. pmc Assessing the impact of missing genotype data in rare variant association analysis
    Reedik Magi
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    BMC Proc 5:S107. 2011
  3. pmc Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Nat Genet 44:981-90. 2012
  4. pmc A comparison of case-only designs for detecting gene x gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S73. 2009
  5. pmc Assessment of sex-specific effects in a genome-wide association study of rheumatoid arthritis
    Joanna J Zhuang
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S90. 2009
  6. pmc The role of CACNA1S in predisposition to malignant hyperthermia
    Danielle Carpenter
    MH Investigation Unit, Academic Unit of Anaesthesia, St James s University Hospital, Leeds, LS9 7TF, UK
    BMC Med Genet 10:104. 2009
  7. pmc Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data
    Caroline Durrant
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, UK
    BMC Genet 6:S100. 2005
  8. pmc Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies
    Fredrik Pettersson
    Dept Bioinformatics, Wellcome Trust Centre, Oxford, UK
    BMC Bioinformatics 9:138. 2008
  9. pmc GWAMA: software for genome-wide association meta-analysis
    Reedik Magi
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    BMC Bioinformatics 11:288. 2010
  10. pmc Identification of novel putative rheumatoid arthritis susceptibility genes via analysis of rare variants
    Andrew P Morris
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    BMC Proc 3:S131. 2009

Detail Information

Publications49

  1. pmc Meta-analysis of sex-specific genome-wide association studies
    Reedik Magi
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 34:846-53. 2010
    ....
  2. pmc Assessing the impact of missing genotype data in rare variant association analysis
    Reedik Magi
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    BMC Proc 5:S107. 2011
    ..According to our results, the mutational load based rare variant analysis method is relatively robust to call-rate and is adequately powered for genome-wide association analysis...
  3. pmc Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Nat Genet 44:981-90. 2012
    ..Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis...
  4. pmc A comparison of case-only designs for detecting gene x gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S73. 2009
    ..Porportional odds and multinomial methods provide new tools for identification of G x G interactions...
  5. pmc Assessment of sex-specific effects in a genome-wide association study of rheumatoid arthritis
    Joanna J Zhuang
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S90. 2009
    ..These signals may represent true sex-specific effects, or may reflect a lack of power to detect association in the smaller sample of males, and thus warrant further investigation...
  6. pmc The role of CACNA1S in predisposition to malignant hyperthermia
    Danielle Carpenter
    MH Investigation Unit, Academic Unit of Anaesthesia, St James s University Hospital, Leeds, LS9 7TF, UK
    BMC Med Genet 10:104. 2009
    ..This study focuses on the gene CACNA1S which encodes the alpha1 subunit of the DHPR, in order to establish whether CACNA1S plays a major role in MH susceptibility in the UK...
  7. pmc Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data
    Caroline Durrant
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, UK
    BMC Genet 6:S100. 2005
    ..As expected, our results suggest that when there is little or no LD between a disease locus and the flanking region, there will be no chance of detecting it unless the disease variant itself is genotyped...
  8. pmc Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies
    Fredrik Pettersson
    Dept Bioinformatics, Wellcome Trust Centre, Oxford, UK
    BMC Bioinformatics 9:138. 2008
    ..Finally significant associations need to be prioritised using functional and biological interpretation methods, browsing available biological annotation, pathway information and patterns of linkage disequilibrium (LD)...
  9. pmc GWAMA: software for genome-wide association meta-analysis
    Reedik Magi
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    BMC Bioinformatics 11:288. 2010
    ..Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies...
  10. pmc Identification of novel putative rheumatoid arthritis susceptibility genes via analysis of rare variants
    Andrew P Morris
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    BMC Proc 3:S131. 2009
    ..We apply our method to WGA SNP genotype data obtained from 868 RA cases and 1194 controls. Our results highlight novel putative RA susceptibility genes that have not previously been identified in large-scale WGA studies...
  11. pmc A powerful approach to sub-phenotype analysis in population-based genetic association studies
    Andrew P Morris
    The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
    Genet Epidemiol 34:335-43. 2010
    ....
  12. pmc Transethnic meta-analysis of genomewide association studies
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
    Genet Epidemiol 35:809-22. 2011
    ..Furthermore, when the similarity in allelic effects between populations is well captured by their relatedness, this approach has increased power and mapping resolution over random-effects meta-analysis...
