Research Interests

Multiethnic cohort collection; influence of ethnicity on disease susceptibility/protection; evolutionary genetics; genetics of skin color; Amylase CNV genetics

Academic Appointments

2009 - present

Postdoctoral Scholar, Tishkoff Laboratory, University of Pennsylvania
Supervisor: Professor Sarah A. Tishkoff

  • Leader of sample collection arm of NIH Pioneer Award project
  • Led four field seasons, totalling 20+ months and enrolling 2,000+ participants, in Ethiopia, Tanzania, Botswana and Cameroon
  • Had major role in preparation and submission of IRB/ethics applications in both USA and host countries
  • Method development and logistics coordination for collection of multiple data and samples types in remote undeveloped areas
  •   DNA, RNA, plasma, saliva
  •   Cell lines - EBV and iPS
  •   Fecal samples for microbiome analysis
  •   Ethnographic and lifestyle data
  •   Various anthropometric data
  •   Challenge tests - glucose and lactose tolerance tests, and taste perception tests
  • Responsible for coordinating freight forwarding to sample location, and cold chain shipment of returning samples
  • Recruited and managed multiple small teams of research assistants
  • Coordinated collaborative research projects across a range of subjects and fields using collected samples (eg. microbiomics, metabolomics)
  • Analysed whole genome and 'SNP chip' data

2003 - 2008

Ph.D. Student, Centre for Cardiovascular Genetics, University College London
Supervisor: Prof Steve Humphries

  • British Heart Foundation student
  • Thesis title: Variation within the IL-18 system and its association with cardiovascular disease and obesity
  • Molecular biology laboratory skills: DNA extraction, high throughput genotyping
  • (PCR, RFLP, TaqMAN), sequencing, QPCR, tissue culture, DNase hypersensitivity assay, ELISA
  • Genetic association analysis at haplotypic and genotypic level
  • Basic population genetics comparing allele frequencies across multiple populations
  • Complex bioinformatics and data-mining

2002 - 2003

Research Assistant, MRC Prion Unit, University College London
Supervisor: Dr. Sarah Lloyd

  • Mouse colony organization and supervision
  • Use and maintenance of MegaBACE capillary genotypers/sequencers

Education

1998 - 2001

BSc Hons. Bristol University (Biochemistry) II.I
Supervisor: Prof George Banting

  • Wide-ranging genetics modules throughout
  • Final year project investigated sub-cellular localization of GFP-tagged membrane proteins.
  • Involved basic molecular biology and fluorescent confocal microscopy

Refereed Journal Publications

  • S.R. Thompson, S.E. Humphries, M.G. Thomas, R. Ekong, A. Tarekegn, E. Bekele, O. Creemer, N. Bradman, and K.R. Veeramah (2013) The frequency of an IL-18-associated haplotype in Africans. Eur J Hum Genet 21(4):465-468. doi:10.1038/ejhg.2012 184.
  • L.B. Scheinfeldt, S. Soi, S.R. Thompson, A. Ranciaro, D. Woldemeskel, W. Beggs, C. Lambert, J.P. Jarvis, D. Abate, G. Belay, S.A. Tishkoff (2012) Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biol. 13:R1 doi:10.1186/gb-2012-13-1-r1
  • S.R. Thompson, P.A. McCaskie, J.P. Beilby, J. Hung, M. Jennens, C. Chapman, P. Thompson, and S.E. Humphries (2007) IL18 haplotypes are associated with serum IL-18 concentrations in a population-based study and a cohort of individuals with prema-
    ture coronary heart disease. Clin Chem 53(12):2078-2085. doi:10.1373/clinchem.2007.092692
  • S.R. Thompson, D. Novick, C.J. Stock, J. Sanders, D. Brull, J. Cooper, P. Woo, G. Miller, M. Rubinstein, and S.E. Humphries (2007) Free interleukin (IL)-18 levels, and the impact of IL18 and IL18BP genetic variation, in CHD patients and healthy men. Arterioscler Thromb Vasc Biol 27(12):2743-2749. doi:10.1161/ATVBAHA.107.149245
  • S.R. Thompson, J. Sanders, J.W. Stephens, G.J. Miller, and S.E. Humphries (2007) A common interleukin-18 haplotype is associated with higher body mass index in subjectswith diabetes and coronary heart disease. Metabolism 56(5):662-669. doi:10.1016/j.metabol.2006.12.015
  • P.T. Wootton, N.L. Arora, F. Drenos, S.R. Thompson, J.A. Cooper, J.W. Stephens, S.J. Hurel, E. Hurt-Camejo, O. Wiklund, S.E. Humphries, and P.J. Talmud (2007) Tagging SNP haplotype analysis of the secretory PLA2-V gene, PLA2G5, shows strong association with LDL and oxLDL levels, suggesting functional distinction from sPLA2-IIA: Results from the UDACS study. Hum Mol Genet 16(12):1437-1444. doi:10.1093/hmg/ddm094
  • P.T. Wootton, F. Drenos, J.A. Cooper, S.R. Thompson, J.W. Stephens, E. Hurt-Camejo, O. Wiklund, S.E. Humphries, and P.J. Talmud (2006) Tagging-SNP haplotype analysis of the secretory PLA2IIa gene PLA2G2A shows strong association with serum levels of sPLA2IIa: results from the UDACS study. Hum Mol Genet 15(2):355-361. doi:10.1093/hmg/ddi453
  • S.E. Lloyd, S.R. Thompson, J.A. Beck, J.M. Linehan, J.D. Wadsworth, S. Brandner, J. Collinge, and E.M. Fisher (2004) Identification and characterization of a novel mouse prion gene allele. Mamm. Genome 15(5):383-389. doi:10.1007/s00335-004-3041-5

