DAVID BALDING
Professor of Statistical Genetics,

Imperial College London

POSTAL ADDRESS:

Department of Epidemiology & Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG

 

Local map

Direct Phone: +44 (0)20 7594 3309
e-mail: D.Balding@ic.ac.uk

PA Madeline Kirk: M.Kirk@ic.ac.uk

phone +44 (0) 20 7594 3319

LINKS:

Centre for Biostatistics

My official IC website

IC Statistical Advisory Service

           

BOOKS:

PEOPLE WORKING WITH ME:

  • Jean-Marie Cornuet, from the Centre de Biologie et de Gestion des Populations at INRA, Montpellier, France, arrived Sept 2006 to commence a 2-year Marie Curie Intra-European Fellowship with us, on a project entitled "Statistical inference in population genetics".
  • Valentina Cipriani, PhD student in the Sezione di Statistica Medica ed Epidemiologia, Università di Pavia, Italy, is visiting for 2007 + 2008.

 

PhD Students (see below for past PhD students):

Post-docs:

Paul O’Reilly (BBSRC, started Oct 2004)

Federico Calboli (BBSRC, started Jan 2005)

William Astle (MRC, started Oct 2004)

Delilah Zabaneh (BHF, started April 05) Now on maternity leave

Charlotte Vignal (part-time, GSK, started Dec 2004)

Adaikalavan Ramasamy (EU, started Jan 08) Joint with NHLI

Shu-Yi Su (started Oct 2005)

Michele Petteni (WT, started Feb 08)

Jon White (part-time, NIAB, started April 07)

 

 

RECENT POSTDOCS AND VISITORS

 

  • Toby Andrew (Sept 05 – Mar 08) is now a Lecturer in Genetic Epidemiology at King’s College London
  • Marc Chadeau (Dec 06 – Feb 08) is now working on another project in the Department.
  • Clive Hoggart (Sept 04 – Feb 08) is now working on another project in the Department.
  • David Welch, EPSRC-funded postdoc, May 2006 – Dec 2007 is now at Penn State U.
  • Tina Müller, PhD student at Dept Statistics, University of Dortmund, Germany visited from August 2006 to December 2006.
  • Scott Sisson from Dept Statistics, UNSW, Sydney, visited June/July 2006.
  • Michael Buckley from CSIRO Mathematical and Information Sciences, Sydney, visited May/July 2006.
  • In Oct 06 Taane Clark (postdoc funded by MRC from Feb 2005) moved to the Sanger Institute, Hinxton.
  • Photo of people working with me in 2000 at Reading (Grainne, Andrew, Patrick, Chiara, Karen, in Three Tuns pub) here.

 

RECENT PUBLICATIONS (since 2005) AND PAPERS IN PRESS (earlier publications)

Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ, Simultaneous Analysis of all SNPs in Genome–Wide and Re–sequencing Association Studies, PLoS Genetics 4(7): e1000130. doi:10.1371/journal.pgen.1000130

O’Reilly PF, Birney E, Balding DJ, Confounding between recombination and selection, and the Ped/Pop method for detecting selection, Genome Research 18: 1304-1313, August 2008, doi:10.1101/gr.067181.107

Chambers JC, Elliott P, Zabaneh D, Zhang W, Li Y, Froguel P, Balding D, Scott J, Kooner JS, Common genetic variation near the melanocortin-4 receptor gene is associated with waist circumference and insulin resistance, Nature Genetics 40, 716 – 718, June  2008. doi:10.1038/ng.156

Calboli FC , Sampson J,  Fretwell N, Balding DJ, Population structure and inbreeding from pedigree analysis of purebred dogs, Genetics, 179(1): 593–601, May 2008.  doi:10.1534/genetics.107.084954

Su SY, Balding DJ, Coin LJM, Disease Association Tests by Inferring Ancestral Haplotypes Using a Hidden Markov Model, Bioinformatics, 24: 972-978, April 2008. doi:10.1093/bioinformatics/btn071

Hoggart CJ, Clark TG, De Iorio M, Whittaker JC, Balding DJ, Genome-Wide Significance for Dense SNP and Resequencing Data, Genetic Epidemiology, 32(2): 179-185, February 2008.