  13. pmc A flexible Bayesian framework for modeling haplotype association with disease, allowing for dominance effects of the underlying causative variants
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
    Am J Hum Genet 79:679-94. 2006
    ....
  14. pmc An evaluation of statistical approaches to rare variant analysis in genetic association studies
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
    Genet Epidemiol 34:188-93. 2010
    ....
  15. pmc Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies
    A P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Am J Hum Genet 70:686-707. 2002
    ..We present detailed simulations to provide evidence of improvements over existing methodology. Furthermore, inferences about the location of the disease locus are shown to remain robust to modeling assumptions...
  16. pmc Little loss of information due to unknown phase for fine-scale linkage-disequilibrium mapping with single-nucleotide-polymorphism genotype data
    A P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
    Am J Hum Genet 74:945-53. 2004
    ..a two-stage approach of inferring haplotypes followed by a haplotype-based analysis can be very inefficient for fine mapping, compared with an analysis based directly on the genotypes...
  17. ncbi request reprint Linkage disequilibrium assessment via log-linear modeling of SNP haplotype frequencies
    Andrew Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Genet Epidemiol 25:106-14. 2003
    ....
  18. doi request reprint Two-stage candidate gene study of chromosome 3p demonstrates an association between nonsynonymous variants in the MST1R gene and Crohn's disease
    John B Beckly
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Inflamm Bowel Dis 14:500-7. 2008
    ....
  19. pmc Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT
    Gabrielle Barnby
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Am J Hum Genet 76:950-66. 2005
    ..0001). Logistic regression analysis of SNP data across GRIN2A and ABAT showed a trend toward haplotypic differences between cases and controls...
  20. doi request reprint Association between genetic variants in myosin IXB and Crohn's disease
    Rachel Cooney
    Wellcome Trust Centre of Human Genetics, University of Oxford, Oxford, UK
    Inflamm Bowel Dis 15:1014-21. 2009
    ..We also investigated subphenotype association and interactions with CARD15, IL23R, ATG16L1, and the IBD5 risk haplotype...
  21. pmc A role for coding functional variants in HNF4A in type 2 diabetes susceptibility
    B Jafar-Mohammadi
    Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, UK
    Diabetologia 54:111-9. 2011
    ..We aimed to evaluate the contribution of these variants to type 2 diabetes susceptibility through large-scale association analysis...
  22. ncbi request reprint A note on the power to detect transmission distortion in parent-child trios via the transmission disequilibrium test
    D M Evans
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    Behav Genet 36:947-50. 2006
    ..The corollary is that genome-wide searches are unlikely to identify loci where the level of distortion is small, although they may serve to identify interesting regions worthy of follow up...
  23. pmc Evidence for genetic regulation of vitamin D status in twins with multiple sclerosis
    Sarah Michelle Orton
    Wellcome Trust Centre for Human Genetics and Department of Clinical Neurology, University of Oxford Oxford, United Kingdom
    Am J Clin Nutr 88:441-7. 2008
    ..Recent epidemiologic, experimental, and clinical evidence support an effect for low environmental supplies of vitamin D in mediating an increased susceptibility to MS...
  24. ncbi request reprint Direct analysis of unphased SNP genotype data in population-based association studies via Bayesian partition modelling of haplotypes
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 29:91-107. 2005
    ..Further, the results of a detailed simulation study suggest that we can identify positive evidence of association for moderate relative disease risks with a sample of 1,000 cases and 1,000 controls...
  25. ncbi request reprint Genotype prediction using a dense map of SNPs
    David M Evans
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Genet Epidemiol 27:375-84. 2004
    ..These results suggest that pair-wise tests of disease-marker association may be inferior to multipoint methods, which take advantage of the information contained within multi-locus haplotypes...
  26. ncbi request reprint How useful is the fine-scale mapping of complex trait linkage peaks? Evaluating the impact of additional microsatellite genotyping on the posterior probability of linkage
    Steven Wiltshire
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 28:1-10. 2005
    ....
  27. pmc Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes
    Caroline Durrant
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Am J Hum Genet 75:35-43. 2004
    ..The results of the simulation study highlight substantial gains in power over single-locus tests for a wide range of disease models, despite overcorrection for multiple testing...
  28. ncbi request reprint Efficiency and consistency of haplotype tagging of dense SNP maps in multiple samples
    Xiayi Ke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    Hum Mol Genet 13:2557-65. 2004
    ..Encouragingly, whatever the density employed, a high level of robustness was observed between UK and CEPH samples, as most of the htSNPs selected in one sample were also appropriate as tags in the other...
