Colin Semple Research Group

Origins and Impacts of Structural Mutations

Professor Colin Semple

Group leader and Head of Bioinformatics

Contact details

Research in a Nutshell 

The emergence of widespread whole genome sequencing has revealed a vast layer of structural mutations: deletions, duplications and other rearrangements of the human genome. These structural alterations affect more of the genome than the short variants that are more familiar but their effects on gene function are poorly understood. We study these alterations in the germline and early embryo, where they can disrupt developmental expression patterns, and also in tumours where complex structural rearrangements can drive cancer progression. We have a particular focus on the chaotic mutational landscapes that evolve in many cancers of unmet need (such as ovarian cancer, glioblastoma and mesothelioma) where tumour genomes become dramatically rearranged. With our clinical collaborators we explore the consequences of these rearrangements for tumour biology and cancer patient outcomes; motivated by four questions. What are the origins of structural mutations? How do they impact gene function? How does structural complexity drive disease progression? How do the diverse constellations of mutations evolving at different scales in tumours combine to create adaptations and vulnerabilities?

People

NameRole
Professor Colin SempleGroup leader and Head of Bioinformatics
Dr Stuart AitkenBioinformatician
Dr Vera KaiserBioinformatician
Dr Devin BendixsenBioinformatician
Matthew BrownPhD student
Ryan SilkPhD student
Scott PirriePhD student
Simon TimminsPhD Student
Alhafidz HamdanECAT fellow
Edward Esiri-BloomCRUK TRACC Fellow

Bioinformatics Analysis Core

NameRole
Dr Jing SuInstitute of Genetics and Cancer Bioinformatics Analysis Core Manager
Dr Philippe GautierBioinformatician
Mr Graeme GrimesBioinformatician
Dr Mihail HalachevNHS/Institute of Genetics and Cancer Translational Bioinformatician
Kevin DonnellyBioinformatician
Murray WhamBioinformatician
Steve FoxInstitute of Genetics and Cancer Data Manager
Hywel Dunn-DaviesInstitute of Genetics and Cancer Statistician

External Links

Key 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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