Ioannidis JPA, Boffetta P, Little J, O’Brien TR, Uitterlinden AG, Vineis P, Balding DJ, Chokkalingam A, Dolan SM, Flanders WD, Higgins JPT, McCarthy MI, McDermott DH, Page GP, Rebbeck TR, Seminara D, Khoury MJ. Assessment of Cumulative Evidence on Genetic Associations: Interim Guidelines, Int. J. Epidem. 37(1):120-132, February 2008  doi:10.1093/ije/dym159

Leschziner GD, Jorgensen AL, Andrew T, Williamson PR + 3 authors + Balding DJ + 3 authors + Johnson MR, Pirmohamed M, The association between polymorphisms in RLIP76 and drug response in epilepsy, Pharmacogenomics, 8(12): 1715-1722, 2007.

Hoggart CJ, Chadeau-Hyams M, Clark TG, Lampariello R, De Iorio M, Whittaker JC, Balding DJ, Sequence-level population simulations over large genomic regions, Genetics 177: 1725–1731, 2007 doi:10.1534/genetics.106.069088

Clark TG, Andrew T, Cooper GM, Marguiles EH, Mullikin JC, Balding DJ. Functional constraint and small insertions and deletions in the ENCODE regions of the human genome Genome Biology, 8:R180, 2007  doi:10.1186/gb-2007-8-9-r180

Graffelman J; Balding DJ; Gonzalez A; Bertranpetit J.  Variation in Estimated Recombination Rates across Human Populations, Human Genetics, 122(3-4):301-310, 2007. doi:10.1007/s00439-007-0391-6

Leschziner GD; Andrew T; Leach JP; Chadwick D; Coffey AJ; Balding DJ; Bentley DR; Pirmohamed M; Johnson MR.  Common ABCB1 polymorphisms are not associated with multidrug resistance in epilepsy using a gene-wide tagging approach, Pharmacogenetics and Genomics 17: 217-220, 2007.

A genome-wide association study identifies novel risk loci for type 2 diabetes, Sladek R, Rocheleau G, Rung J, Dina C + 14 authors + Balding DJ, Meyre D, Polychronakos C, Froguel P, Nature 445: 881-885 2007. doi:10.1038/nature05616

Family-based association analysis with ordered categorical phenotypes, covariates and interactions, Baksh MF, Balding DJ, Vyse TJ & Whittaker JC, Genetic Epidemiology 31(1): 1-8, 2007. doi:10.1002/gepi.20183

A tutorial on statistical methods for population association studies, Balding DJ, Nature Reviews Genetics 7: 781-791, 2006.  doi:10.1038/nrg1916

Clinical factors and ABCB1 polymorphisms in prediction of antiepileptic drug response: a prospective cohort study, Leschziner G, Jorgensen AL, Andrew T, Pirmohamed M, Williamson PR, Marson AG, Coffey AJ, Middleditch C, Rogers J, Bentley DR, Chadwick DW, Balding DJ, Johnson MR, Lancet Neurology 5: 668–76, 2006.

Exon sequencing and high resolution haplotype analysis of ABC transporter genes implicated in drug resistance, Leschzinger G, Zabaneh D, Pirmohamed M, Owen A, Rogers J, Coffey AJ, Balding DJ, Bentley DB & Johnson MR, Pharmacogenetics and Genomics, 16: 439-450, 2006.

Discrimination of half-siblings when maternal genotypes are known, LR Mayor & Balding DJ, Forensic Science International, 159(2-3): 141-147, 2006.

doi:10.1016/j.forsciint.2005.07.007

Fine mapping of disease genes via haplotype clustering, ERB Waldron, JC Whittaker & Balding DJ, Genetic Epidemiology, 30: 170-179, 2006 Software

Logistic regression protects against population structure in genetic association studies, E Setakis, H Stirnadel & Balding DJ, Genome Research, 16: 290-296, 2006.

A family-based association test with a complex phenotype, covariates and interactions: assessing CRP and lupus, Baksh MF, Balding DJ, Vyse TJ & Whittaker JC, Annals of Human Genetics 70: 131-139, 2006.