  29. ncbi request reprint The impact of SNP density on fine-scale patterns of linkage disequilibrium
    Xiayi Ke
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Hum Mol Genet 13:577-88. 2004
    ..The results suggest that very dense marker sets will be required to yield stable views of fine-scale LD in the human genome...
  30. pmc Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
    Proc Natl Acad Sci U S A 100:13442-6. 2003
    ..We further investigate a selection of SNP subsets and find that previously reported methods lead to a 38% savings in SNPs at the cost of an increase of <20% in the width of the location interval...
  31. pmc Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms
    Carl A Anderson
    The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN Oxford, UK
    Am J Hum Genet 83:112-9. 2008
    ..Platforms consisting of around 1 million SNPs offer poor cost efficiency for SNP association in European populations...
  32. pmc Common variants near MC4R are associated with fat mass, weight and risk of obesity
    Ruth J F Loos
    MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
    Nat Genet 40:768-75. 2008
    ....
  33. pmc Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease
    Sheila A Fisher
    Department of Medical and Molecular Genetics, King s College London School of Medicine, 8th Floor Guy s Tower, Guy s Hospital, London SE1 9RT, UK
    Nat Genet 40:710-2. 2008
    ..These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases...
  34. pmc Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants
    Robert Lawrence
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genome Res 15:1503-10. 2005
    ..We describe the distribution of giSNPs on this map of chromosome 20 and illustrate the potential impact they can have on association mapping...
  35. pmc Two-stage two-locus models in genome-wide association
    David M Evans
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 2:e157. 2006
    ....
  36. pmc Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes
    Eleftheria Zeggini
    Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
    Science 316:1336-41. 2007
    ..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes...
  37. pmc A TNF region haplotype offers protection from typhoid fever in Vietnamese patients
    Sarah J Dunstan
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, District 5, Ho Chi Minh City, Vietnam
    Hum Genet 122:51-61. 2007
    ..Finally, individuals that carry the typhoid fever protective haplotype *12122*1111 also produce a relatively low TNF-alpha response to LPS...
  38. pmc The inheritance of resistance alleles in multiple sclerosis
    Sreeram V Ramagopalan
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 3:1607-13. 2007
    ..Restriction of antigen presentation by HLA-DRB1*15 seems an improbably simple mechanism of major histocompatibility complex-associated susceptibility...
  39. pmc Fine mapping versus replication in whole-genome association studies
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Am J Hum Genet 81:995-1005. 2007
    ..Our results provide a basis for the design and interpretation of GWA replication studies and point to the importance of a clear distinction between fine mapping and replication after GWA...
  40. ncbi request reprint Gearing up for genome-wide gene-association studies
    Martin Farrall
    Department of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Hum Mol Genet 14:R157-62. 2005
    ..Expectations are understandably high and it is timely to review the promise and pitfalls of this strategy...
  41. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  42. pmc Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants
    Paul R Burton
    Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
    Nat Genet 39:1329-37. 2007
    ....
  43. ncbi request reprint Coalescent methods for fine-scale disease-gene mapping
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Methods Mol Biol 376:123-40. 2007
    ....
  44. pmc Examining the statistical properties of fine-scale mapping in large-scale association studies
    Steven Wiltshire
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 32:204-14. 2008
    ..Our findings help inform the interpretation and design of dense SNP-mapping follow-up studies, thus facilitating discrimination between a genuine genetic effect and chance fluctuation (false positive)...
  45. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  46. ncbi request reprint An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets
    Eleftheria Zeggini
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Genet 37:1320-2. 2005
    ....
  47. ncbi request reprint Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice
    Binnaz Yalcin
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Nat Genet 36:1197-202. 2004
    ..We then use quantitative complementation to show that Rgs2 is a quantitative trait gene. This combined genetic and functional approach should be applicable to the analysis of any quantitative trait...
  48. ncbi request reprint Chronic PKC-beta2 activation in HT-29 Cl.19a colonocytes prevents cAMP-mediated ion secretion by inhibiting apical membrane CFTR targeting
    James R Broughman
    Department of Integrative Biology, University of Texas Health Science Center, Houston, TX 77030, USA
    Am J Physiol Gastrointest Liver Physiol 291:G331-44. 2006
    ..Thus PKC-beta2 is hypothesized to participate in the regulation of CFTR apical plasma membrane targeting within the constitutive cellular biosynthetic pathway...