Articles in Press

  • M.C. Campbell, A. Ranciaro, D. Zinshteyn, R. Rawlings-Goss, J. Hirbo, S.R. Thompson, D. Woldemeskel, A. Froment, J.B. Rucker, S. Omar, J. Bodo, T. Nyambo, G. Belay, D. Drayna, P.A.S. Breslin, and S.A. Tishkoff (2013) Origin and differential selection of allelic variation at TAS2R16 associated with salicin bitter taste sensitivity in Africa. Mol Bio Evol

Articles in Preparation

  • S. Soi, L. Scheinfeldt, C. Lambert, A. Ranciaro, S.R. Thompson, J. Hirbo, W. Beggs, M. Ibrahim, T. Nyambo, S. Omar, C. Wambebe, D. Meskel, G. Belay, A. Froment, J. Kim, and S. Tishkoff. Genetic evidence supports common ancestry of geographically distant East African hunting-gathering populations.
  • L. Scheinfeldt, S. Soi, C. Lambert, D. Hu, A. Coulibaly, H. Hutton, C. Elbers, W. Ko, W. Beggs, A. Ranciaro, S.R. Thompson, J. Hirbo, J.M. Bodo, O. Doumbo, M. Ibrahim, A. Froment, G. Lema, T. Nyambo, S. Omar, C. Wambebe, D. Meskel, G. Belay, and S. Tishkoff. Genome-wide signatures of positive selection in diverse African populations provide insight into local adaptation and pathogen resistance

Conferences

2010

American Society of Human Genetics, Annual Meeting, Washington DC, Delegate

2007

[European Atherosclerosis Society, Summer Conference, Helsinki, Poster Presentation

2006

International Atherosclerosis Society, Summer Conference, Rome, Oral Presentation

2005

European Atherosclerosis Society, Summer Conference 2005, Prague, Poster Presentation

2004

Genomes to Systems, Manchester, Delegate

2004-2007

British Atherosclerosis Society, numerous conferences, Delegate and Poster Presentation

Book Chapters

  • S.R. Thompson and S.E. Humphries (2007) Familiäre belastung [family history]. In P Schwandt and K.G. Parhofer, editors, Handbuch der Fettstoffwechselstörungen [Handbook of fat metabolism disorders] vol. 3.

Review Articles

  • S.R. Thompson and S.E. Humphries (2007) Interleukin-18 genetics and inflammatory disease susceptibility. Genes Immundoi:10.1038/sj.gene.6364366

Grants

2003, British Heart Foundation, Was granted a BHF PhD studentship following preparation and submission of a grant application assessing the role of variation with IL18 on cardiovascular disease.

Teaching Experience

2006, 2007: Summer School, Lectured and taught a workshop on linkage disequilibrium to first year PhD students

Computer Skills

 

Data Analysis:

  • R - mathematical programming language
  • SPSS - basic statistics and data manipulation
  • REST - QPCR data analysis using Pfaffl exact method
  • CNV analysis
 

Haplotype and SNP Analysis:

  • EMMAX - GWAS analysis in multiethnic cohorts
  • Thesias and SimHap - haplotype-based association analysis
  • Arlequin - general population genetics (AMOVA, Mantel test etc.)
  • PHASE and PL-EM - haplotype inference
  • Haploview - linkage disequilibrium visualization
  • BEST and STRAM - tSNP selection
 

Programming Languages:

  • Python
  • Bash
 

Bioinformatics:

  • UCSC Genome Browser, Ensembl, cisRED, VISTA, HapMap, SNPper, TransFac, db-SNP
 

Miscellaneous

  • Adobe Illustrator and Photoshop - Vector graphics and image manipulation
  • Microsoft Word, Excel, and Powerpoint
  • LATEX- complex document preparation

Personal Interests

I enjoy cycle touring and recently spent five months cycling and trekking through south America. Prior to this, in 2008–2009, I cycled from England to Kenya over six months raising money to build a school in Kenya.

I also enjoy swimming, photography, and spending time walking in the outdoors