SOFTWARE

  • FREGENE C++ software for simulating sequence-like data in large genomic regions in entire populations (say, 1 Mb in 100K individuals, or 20 Mb in 5K individuals), under a flexible range of scenarios for recombination (including gene conversion), demography (population growth and structure) and selection (directional and balancing) is available from the Bargen project webpage at the EBI.  A paper describing its use together with a rescaling technique that greatly reduces computing times, has been accepted to appear in Genetics (Hoggart et al 2007).
  • HAPCLUSTER software for confirming and fine-mapping genetic associations in candidate regions, using haplotype clustering, is available from Thomas Mailund's homepage.  The original R code described in Waldron, Whittaker and Balding (2006) only analysed phased haplotype data, and implemented a general risk model (separate risk for each genotype at the postulated causal locus).  Thomas has recoded it in C++ and extended it to handle unphased genotype data, to output the Bayes Factor assessing the evidence against the null hypothesis of no association, and to implement an allelic disease model.  The latter should give more power for near-multiplicative disease risks, but may be affected by deviations from Hardy-Weinberg equilibrium.  The latest version (2.1.5) also allows unphenotyped individuals, to facilitate imputation e.g. from HapMap individuals.
  • BAYESFST software for Bayesian hierarchical inference for Fst, described in Theoretical Population Biology, 63(3): 221-230, 2003 and Molecular Ecology, 13: 969-980, 2004, is available here.
  • MAC5 software for phylogenetic inference, described in McGuire, Denham & Balding (2001a,b) may be downloaded from here.
  • C programs described in Ayres & Balding, Heredity, 1998, and Ayres & Balding, Genetics, 2001, are available here.
  • BATWING software, a development of that described in Wilson & Balding, Genetics,1998, may be downloaded from Ian Wilson's home page.

PROFESSIONAL SOCIETIES:

JOURNALS:

Fellow of the Royal Statistical Society (member of Council 1999-2004).

AE of International Statistical Review (1999 – 2005)

Member of the International Statistical Institute.

AE of Biostatistics (2000 – 2004)

Member of the International Biometric Society (British & Irish President 2006-08)

AE of Human Genomics (2003 – 2006)

Member of the International Genetic Epidemiology Society

AE of Annals of Human Genetics (2004 – )

BACKGROUND:

 

PAST PhD STUDENTS:

  • Dr David Wright (EPSRC, 1990 – 1995).  Now Senior Statistical Assessor and Scientific Advice Coordinator at Medicines and Healthcare products Regulatory Agency, London
  • Dr Karen Ayres (EPSRC, 1995 – 1998).   Now Lecturer in Applied Statistics, University of Reading
  • Dr Martyn Byng (BBSRC, 1997 – 2001).  Now Senior Technical Consultant at NAG, Oxford.
  • Jacky Civil (BBSRC/GSK, 2000 – 2004; did not submit).  Now with Data Sciences Group at Unilever, Beds UK.
  • Dr Lianne Mayor (MRC, 2002 – 2006).  Now at Deloitte, Reading.
  • Dr Ed Waldron (BBSRC/GSK, 2003-2007).  Now Statistician at Takeda R&D, London.

CONSULTING and SHORT COURSES

I offer a statistical consulting service, primarily to lawyers. Most often I advise on statistical aspects of the interpretation of DNA profile evidence, but I have also provided advice on a variety of other statistical aspects of forensic science, epidemiology and other fields.

I teach a one-day short course on "Weight-of-evidence for forensic DNA profiles", based on my bookof the same name, which was last presented at UNSW, Sydney, on July 6 2005.

I also co-teach a two-day short course "Statistical Analysis of Genetic Association Studies", which was last presented at St Mary’s, London, on 28/29 Sept 2006.

PREVIOUS PUBLICATIONS

2003-2005

·         Paternity index calculations when some individuals share common ancestry, KL Ayres & Balding DJ, Forensic Science International, 151(1): 101-103, 2005.

·         The impact of low-cost, genome-wide resequencing on association studies, Balding DJ, editorial for Human Genomics, 2(2): 79-80, 2005.

·         A question of identity, Balding DJ, Significance, 2(1): 20-23, March 2005.

·         Identifying adaptive genetic divergence among populations from genome scans, MA Beaumont & DJB, Molecular Ecology, 13: 969-980,2004. Software

·         Clustering of protein domains in the human genome, LR Mayor, KP Fleming, A Müller, DJB & MJ Sternberg, Journal of Molecular Biology, 340(5): 991-1004,2004.

·         Little loss of information due to unknown phase for fine-scale LD mapping with SNP genotype data,  AP Morris, JC Whittaker & DJB, American Journal of Human Genetics, 74(5): 945-953,2004.

·         Multipoint LD mapping narrows location interval and identifies mutation heterogeneity, A. Morris, J. Whittaker, C-F Xu, L Hosking& DJB, Proceedings of the NationalAcademy of Sciences of the USA 100(23):13442–13446, 2003.

