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Researchers at UCD

Simon Furney

Conway Institute of Biomolecular & Biomedical Research

Tel:
Email: simon.furney@ucd.ie

Biography

Independent  Senior Research Fellow in Cancer Genomics, School of Medicine and Medical Science, University College Dublin, from May 1st 2014.
 
 I am funded by a European Commission Marie Curie Fellowship. My research focuses on Evolutionary Cancer Genomics and Personalised Medicine.

 

Senior Post-doctoral Scientist in Cancer Genomics, Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, UK, October 2012 - April 2014. Principal Investigator: Prof. Richard Marais.

 

I led the analysis of a number of next generation sequencing projects in the Molecular Oncology Group to identify potential oncogenic somatic variants in cutaneous and rare melanomas. This has involved the analysis of whole genome sequences from >60 samples, whole exome sequences from >250 samples and integration with RNA-seq and SNP array data. In addition I am using next generation sequencing data to identify mechanisms of resistance to drugs in tumours, and to understand tumour heterogeneity. As well as the publications listed in my CV, I have several other manuscripts in preparation from this work.

 

Post-doctoral Fellow in Cancer Genomics, Signal Transduction Team, Institute of Cancer Research London, November 2010 - September 2012. Principal Investigator: Prof. Richard Marais.

 

I led next generation sequencing projects in the Signal Transduction Team to identify potential oncogenic somatic variants in cutaneous and rare melanomas. The work I undertook at the Institute of Cancer Research has resulted in five peer-reviewed research articles to date (four as first author).

                                                                      

Post-doctoral bioinformatician, National Institute for Health Research Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, July 2008 - October 2010. Principal Investigator: Prof. Simon Lovestone.

 

In this position I was responsible for the integration of large-scale patient data in Alzheimer's disease to identify causative genetic variants and predictive biomarkers. I analysed >1000 samples in an imaging-genetics study, and combined gene expression and neuroimaging data, proteomics and imaging data, and gene expression and genetic data (eQTL analysis) in other projects. My research in this field has resulted in nine peer-reviewed research articles to date (three as first author).

 

Postdoctoral researcher, Biomedical Genomics Group, University Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), March 2007- April 2008. Principal Investigator: Prof. Nuria Lopez-Bigas.

 

In this post I conducted in silico prediction of cancer genes, prioritisation of candidate cancer genes using public data, and integration of expression and aCGH data from tumour samples, resulting in the publication of two peer-reviewed research articles (one as first author) and a first author review article.

 

 

Publications

     

