Jonathan Marchini

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. doi request reprint Genotype imputation for genome-wide association studies
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford, UK
    Nat Rev Genet 11:499-511. 2010
  2. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
  3. pmc Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    Chris C A Spencer
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000477. 2009
  4. ncbi request reprint Joint genotype calling with array and sequence data
    Jared O'Connell
    Wellcome Trust Center of Human Genetics, Oxford, United Kingdom
    Genet Epidemiol 36:527-37. 2012
  5. ncbi request reprint Comparing methods of analyzing fMRI statistical parametric maps
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Neuroimage 22:1203-13. 2004
  6. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
  7. ncbi request reprint A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
  8. ncbi request reprint Genome-wide strategies for detecting multiple loci that influence complex diseases
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 37:413-7. 2005
  9. doi request reprint Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold
    Androniki Menelaou
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Bioinformatics 29:84-91. 2013
  10. pmc A model-based approach to capture genetic variation for future association studies
    Susana Eyheramendy
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genome Res 17:88-95. 2007

Detail Information

Publications29

  1. doi request reprint Genotype imputation for genome-wide association studies
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford, UK
    Nat Rev Genet 11:499-511. 2010
    ....
  2. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
    ....
  3. pmc Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    Chris C A Spencer
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000477. 2009
    ..Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated...
  4. ncbi request reprint Joint genotype calling with array and sequence data
    Jared O'Connell
    Wellcome Trust Center of Human Genetics, Oxford, United Kingdom
    Genet Epidemiol 36:527-37. 2012
    ..This method provides a foundation for future efforts to fuse genetic data from different sources, for example, when combining data from exome sequencing and exome microarrays...
  5. ncbi request reprint Comparing methods of analyzing fMRI statistical parametric maps
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Neuroimage 22:1203-13. 2004
    ..Within this framework, we highlight the role of the loss function, which explicitly penalizes the types of errors that may occur in a given analysis...
  6. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  7. ncbi request reprint A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  8. ncbi request reprint Genome-wide strategies for detecting multiple loci that influence complex diseases
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 37:413-7. 2005
    ..These results suggest that searching for interactions among genetic loci can be fruitfully incorporated into analysis strategies for genome-wide association studies...
  9. doi request reprint Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold
    Androniki Menelaou
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Bioinformatics 29:84-91. 2013
    ..When sequencing data are available from trios, Mendelian transmission constraints are easily accommodated into the updates. The method is highly parallelizable, as it analyses one position at a time...
  10. pmc A model-based approach to capture genetic variation for future association studies
    Susana Eyheramendy
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genome Res 17:88-95. 2007
    ..We also propose new methods to select the tagging SNPs. We empirically show by using HapMap data that our approach is able to capture significantly more genetic variation than methods based solely on a pairwise LD measure...
  11. 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
    ....
  12. pmc Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array
    Niall Cardin
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, United Kingdom
    Genet Epidemiol 35:536-48. 2011
    ..We illustrate the methods performance using real data from the Wellcome Trust Case Control Consortium's CNV association study and using simulated data...
  13. pmc Meta-analysis and imputation refines the association of 15q25 with smoking quantity
    Jason Z Liu
    Department of Statistics, University of Oxford, Oxford, UK
    Nat Genet 42:436-40. 2010
    ..Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3...
  14. pmc HAPGEN2: simulation of multiple disease SNPs
    Zhan Su
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
    Bioinformatics 27:2304-5. 2011
    ..However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application...
  15. doi request reprint Modeling interactions with known risk loci-a Bayesian model averaging approach
    Teresa Ferreira
    Department of Statistics, University of Oxford, UK
    Ann Hum Genet 75:1-9. 2011
    ..We show that the method has good power both when the association is the result of marginal effects only, and when interaction with a known locus occurs. The method is implemented as an option in the program SNPTEST...
  16. pmc Haplotype estimation using sequencing reads
    Olivier Delaneau
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Am J Hum Genet 93:687-96. 2013
    ..When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. ..
  17. doi request reprint Multiway admixture deconvolution using phased or unphased ancestral panels
    Claire Churchhouse
    Department of Statistics, University of Oxford, United Kingdom
    Genet Epidemiol 37:1-12. 2013
    ....
  18. ncbi request reprint The effects of human population structure on large genetic association studies
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 36:512-7. 2004
    ..The results of our analysis can guide the design of large-scale association studies...
  19. pmc Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer
    Ian P M Tomlinson
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 7:e1002105. 2011
    ....
  20. pmc The effect of genome-wide association scan quality control on imputation outcome for common variants
    Lorraine Southam
    Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
    Eur J Hum Genet 19:610-4. 2011
    ..A minority of common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency. These findings may not generalise to the imputation of low frequency and rare variants...
  21. ncbi request reprint A general approach for haplotype phasing across the full spectrum of relatedness
    Jared O'Connell
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 10:e1004234. 2014
    ..The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics. ..
  22. pmc Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
    Jeffrey C Barrett
    Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Nat Genet 40:955-62. 2008
    ..The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development...
  23. pmc Comparing algorithms for genotype imputation
    Jonathan Marchini
    Am J Hum Genet 83:535-9; author reply 539-40. 2008
  24. pmc A robust statistical method for case-control association testing with copy number variation
    Chris Barnes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 40:1245-52. 2008
    ..We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools...
  25. 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
    ....
  26. 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
    ....
  27. pmc A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC
    Paul I W de Bakker
    Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 38:1166-72. 2006
    ....
  28. 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...
  29. ncbi request reprint Intra-individual variation in resting metabolic rate during the menstrual cycle
    C Jeya K Henry
    Nutrition and Food Science Group, School of Biological and Molecular Sciences, Oxford Brookes University, Gipsy Lane Campus, Headington, OX3 0BP
    Br J Nutr 89:811-7. 2003
    ..In conclusion, the findings from our present study show that RMR cannot be assumed to be 'stable' in all women. The implications of intra-individual variation in RMR and its impact on energy balance needs further research...