Royal College of Surgeons in Ireland Coláiste Ríoga na Máinleá in Éirinn

FUNDED PhD: Dr Simon Furney - Cancer Genomics and Bioinformatics

This PhD project will investigate mutational rates and signatures in cancer genomes to identify novel cancer genes and mechanisms of tumour development and evolution.

Project title

Bioinformatic identification of mechanisms of tumour development and evolution from cancer genome sequencing data.

Project description

Genome and exome sequencing studies have confirmed vast heterogeneity in mutational rates and signatures in cancer genomes. For example, colorectal cancer genomes with mutations in mismatch repair genes show high mutational burdens.Tumours exposed to mutagenic environmental factors such as ultraviolet light in melanomas and tobacco smoke in lung cancers also have elevated mutation rates.

This PhD project will investigate mutational rates and signatures in cancer genomes to identify novel cancer genes and mechanisms of tumour development and evolution.

The student will probe thousands of publically available cancer genome sequences using existing and novel bioinformatics approaches. The project builds on the Principal Investigator’s expertise in Bioinformatics, Cancer gene prioritization and Next Generation Sequencing Data analysis [1-7] and will be based in the Cancer Genomics & Bioinformatics Research Group under the supervision of Dr Simon Furney.

The successful candidate should be able to demonstrate the following: 

Essential

  • An Honours Bachelor degree (First Class OR very good Upper Second Class degree) in Genomics, Genetics or Bioinformatics or similar subject

  • A passion for biology and genomics

  • Strong interest in cancer research

  • Expertise in/aptitude for programming and scripting

  • Good communication skills

  • Strong organisational and administrative skills

  • Ability to work on one’s own initiative as well as in a multidisciplinary, team environment

  • Willingness to undertake training and career development

  • English language requirements for candidates who do not speak English as their first language: an IELTS score of 6.5 or above

Desirable

  • MSc in Bioinformatics or Computational Biology

  • An aptitude for mathematics/statistics

Application process

Please apply with an up-to-date CV, a 500-word statement outlining your interest in and suitability for the position, complete the application form and go to the RCSI School of Postgraduate Studies recruitment portal to apply for this scholarship.

Informal enquiries can be directed to simonfurney@rcsi.ie.

 

Application deadline: Friday, 21 April 2017 at 5pm.

Interview date: early May 2017

 

  • Department: Physiology and Medical Physics

  • Tenure: Four years

  • Reporting to: Dr Simon Furney

  • Salary: €18,000/year (plus fees) for up to a maximum of four years. 

  • Start date: October 2017

References
  1. Furney SJ, Calvo B, Larranaga P, Lozano JA, Lopez-Bigas N: Prioritization of candidate cancer genes--an aid to oncogenomic studies. Nucleic Acids Res 2008, 36(18):e115.

  2. Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N: IntOGen: integration and data mining of multidimensional oncogenomic data. Nat Methods 2010, 7(2):92-93.

  3. Turajlic S, Furney SJ, Lambros MB, Mitsopoulos C, Kozarewa I, Geyer FC, Mackay A, Hakas J, Zvelebil M, Lord CJ et al: Whole genome sequencing of matched primary and metastatic acral melanomas. Genome Res 2012, 22(2):196-207.

  4. Furney SJ, Pedersen M, Gentien D, Dumont AG, Rapinat A, Desjardins L, Turajlic S, Piperno-Neumann S, de la Grange P, Roman-Roman S et al: SF3B1 mutations are associated with alternative splicing in uveal melanoma. Cancer Discov 2013, 3(10):1122-1129.

  5. Turajlic S, Furney SJ, Stamp G, Rana S, Ricken G, Oduko Y, Saturno G, Springer C, Hayes A, Gore M et al: Whole-genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition. Ann Oncol 2014, 25(5):959-967.

  6. Viros A, Sanchez-Laorden B, Pedersen M, Furney SJ, Rae J, Hogan K, Ejiama S, Girotti MR, Cook M, Dhomen N et al: Ultraviolet radiation accelerates BRAF-driven melanomagenesis by targeting TP53. Nature 2014, 511(7510):478-482.

  7. Piraino SW and Furney SJ. Identification of coding and non-coding mutational hotspots in cancer genomes. BMC Genomics, 2017, 5;18(1):17.

Mentors Dr Simon Furney