Peer Reviewed Journals

Nho K, Kim S, Risacher SL, Shen L, Corneveaux JJ, Swaminathan S, Lin H, Ramanan VK, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR Jr, Weiner MW, Baldwin CT, Lunetta KL, Farrer LA; MIRAGE (Multi-Institutional Research on Alzheimer Genetic Epidemiology) Study, Furney SJ, Lovestone S, Simmons A, Mecocci P, Vellas B, Tsolaki M, Kloszewska I, Soininen H; AddNeuroMed Consortium, McDonald BC, Farlow MR, Ghetti B; Indiana Memory and Aging Study, Huentelman MJ, Saykin AJ; Alzheimer's Disease Neuroimaging Initiative. (2015) 'Protective variant for hippocampal atrophy identified by whole exome sequencing'. Annals of Neurology, . [Details]
Korfi K, Mandal A, Furney SJ, Wiseman D, Somervaille TC, Marais R (2015) 'A personalised medicine approach for ponatinib-resistant chronic myeloid leukaemia'. Annals of Oncology, . [Details]
Viros A, Sanchez-Laorden B, Pedersen M, Furney SJ, Rae J, Hogan K, Ejiama S, Girotti MR, Cook M, Dhomen N, Marais R (2014) 'Ultraviolet radiation accelerates BRAF-driven melanomagenesis by targeting TP53'. Nature, . [Details]
Furney SJ, Turajlic S, Stamp G, Meirion Thomas J, Hayes A, Strauss D, Gavrielides M, Xing W, Gore M, Larkin J, Marais R (2014) 'The mutational burden of acral melanoma revealed by whole genome sequencing and comparative analysis'. Pigment Cell & Melanoma Research, . [Details]
Turajlic, S., Furney, S. J., Stamp, G., Rana, S., Ricken, G., Oduko, Y., Saturno, G., Springer, C., Hayes, A., Gore, M., Larkin, J., Marais, R. (2014) 'Whole-genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition'. Ann Oncol, 25 (5):959-67. Available Online [Details]
Killick, R., Ribe, E. M., Al-Shawi, R., Malik, B., Hooper, C., Fernandes, C., Dobson, R., Nolan, P. M., Lourdusamy, A., Furney, S., Lin, K., Breen, G., Wroe, R., To, A. W., Leroy, K., Causevic, M., Usardi, A., Robinson, M., Noble, W., Williamson, R., Lunnon, K., Kellie, S., Reynolds, C. H., Bazenet, C., Hodges, A., Brion, J. P., Stephenson, J., Simons, J. P., Lovestone, S. (2014) 'Clusterin regulates beta-amyloid toxicity via Dickkopf-1-driven induction of the wnt-PCP-JNK pathway'. Mol Psychiatry, 19 (1):88-98. Available Online [Details]
Proitsi, P., Lee, S. H., Lunnon, K., Keohane, A., Powell, J., Troakes, C., Al-Sarraj, S., Furney, S., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Lovestone, S., Hodges, A., AddNeuroMed, Consortium (2014) 'Alzheimer's disease susceptibility variants in the MS4A6A gene are associated with altered levels of MS4A6A expression in blood'. Neurobiol Aging, 35 (2):279-90. Available Online [Details]
Furney, S. J., Pedersen, M., Gentien, D., Dumont, A. G., Rapinat, A., Desjardins, L., Turajlic, S., Piperno-Neumann, S., de la Grange, P., Roman-Roman, S., Stern, M. H., Marais, R. (2013) 'SF3B1 mutations are associated with alternative splicing in uveal melanoma'. Cancer Discov, 3 (10):1122-9. Available Online [Details]
Nho, K., Corneveaux, J. J., Kim, S., Lin, H., Risacher, S. L., Shen, L., Swaminathan, S., Ramanan, V. K., Liu, Y., Foroud, T., Inlow, M. H., Siniard, A. L., Reiman, R. A., Aisen, P. S., Petersen, R. C., Green, R. C., Jack, C. R., Weiner, M. W., Baldwin, C. T., Lunetta, K., Farrer, L. A., Multi-Institutional Research on Alzheimer Genetic Epidemiology, Study, Furney, S. J., Lovestone, S., Simmons, A., Mecocci, P., Vellas, B., Tsolaki, M., Kloszewska, I., Soininen, H., AddNeuroMed, Consortium, McDonald, B. C., Farlow, M. R., Ghetti, B., Indiana, Memory, Aging, Study, Huentelman, M. J., Saykin, A. J., Alzheimer's Disease Neuroimaging, Initiative (2013) 'Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in mild cognitive impairment'. Mol Psychiatry, 18 (7):781-7. Available Online [Details]
Nho, K., Corneveaux, J. J., Kim, S., Lin, H., Risacher, S. L., Shen, L., Swaminathan, S., Ramanan, V. K., Liu, Y., Foroud, T., Inlow, M. H., Siniard, A. L., Reiman, R. A., Aisen, P. S., Petersen, R. C., Green, R. C., Jack, C. R., Weiner, M. W., Baldwin, C. T., Lunetta, K., Farrer, L. A., Multi-Institutional Research on Alzheimer Genetic Epidemiology, Study, Furney, S. J., Lovestone, S., Simmons, A., Mecocci, P., Vellas, B., Tsolaki, M., Kloszewska, I., Soininen, H., AddNeuroMed, Consortium, McDonald, B. C., Farlow, M. R., Ghetti, B., Indiana, Memory, Aging, Study, Huentelman, M. J., Saykin, A. J., Alzheimer's Disease Neuroimaging, Initiative (2013) 'Identification of functional variants from whole-exome sequencing, combined with neuroimaging genetics'. Mol Psychiatry, 18 (7). Available Online [Details]
Lunnon, K., Sattlecker, M., Furney, S. J., Coppola, G., Simmons, A., Proitsi, P., Lupton, M. K., Lourdusamy, A., Johnston, C., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Geschwind, D., Lovestone, S., Dobson, R., Hodges, A., dNeuroMed, Consortium (2013) 'A blood gene expression marker of early Alzheimer's disease'. J Alzheimers Dis, 33 (3):737-53. Available Online [Details]
Furney, S. J., Turajlic, S., Stamp, G., Nohadani, M., Carlisle, A., Thomas, J. M., Hayes, A., Strauss, D., Gore, M., van den Oord, J., Larkin, J., Marais, R. (2013) 'Genome sequencing of mucosal melanomas reveals that they are driven by distinct mechanisms from cutaneous melanoma'. J Pathol, 230 (3):261-9. Available Online [Details]
