Dr Susie Cooke

  • Head of Medical Genomics- Glasgow Precision Oncology Laboratory (Translational Research Centre)

Biography

Susie is a biologist turned bioinformatician whose main interest is in facilitating the move of next-generation sequencing into the clinic to help cancer patients. She completed a PhD in cancer genomics at the University of Cambridge and worked for Cancer Research UK, the Wellcome Trust Sanger Institute and in the biotech industry before moving to University of Glasgow. Susie now leads the Medical Genomics arm of the Glasgow Precision Oncology Laboratory, including overseeing the high-throughput sequencing and bioinformatics teams. Her main research focus is the development of clinical-grade analysis pipelines to allow custom oncology sequencing assays to be used safely in clinical trials and clinical practice.


Publications

List by: Type | Date

Jump to: 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006
Number of items: 36.

2019

Dreyer, S.B., Jamieson, N.B. , Cooke, S.L. , Valle, J.W., McKay, C.J., Biankin, A.V. and Chang, D.K. (2019) PRECISION-Panc: the next generation therapeutic development platform for pancreatic cancer. Clinical Oncology, (doi:10.1016/j.clon.2019.07.011) (PMID:31378449) (In Press)

Dreyer, S. B. et al. (2019) Feasibility and clinical utility of endoscopic ultrasound guided biopsy of pancreatic cancer for next-generation molecular profiling. Chinese Clinical Oncology, 8(2), 16. (doi:10.21037/cco.2019.04.06) (PMID:31070037)

2018

Dreyer, S. B. et al. (2018) Precision oncology in surgery: patient selection for operable pancreatic cancer. Annals of Surgery, (doi:10.1097/SLA.0000000000003143) (PMID:30570546) (Early Online Publication)

2017

Cooke, S. L. et al. (2017) The driver mutational landscape of ovarian squamous cell carcinomas arising in mature cystic teratoma. Clinical Cancer Research, 23(24), pp. 7633-7640. (doi:10.1158/1078-0432.CCR-17-1789) (PMID:28954785)

Behjati, S. et al. (2017) Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma. Nature Communications, 8(1), 15936. (doi:10.1038/ncomms15936) (PMID:28643781) (PMCID:PMC5490007)

2016

Behjati, S. et al. (2016) Mutational signatures of ionizing radiation in second malignancies. Nature Communications, 7(1), 12605. (doi:10.1038/ncomms12605) (PMID:27615322) (PMCID:PMC5027243)

Shlien, A. et al. (2016) Direct transcriptional consequences of somatic mutation in breast cancer. Cell Reports, 16(7), pp. 2032-2046. (doi:10.1016/j.celrep.2016.07.028) (PMID:27498871) (PMCID:PMC4987284)

Greenman, C. D., Cooke, S.L. , Marshall, J., Stratton, M. R. and Campbell, P. J. (2016) Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process. Journal of Mathematical Biology, 72(1-2), pp. 47-86. (doi:10.1007/s00285-015-0875-2)

2015

Cooper, C. S. et al. (2015) Erratum: Corrigendum: Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47(6), p. 689. (doi:10.1038/ng0615-689b) (PMID:26018901)

Kemp, C. et al. (2015) Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis. PLoS Medicine, 12(2), e1001789. (doi:10.1371/journal.pmed.1001789) (PMID:25710373) (PMCID:PMC4339382)

Cooper, C. S. et al. (2015) Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47(4), pp. 367-372. (doi:10.1038/ng.3221) (PMID:25730763) (PMCID:PMC4380509)

2014

Tubio, J.M.C. et al. (2014) Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science, 345(6196), p. 1251343. (doi:10.1126/science.1251343) (PMID:25082706) (PMCID:PMC4380235)

Cooke, S. L. et al. (2014) Processed pseudogenes acquired somatically during cancer development. Nature Communications, 5, 3644. (doi:10.1038/ncomms4644) (PMID:24714652) (PMCID:PMC3996531)

Behjati, S. et al. (2014) Recurrent PTPRB and PLCG1 mutations in angiosarcoma. Nature Genetics, 46(4), pp. 376-379. (doi:10.1038/ng.2921) (PMID:24633157) (PMCID:PMC4032873)

Papaemmanuil, E. et al. (2014) RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nature Genetics, 46(2), pp. 116-125. (doi:10.1038/ng.2874) (PMID:24413735) (PMCID:PMC3960636)

Meier, B. et al. (2014) C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome Research, 24(10), pp. 1624-1636. (doi:10.1101/gr.175547.114) (PMID:25030888) (PMCID:PMC4199376)

