MRC Human Genetics Unit
Medical Research Council Human Genetics Unit
MRC Human Genetics Unit
Institute of Genetics and Cancer
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Colin Semple Research Group

Origins and Impacts of Regulatory Mutations

C.Semple group
Professor Colin Semple - Group leader and Head of Bioinformatics

Section: Biomedical Genomics

Research in a Nutshell 

The genes embedded in your genome have complex patterns of activity and particular constellations of genes must be active at particular times for biological processes, such as embryonic development, to conclude successfully. I am interested in the fundamental biology of gene regulation: when, how and why genes are turned on and off. We try to understand the mechanisms underlying gene regulation, using computational analyses of genomic datasets. This can provide new insights into human evolution and help us interpret disease processes with aberrant regulation, such as cancers and developmental disorders. We focus on relatively poorly studied cancers, such as ovarian cancer and the brain cancer glioblastoma, where the tumour genomes become dramatically rearranged as they evolve during disease progression. With our clinical and experimental collaborators we explore the consequences of these rearrangements for gene functions, and for cancer patient outcomes. The aim is to better understand tumour biology, to reveal new vulnerabilities that can be targeted in cancer treatments.

Group External Website

People

  
Professor Colin Semple Group leader and Head of Bioinformatics
Dr Stuart Aitken    Bioinformatician
Dr Vera Kaiser  Bioinformatician
Dr Devin Bendixsen Bioinformatician

Matthew Brown

 PhD student
Ryan Silk PhD student
Scott Pirrie PhD student
Alhafidz Hamdan ECAT fellow
Mitchell Foster ECAT fellow
Edward Esiri-Bloom CRUK TRACC Fellow

Bioinformatics Analysis Core

  
Dr Alison Meynert Institute of Genetics and Cancer Bioinformatics Analysis Core Manager
Dr Philippe Gautier  Bioinformatician
Mr Graeme Grimes Bioinformatician
Dr Mihail Halachev  NHS/Institute of Genetics and Cancer Translational Bioinformatician
Hannes Becher Institute of Genetics and Cancer Statistician
Murray Wham Bioinformatician

Contact

Colin.Semple@ed.ac.uk

Publications

  1. Kaiser VB, Talmane L, Kumar Y, Semple F, MacLennan M, DDD Study, FitzPatrick DR, Taylor MS*, Semple CA*. (2021) Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome. Genome Research 31: 1-14.
  2. Ewing A, Meynert A, Churchman M, Grimes GR, Hollis RL, Herrington CS, Rye T, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Dowson S, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D, McMahon L, Matakidou A, Dougherty B, March R, Barrett JC, McNeish IA, SGP, Biankin AV, Roxburgh P, Gourley C*, Semple CA*. (2021) Structural variants at the BRCA1/2 loci   are a common source of homologous repair deficiency in high grade serous ovarian carcinoma. Clinical Cancer Research 27: 3201-3214.
  3. Aitken SA, Anderson CJ, Connor F, Pich O, Sundaram V, Feig C, Rayner TF, Lukk M,   Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes S, Davies SE, Drews RM, Ewing A, Kaiser VB, Khamseh A, Lopez-Arribillaga E, Redmond AM, Santoyo-Lopez J, Sentis I, Talmane L, Yates AD, Semple CA, Lopez- Bigas N, Flicek P, Odom DT, Taylor MS. (2020) Pervasive lesion segregation shapes cancer genome evolution. Nature 583: 265-270.
  4. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature 578: 82-93.
  5. Ballinger TJ, Bouwman BAM, Mirzazadeh R, Garnerone S, Crosetto N, Semple CA. (2019) Modeling double strand break susceptibility to interrogate structural variation in cancer. Genome Biology 20:28.

Full publication list can be found on Research Explorer: Colin Semple — University of Edinburgh Research Explorer

Collaborations

  • Professor Wendy Bickmore, MRC Human Genetics Unit
  • Professor Malcolm Dunlop, MRC Human Genetics Unit
  • Professor David Fitzpatrick, MRC Human Genetics Unit
  • Professor Chris Haley, MRC Human Genetics Unit
  • Professor Martin Taylor, MRC Human Genetics Unit
  • Dr Nicola Crosetto, Karolinska Institute, Sweden
  • Professor Charlie Gourley, Cancer Research UK Edinburgh Centre
  • Professor Piero Carninci, RIKEN  Center for Life Science Technologies, Japan

Partners and Funders

Scientific Themes

Medical Genomics, Bioinformatics, Transcriptomics, Epigenomics

Technology Expertise

Computational Biology

 

 
 
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