·         Gametic phase estimation over large genomic regions using an adaptive window approach, L. Excoffier, G. Laval & DJB, Human Genomics 1(1): 7-19, 2003.

·         Handbookof Statistical Genetics, 2nd edition, DJB, M. Bishop, & C. Cannings (Eds), Chichester: Wiley, 2003.

·         Inferences from DNA data: population histories, evolutionary processes, and forensic match probabilities, I.J. Wilson, M.E. Weale & DJB, read before the Royal Statistical Society, November 2002, Journal of the Royal Statistical Society A 166(2): 155-187, 2003 (see also discussion pp 188-202).

·         Likelihood-based inference for genetic correlation coefficients, DJB, Theoretical Population Biology, 63(3): 221-230, 2003.

·         Chromosome-wide distribution of haplotype blocks and the role of recombination hotspots, M.S. Phillips, R. Lawrence, R. Sachidanandam, A.P. Morris, DJB, + 29 authors + L.R. Cardon, Nature Genetics, 33: 382-387,2003.

2000-2002

  • Approximate Bayesian computation in population genetics, M.A. Beaumont, W. Zhang, & DJB, Genetics, 162: 2025-2035, 2002.
  • Implications for DNA identification arising from an analysis of Australian forensic databases, K.L. Ayres, J. Chaseling, & DJB, Forensic Science International, 129: 90-98, 2002.
  • Coalescent theory and modeling, DJB, pp 170-175 of Encyclopedia of Evolution, M. Pagel ed, Oxford UP, 2002.
  • Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms, C. Romualdi, DJB, I.S. Nasidze, G. Risch, M. Robichaux, S. Sherry, M. Stoneking, M.A. Batzer & G. Barbujani, Genome Research, 12: 602-612, 2002.
  • Fine scale mapping of disease loci via shattered coalescent modelling of genealogies, A.P. Morris, J.C. Whittaker & DJB, American Journal of Human Genetics, 70: 686-707, 2002.
  • The DNA database search controversy, DJB, Biometrics, 58: 241-244, 2002.
  • MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps. G. McGuire, M.C. Denham, & DJB, Bioinformatics , Vol 17, pp 479-480, 2001.
  • Models of evolution for DNA sequences including gaps, G. McGuire, M.C. Denham & DJB, Molecular Biology and Evolution, Vol 18, pp 481-490, 2001.
  • Measuring gametic disequilibrium from multi-locus data, K.L. Ayres & DJB, Genetics, Vol. 157, pp 413-423, 2001. C programs
  • Handbook of Statistical Genetics, DJB, M. Bishop, & C. Cannings (Eds), Chichester: Wiley, 2001.
  • Analysis of infectious disease data from household outbreaks by Markov chain Monte Carlo methods. P.D. O'Neill, DJB, N.G. Becker, M. Eerola, & D. Mollison, Applied Statistics, Vol 49, pp 517-542, 2000.
  • Bayesian fine scale mapping of disease loci using hidden Markov models, A.P. Morris, J.C. Whittaker & DJB, American Journal of Human Genetics, Vol 67, pp 155-169, 2000.
  • Interpreting DNA evidence: can probability theory help? Chap. 3, pp 51-70, of Statistical Science in the Courtroom, J.L. Gastwirth ed, Springer-Verlag, New York, 2000.

1997-1999

  • When can a DNA profile be regarded as unique? Science & Justice, Vol. 39, pp 257-260, 1999.
  • Forensic applications of microsatellite markers. pp 198-210 of Microsatellites: evolution and applications, D. Goldstein and C. Schlotterer eds, Oxford UP, 1999.
  • Genealogical inference from microsatellite data . I.J. Wilson and DJB, Genetics, 150, pp 499-510, 1998.
  • Measuring departures from Hardy-Weinberg: a Markov Chain Monte Carlo method for estimating the inbreeding coefficient. K.L. Ayres and DJB, Heredity, 80, pp 769-777, 1998.
  • Inferring coalescence times from DNA sequence data. Simon Tavaré, DJB, R.C. Griffiths and Peter Donnelly, Genetics 145 pp 505-518, 1997.
  • Significant genetic correlations among Caucasians at forensic DNA loci. DJB and R.A. Nichols Heredity 78, pp 583-589, 1997.
  • Errors and misunderstandings in the second NRC report. Jurimetrics, 37, pp 469-476, 1997.
  • The design of pooling experiments for screening a clone map. DJB and D.C. Torney, Fungal Genetics and Biology, 21, pp 302-307, 1997.