2013

Behjati, S. et al. (2013) Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nature Genetics, 45(12), pp. 1479-1482. (doi:10.1038/ng.2814) (PMID:24162739) (PMCID:PMC3839851)

Tarpey, P. S. et al. (2013) Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Nature Genetics, 45(8), pp. 923-926. (doi:10.1038/ng.2668) (PMID:23770606) (PMCID:PMC3743157)

Voet, T. et al. (2013) Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Research, 41(12), pp. 6119-6138. (doi:10.1093/nar/gkt345) (PMID:23630320) (PMCID:PMC3695511)

2012

Schulte, I. et al. (2012) Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. BMC Genomics, 13(1), 719. (doi:10.1186/1471-2164-13-719) (PMID:23260012) (PMCID:PMC3548764)

McBride, D. J. et al. (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. Journal of Pathology, 227(4), pp. 446-455. (doi:10.1002/path.4042) (PMID:22514011) (PMCID:PMC3428857)

Persson, M. et al. (2012) Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma. Genes, Chromosomes and Cancer, 51(8), pp. 805-817. (doi:10.1002/gcc.21965) (PMID:22505352)

Nik-Zainal, S. et al. (2012) Mutational processes molding the genomes of 21 breast cancers. Cell, 149(5), pp. 979-993. (doi:10.1016/j.cell.2012.04.024) (PMID:22608084) (PMCID:PMC3414841)

Nik-Zainal, S. et al. (2012) The life history of 21 breast cancers. Cell, 149(5), pp. 994-1007. (doi:10.1016/j.cell.2012.04.023) (PMID:22608083) (PMCID:PMC3428864)

Ng, C. K.Y. et al. (2012) The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer. Journal of Pathology, 226(5), pp. 703-712. (doi:10.1002/path.3980) (PMID:22183581)

Cooke, S. and Campbell, P. (2012) Circulating DNA and next-generation sequencing. In: Schlag, P.-M. and Senn, H.-J. (eds.) Minimal Residual Disease and Circulating Tumor Cells in Breast Cancer. Series: Recent results in cancer research (195). Springer. ISBN 9783642281600

2011

Cooke, S. L. and Brenton, J. D. (2011) Evolution of platinum resistance in high-grade serous ovarian cancer. Lancet Oncology, 12(12), pp. 1169-1174. (doi:10.1016/S1470-2045(11)70123-1) (PMID:21742554)

Cooke, S.L. , Temple, J., MacArthur, S., Zahra, M.A., Tan, L.T., Crawford, R.A.F., Ng, C.K.Y., Jimenez-Linan, M., Sala, E. and Brenton, J.D. (2011) Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer. British Journal of Cancer, 104(2), pp. 361-368. (doi:10.1038/sj.bjc.6605971) (PMID:21063398) (PMCID:PMC3031882)

2010

Cooke, S.L. , Ng, C.K.Y., Melnyk, N., Garcia, M.J., Hardcastle, T., Temple, J., Langdon, S., Huntsman, D. and Brenton, J.D. (2010) Genomic analysis of genetic heterogeneity and evolution in high-grade serous ovarian carcinoma. Oncogene, 29, pp. 4905-4913. (doi:10.1038/onc.2010.245) (PMID:20581869) (PMCID:PMC2933510)

2009

Schrader, K. A. et al. (2009) The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors. PLoS ONE, 4(11), e7988. (doi:10.1371/journal.pone.0007988) (PMID:19956657) (PMCID:PMC2777318)

2008

Cooke, S. L. , Pole, J. C.M., Chin, S.-F., Ellis, I. O., Caldas, C. and Edwards, P. A.W. (2008) High-resolution array CGH clarifies events occurring on 8p in carcinogenesis. BMC Cancer, 8, 288. (doi:10.1186/1471-2407-8-288) (PMID:18840272) (PMCID:PMC2576333)

Howarth, K.D. et al. (2008) Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene, 27, pp. 3345-3359. (doi:10.1038/sj.onc.1210993) (PMID:18084325) (PMCID:PMC2423006)

Cooke, S. L. , Northup, J. K., Champaige, N. L., Zinser, W., Edwards, P. A.W., Lockhart, L. H. and Velagaleti, G. V.N. (2008) Molecular cytogenetic characterization of a unique and complex de novo 8p rearrangement. American Journal of Medical Genetics: Part A, 146A(9), pp. 1166-1172. (doi:10.1002/ajmg.a.32248) (PMID:18302246)

Wakefield, L., Robinson, J., Long, H., Ibbitt, J. C., Cooke, S. , Hurst, H. C. and Sim, E. (2008) Arylamine N-acetyltransferase 1 expression in breast cancer cell lines: A potential marker in estrogen receptor-positive tumors. Genes, Chromosomes and Cancer, 47(2), pp. 118-126. (doi:10.1002/gcc.20512) (PMID:17973251)

