Alice Mann | PhD Student

Mann, Alice

Alice is a PhD student in Professor Nicole Soranzo's team. Alice's project combines wetlab and computational approaches to investigate the functional impact of genetic variation in haematopoietic cells. Through integrating genome-wide association studies with epigenome datasets, she hopes to better understand the mechanisms of regulatory variation in particular immune cells, such as neutrophils, monocytes and T cells.

I started as a PhD student in the WTSI PhD programme in October 2013 and began my PhD project with Professor Nicole Soranzo in May 2014. My main interest is in understanding the effect of variation in regulatory features of the genome such as active enhancers. With a background in molecular and cellular Biochemistry, I am to use my understanding of the biology behind transcription and gene regulation to investigate the mechanism of potential causal regulatory variants. Using these different approaches I hope to answer the following key questions:

  • Are cell-type specific regulatory features enriched in variants that may play a role in those particular cell-types and can this enrichment indicate which variants are functional and the potential mode of action?
  • Are these regulatory features enriched in disease-associated variants?
  • Can we identify genetic variants that are directly linked to cell-function by analysing neutrophil-specific quantitative trait loci (QTL) data?
  • Can we integrate data from a variety of projects such as the Blueprint consortium, INTERVAL and UK Biobank to identify potential causal variants and further define the mechanism of action using a detailed experimental follow-up approach?

The skills involved in addressing these questions involve the analysis of genetic data as well as experimental genomics approaches such as RNA-seq and ChIP-seq.

Publications

  • From GWAS to function: lessons from blood cells.

    Vasquez LJ, Mann AL, Chen L and Soranzo N

    ISBT science series 2016;11;Suppl Suppl 1;211-219

  • The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

    Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D et al.

    Cell 2016;167;5;1415-1429.e19

  • Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

    Chen L, Ge B, Casale FP, Vasquez L, Kwan T et al.

    Cell 2016;167;5;1398-1414.e24

  • Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

    Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM et al.

    Genome biology 2017;18;1;18

  • Common genetic variation drives molecular heterogeneity in human iPSCs.

    Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K et al.

    Nature 2017;546;7658;370-375

Mann, Alice
Alice's Timeline
2014

Joined Human Complex Traits Group for PhD project

2013

WTSI PhD Programme

Master of Biochemistry, University of Oxford

2010

Year In Industry Student at TTP LabTech