1994-1996

  • Optimal pooling designs with error detection. DJB & D.C. Torney, J. Comb. Th. A 74, pp 131-140, 1996.
  • Evaluating DNA profile evidence when the suspect is identified through a database search. DJB & P. Donnelly, J. Forensic Sci., 41, pp 603-607, 1996.
  • Population genetics of STR loci in Caucasians. DJB, M. Greenhalgh & R.A. Nichols, Int. J. Legal Med., 108, pp 300-305, 1996.
  • Estimating the age of the common ancestor of men from the ZFY intron. P. Donnelly, S. Tavaré, DJB & R. Griffiths, Science, 272, pp 1357-1359, 1996.
  • A comparative survey of non-adaptive pooling designs, pp 133-154 of "Genetic mapping and DNA sequencing", IMA Volumes in Mathematics and its Applications, T.P. Speed & M.S. Waterman eds, New York: Springer-Verlag, 1996, DJB, W.J. Bruno, E. Knill & D.C. Torney.
  • Inference in forensic identification. DJB & P. Donnelly, J. Roy. Statist. Soc. A 158, 1995, pp 21-53; Discussion paper, read to the Society April 1994.
  • Efficient pooling designs for library screening. W.J. Bruno, E. Knill, D.C. Bruce, DJB, N.A. Doggett, W.W. Sawhill, R.L. Stallings, C.C. Whittaker & D.C. Torney, Genomics 26, pp 21-30, 1995.
  • A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. DJB & R.A. Nichols, Genetica 96, pp 3-12, 1995.   ERRATUM: Table 2 of this article contains an error: in case Mother = AA, Alleged Father = AB, and Child = AB the 2 in the numerator should be deleted, so that the correct LR is 2(F+(1-F)pB)/(1+3F).  This correction is now published in the journal: GENETICA 133(1) May 2008.
  • Estimating products in forensic identification using DNA profiles. DJB, J. Amer. Statist. Assoc. 90, pp 839-844, 1995.
  • Inferring identity from DNA profile evidence. DJB & P. Donnelly, Proc. Natl. Acad. Sci. USA 92, pp 11741-11745, 1995.
  • DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. DJB & R.A. Nichols, Forensic Sci. Inter., 64, pp 125-140, 1994.
  • How convincing is DNA evidence?. DJB & P. Donnelly, Nature, 368, pp 285-286, 24 March 1994.
  • Design and analysis of chromosome physical mapping experiments. DJB, Phil. Trans. Roy. Soc. B 244, pp 329-335, 1994.
  • The prosecutor's fallacy and DNA evidence. DJB & P. Donnelly, Crim. Law Rev., October 1994, pp 711-721.

1985 - 1993

  • Computations for mapping genomes with clones. C.C. Whittaker, M.O. Mundt, V. Faber, DJB, R.L. Dougherty, R.L. Stallings, S.W. White & D.C. Torney. Int. J. Genome Res., 1, pp 195-226, 1993.
  • Detecting gene conversion: Primate visual pigment genes. DJB & R.A. Nichols, & D. Hunt. Proc. Roy. Soc. B 249, pp 275-280, 1992.
  • Effects of population structure on DNA fingerprint analysis in forensic science. R.A. Nichols & DJB, Heredity, 66 pp 297-302, 1991.
  • Statistical analysis of fingerprint data for ordered clone physical mapping of human chromosomes. DJB & D.C. Torney, Bull. Math. Biol. 53, pp 853-879, 1991.
  • Diffusion-controlled reactions in one dimension: Exact solutions and deterministic approximations. DJB & N.J.B. Green, Phys. Rev. A 40, pp 4585-4592, 1989.
  • Invasion processes and binary annihilation in one dimension. DJB, P. Clifford & N.J.B. Green. Phys. Lett. A 126, pp 481-483, 1988.
  • Diffusion-reaction in one dimension. DJB, J. Appl. Prob. 25, pp 733-743, 1988.
  • Risk factors and heart disease mortality. H. Alexander, DJB, A. Dobson, R. Gibberd, D. Lloyd & S. Leeder, Med. J. Aust. 144, pp 20-22, 1986.
  • A mathematical model of tumour-induced capillary growth. DJB & D.L.S. McElwain. J. Theor. Biol. 114, pp 53-73, 1985.
 
last updated 4 August 2008.