Work Summary:

I previously worked on the analysis of data from the International HapMap Project and the Wellcome Trust Case Control Consortium. As part of Peter Donnelly’s group, I am now analysing 15 association studies exploring both disease and nondisease phenotypes. Although most of these studies are of non-infectious disease in Europeans, we are also looking at communicable disease susceptibility in Asian, South American and African populations.

In parallel, I am working with Dominic Kwiatkowski on genetic susceptibility to severe malaria in Africa. By combining results from these studies with other large-scale population data, I hope to gain insights into disease mechanisms and the evolutionary processes influencing the distribution of genetic risk factors across populations.

Software

Aberrant is a R package for automatically indentiying outliers from otherwise Guassian distributions. It is designed for excluding samples from genome-wide association studies which have summary statistics of variation which differ from the sample at large.

Celine Bellenguez, Amy Strange, Colin Freeman, Wellcome Trust Case Control Consortium 2, Peter J Donnelly and Chris CA Spencer. (2011) A robust clustering algorithm for identifying problematic samples in genome-wide association studies. Sumbitted

Download : aberrant_1.0.tar.gz

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SelSim is a command line program for simulating data from the coalescent with recombination and a single locus under natural selection. Both stochastic and deterministic models of selection are available. The program is no longer supported.

Spencer C., Coop, G. (2005)  SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics. 2004 Dec 12;20(18):3673-5.

Website : SelSim

Selected Publications:

C.C.Spencer et al. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 2009 May;5(5):e1000477

Spencer, Chris CA (July 2008) Recombination and Human Genetic Diversity. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd:Chichester.

McVean, G. and C.C. Spencer, Scanning the human genome for signals of selection. Curr Opin Genet Dev, 2006. 16(6): p. 624-9.

Spencer, C.C., Human polymorphism around recombination hotspots. Biochem Soc Trans, 2006. 34(Pt 4): p. 535-6.

Myers, S., et al., The distribution and causes of meiotic recombination in the human genome. Biochem Soc Trans, 2006. 34(Pt 4): p. 526-30.

Spencer, C.C., et al., The influence of recombination on human genetic diversity. PLoS Genet, 2006. 2(9): p. e148.

Spencer, C.C. and G. Coop, SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics, 2004. 20(18): p. 3673-5.

Hanchard, N.A., et al., Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet, 2006. 78(1): p. 153-9.

Consotrium Publications:

Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet, 2008. Sep;40(9):1053-5

The Wellcome Trust Cases-Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 2007. 447(7145): p. 661-78.

The Wellcome Trust Cases-Control Consortium, et al., Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet, 2007. 39(11): p. 1329-37.

The International HapMap Consortium, A second generation human haplotype map of over 3.1 million SNPs. Nature, 2007. 449(7164): p. 851-61.

The DNA sequence and biological annotation of human chromosome 1. Nature, 2006. 441(7091):315-21

The International HapMap Consortium, A haplotype map of the human genome. Nature, 2005. 437(7063): p. 1299-320.

Keywords

• Genome-Wide Association Studies
• Population Genetics
• Bayesian Statistics