Research Topics
Genomes and Genes
Species | David J BaldingSummaryAffiliation: Imperial College Country: UK Publications
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Detail Information
Publications
Likelihood-based inference for genetic correlation coefficientsDavid J Balding
Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, Norfolk Place, London W2 1PG, UK
Theor Popul Biol 63:221-30. 2003..This framework can be used, for example, to detect environment-related diversifying selection...- A tutorial on statistical methods for population association studiesDavid J Balding
Department of Epidemiology and Public Health, Imperial College, St Marys Campus, Norfolk Place, London W2 1PG, UK
Nat Rev Genet 7:781-91. 2006..My goal is to outline the key methods with a brief discussion of problems (population structure and multiple testing), avenues for solutions and some ongoing developments... 
Interpreting low template DNA profilesDavid J Balding
Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, Norfolk Place, London W21PG, UK
Forensic Sci Int Genet 4:1-10. 2009..We illustrate that ignoring the possibility of drop-in is usually unfair to defendants, and argue that under circumstances in which the prosecution relies on drop-out, it may be unsatisfactory to ignore any possibility of drop-in...
Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studiesClive J Hoggart
Department of Epidemiology and Public Health, Imperial College, London, United Kingdom
PLoS Genet 4:e1000130. 2008....- Genome-wide significance for dense SNP and resequencing dataClive J Hoggart
Department of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK
Genet Epidemiol 32:179-85. 2008..We compare our results for sequence data to those derived by the HapMap Consortium and find notable differences which may be due to the small sample sizes used in the HapMap estimate... - Fregene: simulation of realistic sequence-level data in populations and ascertained samplesMarc Chadeau-Hyam
Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, Norfolk Place, London, W2 1PG, UK
BMC Bioinformatics 9:364. 2008..We describe here main functionalities of both FREGENE and SAMPLE, a companion program that can replicate association study datasets... - Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regionsShu Yi Su
Department of Epidemiology and Public Health, Imperial College, London, W2 1PG, UK
BMC Bioinformatics 9:513. 2008..It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences... - A genome-wide association study of the metabolic syndrome in Indian Asian menDelilah Zabaneh
Department of Epidemiology and Public Health, Imperial College London, London, UK
PLoS ONE 5:e11961. 2010..Further, we found little evidence of a common genetic basis for metabolic syndrome traits in our sample of Indian Asian men... - Inferring combined CNV/SNP haplotypes from genotype dataShu Yi Su
Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London W2 1PG, UK
Bioinformatics 26:1437-45. 2010..Thus, haplotypic phase of CNVs and SNPs are inferred simultaneously. A sampling algorithm is employed to obtain a measure of confidence/credibility of each estimate... - Sequence-level population simulations over large genomic regionsClive J Hoggart
Department of Epidemiology and Public Health, Imperial College, London W2 1PG, United Kingdom
Genetics 177:1725-31. 2007.... - Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computationJean Marie Cornuet
Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, Norfolk Place, London W2 1PG, UK
Bioinformatics 24:2713-9. 2008..AVAILABILITY: The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc... - Confounding between recombination and selection, and the Ped/Pop method for detecting selectionPaul F O'Reilly
Department of Epidemiology and Public Health, Imperial College London, UK
Genome Res 18:1304-13. 2008..We apply the method to human HapMap and Perlegen data sets, finding confirmation of reported candidates as well as identifying new loci that may have undergone recent intense selection... - cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVsLachlan J M Coin
Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary s Hospital, London, UK
Nat Methods 7:541-6. 2010..Combining data from multiple platforms additionally improved sensitivity... - A genome-wide association study of neuroticism in a population-based sampleFederico C F Calboli
Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
PLoS ONE 5:e11504. 2010..Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism... - Functional constraint and small insertions and deletions in the ENCODE regions of the human genomeTaane G Clark
Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London, W2 1PG, UK
Genome Biol 8:R180. 2007..We relate indels to known genomic annotation features and measures of evolutionary constraint... - Population structure and inbreeding from pedigree analysis of purebred dogsFederico C F Calboli
Department of Epidemiology and Public Health, Imperial College, London W2 1PG, United Kingdom
Genetics 179:593-601. 2008..As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare... - Disease association tests by inferring ancestral haplotypes using a hidden markov modelShu Yi Su
Department of Epidemiology and Public Health, Imperial College, London W2 1PG, UK
Bioinformatics 24:972-8. 2008..Haplotype-based methods provide a promising approach; however, they suffer from statistical problems such as abundance of rare haplotypes and ambiguity in defining haplotype block boundaries... - Using penalised logistic regression to fine map HLA variants for rheumatoid arthritisCharlotte M Vignal