Furney, S. J., Turajlic, S., Fenwick, K., Lambros, M. B., MacKay, A., Ricken, G., Mitsopoulos, C., Kozarewa, I., Hakas, J., Zvelebil, M., Lord, C. J., Ashworth, A., Reis-Filho, J. S., Herlyn, M., Murata, H., Marais, R. (2012) 'Genomic characterisation of acral melanoma cell lines'. Pigment Cell Melanoma Res, 25 (4):488-92. Available Online [Details]
Turajlic, S., Furney, S. J., Lambros, M. B., Mitsopoulos, C., Kozarewa, I., Geyer, F. C., Mackay, A., Hakas, J., Zvelebil, M., Lord, C. J., Ashworth, A., Thomas, M., Stamp, G., Larkin, J., Reis-Filho, J. S., Marais, R. (2012) 'Whole genome sequencing of matched primary and metastatic acral melanomas'. Genome Res, 22 (2):196-207. Available Online [Details]
Furney, S. J., Gundem, G., Lopez-Bigas, N. (2012) 'Oncogenomics methods and resources'. Cold Spring Harb Protoc, 2012 (5). Available Online [Details]
Natrajan, R., Mackay, A., Lambros, M. B., Weigelt, B., Wilkerson, P. M., Manie, E., Grigoriadis, A., A'Hern, R., van der Groep, P., Kozarewa, I., Popova, T., Mariani, O., Turajlic, S., Furney, S. J., Marais, R., Rodruigues, D. N., Flora, A. C., Wai, P., Pawar, V., McDade, S., Carroll, J., Stoppa-Lyonnet, D., Green, A. R., Ellis, I. O., Swanton, C., van Diest, P., Delattre, O., Lord, C. J., Foulkes, W. D., Vincent-Salomon, A., Ashworth, A., Henri Stern, M., Reis-Filho, J. S. (2012) 'A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers'. J Pathol, 227 (1):29-41. Available Online [Details]
Lunnon, K., Ibrahim, Z., Proitsi, P., Lourdusamy, A., Newhouse, S., Sattlecker, M., Furney, S., Saleem, M., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Coppola, G., Geschwind, D., Simmons, A., Lovestone, S., Dobson, R., Hodges, A., AddNeuroMed, Consortium (2012) 'Mitochondrial dysfunction and immune activation are detectable in early Alzheimer's disease blood'. J Alzheimers Dis, 30 (3):685-710. Available Online [Details]
Furney, S. J., Kronenberg, D., Simmons, A., Guntert, A., Dobson, R. J., Proitsi, P., Wahlund, L. O., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Spenger, C., Lovestone, S. (2011) 'Combinatorial markers of mild cognitive impairment conversion to Alzheimer's disease--cytokines and MRI measures together predict disease progression'. J Alzheimers Dis, 26 Suppl 3 :395-405. Available Online [Details]
Furney, S. J., Simmons, A., Breen, G., Pedroso, I., Lunnon, K., Proitsi, P., Hodges, A., Powell, J., Wahlund, L. O., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Spenger, C., Lathrop, M., Shen, L., Kim, S., Saykin, A. J., Weiner, M. W., Lovestone, S., Alzheimer's Disease Neuroimaging, Initiative, AddNeuroMed, Consortium (2011) 'Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease'. Mol Psychiatry, 16 (11):1130-8. Available Online [Details]
Gundem, G., Perez-Llamas, C., Jene-Sanz, A., Kedzierska, A., Islam, A., Deu-Pons, J., Furney, S. J., Lopez-Bigas, N. (2010) 'IntOGen: integration and data mining of multidimensional oncogenomic data'. Nat Methods, 7 (2):92-3. Available Online [Details]
Thambisetty, M., Simmons, A., Velayudhan, L., Hye, A., Campbell, J., Zhang, Y., Wahlund, L. O., Westman, E., Kinsey, A., Guntert, A., Proitsi, P., Powell, J., Causevic, M., Killick, R., Lunnon, K., Lynham, S., Broadstock, M., Choudhry, F., Howlett, D. R., Williams, R. J., Sharp, S. I., Mitchelmore, C., Tunnard, C., Leung, R., Foy, C., O'Brien, D., Breen, G., Furney, S. J., Ward, M., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Hodges, A., Murphy, D. G., Parkins, S., Richardson, J. C., Resnick, S. M., Ferrucci, L., Wong, D. F., Zhou, Y., Muehlboeck, S., Evans, A., Francis, P. T., Spenger, C., Lovestone, S. (2010) 'Association of plasma clusterin concentration with severity, pathology, and progression in Alzheimer disease'. Arch Gen Psychiatry, 67 (7):739-48. Available Online [Details]
Furney, S. J., Calvo, B., Larranaga, P., Lozano, J. A., Lopez-Bigas, N. (2008) 'Prioritization of candidate cancer genes--an aid to oncogenomic studies'. Nucleic Acids Res, 36 (18). Available Online [Details]
Furney, S. J., Madden, S. F., Kisiel, T. A., Higgins, D. G., Lopez-Bigas, N. (2008) 'Distinct patterns in the regulation and evolution of human cancer genes'. In Silico Biol, 8 (1):33-46. Available Online [Details]
Calvo, B., Lopez-Bigas, N., Furney, S. J., Larranaga, P., Lozano, J. A. (2007) 'A partially supervised classification approach to dominant and recessive human disease gene prediction'. Comput Methods Programs Biomed, 85 (3):229-37. Available Online [Details]
Furney, S. J.,Higgins, D. G.,Ouzounis, C. A.,Lopez-Bigas, N.; (2006) 'Structural and functional properties of genes involved in human cancer'. BMC Genomics, 7 . [Details]
Furney, S. J., Alba, M. M., Lopez-Bigas, N. (2006) 'Differences in the evolutionary history of disease genes affected by dominant or recessive mutations'. BMC Genomics, 7 . Available Online [Details]
                                                                                             

Research

Research Interests

Cancer Genomics and Bioinformatics, in particular the use of Next Generation Sequencing technologies in Cancer, such as Whole Genome Sequencing, Whole Exome Sequencing and RNA-seq.

Evolutionary Cancer Genomics.

Personalised Cancer Medicine.

Students:

Scott Piraino.