Department of Epidemiology and Public Health, Imperial College London, UK
Ann Hum Genet 75:655-64. 2011..We conclude that SNP selection using penalised regression shows a substantial benefit over single-SNP analyses in identifying risk loci in regions of high LD, and the flexibility of the NEG conveys additional advantages... - Exon sequencing and high resolution haplotype analysis of ABC transporter genes implicated in drug resistanceGuy Leschziner
Imperial College, London, UK
Pharmacogenet Genomics 16:439-50. 2006.... - Clustering of protein domains in the human genomeLianne R Mayor
Department of Epidemiology and Public Health, Imperial College, St Mary's Campus, London W2 1PG, UK
J Mol Biol 340:991-1004. 2004..Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies... - Discrimination of half-siblings when maternal genotypes are knownLianne R Mayor
Department of Epidemiology and Public Health, Imperial College, St. Mary's Campus, Norfolk Place, London W2 1PG, UK
Forensic Sci Int 159:141-7. 2006..We illustrate that using an appropriate value of theta can reduce the average misclassification rate... - Admixture provides new insights into recombinationPaul F O'Reilly
Department of Epidemiology and Biostatistics, Imperial College, London, UK
Nat Genet 43:819-20. 2011..The publication of the first admixture-derived human genetic maps offers a new approach for inferring recombination events and provides insight into variation in recombination rate patterns across populations... - Logistic regression protects against population structure in genetic association studiesEfrosini Setakis
Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, London W2 1PG, United Kingdom
Genome Res 16:290-6. 2006.... - Implications for DNA identification arising from an analysis of Australian forensic databasesKaren L Ayres
School of Applied Statistics, The University of Reading, P O Box 240, Earley Gate, UK
Forensic Sci Int 129:90-8. 2002.... - Approximate Bayesian computation in population geneticsMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
Genetics 162:2025-35. 2002..We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC... - Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneityAndrew 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... - Identifying adaptive genetic divergence among populations from genome scansMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
Mol Ecol 13:969-80. 2004..Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate... - Variation in estimated recombination rates across human populationsJan Graffelman
Department of Statistics and Operations Research, Universitat Politecnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain
Hum Genet 122:301-10. 2007..Several results from studies on the population history of humans are in accordance with our analysis. Our results suggest that between-population variation in DNA sequences may underly recombination rate variation... - Family-based association analysis with ordered categorical phenotypes, covariates and interactionsM Fazil Baksh
Section of Applied Statistics, The University of Reading, Reading, UK
Genet Epidemiol 31:1-8. 2007..By including sex interactions in the analysis, we show that the polymorphism is associated with anti-nuclear autoantibody (ANA) production in females, while there appears to be no effect in males... - The DNA database search controversyDavid J Balding
Department of Applied Statistics, University of Reading, UK
Biometrics 58:241-4. 2002..I outline reasons why Stockmarr and the NRC report are wrong. I also briefly discuss possible reasons why forensic applications tend to be problematic for statisticians... - Paternity index calculations when some individuals share common ancestryKaren L Ayres
Forensic Sci Int 151:101-3. 2005 - Clinical factors and ABCB1 polymorphisms in prediction of antiepileptic drug response: a prospective cohort studyGuy Leschziner
Division of Neurosciences, Imperial College London, London, UK
Lancet Neurol 5:668-76. 2006..We aimed to determine the effect of the ABCB1 gene on epilepsy drug response, using a unique large cohort of epilepsy patients with prospectively measured seizure and drug response outcomes... - A genome-wide association study identifies novel risk loci for type 2 diabetesRobert Sladek
Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal H3A 1A4, Canada
Nature 445:881-5. 2007..These associations explain a substantial portion of disease risk and constitute proof of principle for the genome-wide approach to the elucidation of complex genetic traits... - Common ABCB1 polymorphisms are not associated with multidrug resistance in epilepsy using a gene-wide tagging approachGuy D Leschziner
Imperial College London, London, UK
Pharmacogenet Genomics 17:217-20. 2007..In addition, no evidence for a role of other common ABCB1 polymorphisms was found using a potentially more powerful gene-wide tagging approach... - The association between polymorphisms in RLIP76 and drug response in epilepsyGuy D Leschziner
Imperial College London, Division of Neuroscience, Charing Cross Campus, Room 10E07, St Dunstan s Road, London W6 8RF, UK
Pharmacogenomics 8:1715-22. 2007..We aimed to look for an association with outcomes reflecting drug response in a larger prospective cohort, with gene-wide coverage...