2007

Paterson, A. L. et al. (2007) Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event. Genes, Chromosomes and Cancer, 46(5), pp. 427-439. (doi:10.1002/gcc.20424) (PMID:17285574)

2006

Pole, J.C.M., Courtay-Cahen, C., Garcia, M.J., Blood, K.A., Cooke, S.L. , Alsop, A.E., Tse, D.M.L., Caldas, C. and Edwards, P.A.W. (2006) High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation. Oncogene, 25, pp. 5693-5706. (doi:10.1038/sj.onc.1209570) (PMID:16636668)

This list was generated on Thu Dec 5 18:54:08 2019 GMT.
Number of items: 36.

Articles

Dreyer, S.B., Jamieson, N.B. , Cooke, S.L. , Valle, J.W., McKay, C.J., Biankin, A.V. and Chang, D.K. (2019) PRECISION-Panc: the next generation therapeutic development platform for pancreatic cancer. Clinical Oncology, (doi:10.1016/j.clon.2019.07.011) (PMID:31378449) (In Press)

Dreyer, S. B. et al. (2019) Feasibility and clinical utility of endoscopic ultrasound guided biopsy of pancreatic cancer for next-generation molecular profiling. Chinese Clinical Oncology, 8(2), 16. (doi:10.21037/cco.2019.04.06) (PMID:31070037)

Dreyer, S. B. et al. (2018) Precision oncology in surgery: patient selection for operable pancreatic cancer. Annals of Surgery, (doi:10.1097/SLA.0000000000003143) (PMID:30570546) (Early Online Publication)

Cooke, S. L. et al. (2017) The driver mutational landscape of ovarian squamous cell carcinomas arising in mature cystic teratoma. Clinical Cancer Research, 23(24), pp. 7633-7640. (doi:10.1158/1078-0432.CCR-17-1789) (PMID:28954785)

Behjati, S. et al. (2017) Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma. Nature Communications, 8(1), 15936. (doi:10.1038/ncomms15936) (PMID:28643781) (PMCID:PMC5490007)

Behjati, S. et al. (2016) Mutational signatures of ionizing radiation in second malignancies. Nature Communications, 7(1), 12605. (doi:10.1038/ncomms12605) (PMID:27615322) (PMCID:PMC5027243)

Shlien, A. et al. (2016) Direct transcriptional consequences of somatic mutation in breast cancer. Cell Reports, 16(7), pp. 2032-2046. (doi:10.1016/j.celrep.2016.07.028) (PMID:27498871) (PMCID:PMC4987284)

Greenman, C. D., Cooke, S.L. , Marshall, J., Stratton, M. R. and Campbell, P. J. (2016) Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process. Journal of Mathematical Biology, 72(1-2), pp. 47-86. (doi:10.1007/s00285-015-0875-2)

Cooper, C. S. et al. (2015) Erratum: Corrigendum: Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47(6), p. 689. (doi:10.1038/ng0615-689b) (PMID:26018901)

Kemp, C. et al. (2015) Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis. PLoS Medicine, 12(2), e1001789. (doi:10.1371/journal.pmed.1001789) (PMID:25710373) (PMCID:PMC4339382)

Cooper, C. S. et al. (2015) Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47(4), pp. 367-372. (doi:10.1038/ng.3221) (PMID:25730763) (PMCID:PMC4380509)

Tubio, J.M.C. et al. (2014) Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science, 345(6196), p. 1251343. (doi:10.1126/science.1251343) (PMID:25082706) (PMCID:PMC4380235)

Cooke, S. L. et al. (2014) Processed pseudogenes acquired somatically during cancer development. Nature Communications, 5, 3644. (doi:10.1038/ncomms4644) (PMID:24714652) (PMCID:PMC3996531)

Behjati, S. et al. (2014) Recurrent PTPRB and PLCG1 mutations in angiosarcoma. Nature Genetics, 46(4), pp. 376-379. (doi:10.1038/ng.2921) (PMID:24633157) (PMCID:PMC4032873)

Papaemmanuil, E. et al. (2014) RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nature Genetics, 46(2), pp. 116-125. (doi:10.1038/ng.2874) (PMID:24413735) (PMCID:PMC3960636)

Meier, B. et al. (2014) C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome Research, 24(10), pp. 1624-1636. (doi:10.1101/gr.175547.114) (PMID:25030888) (PMCID:PMC4199376)

Behjati, S. et al. (2013) Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nature Genetics, 45(12), pp. 1479-1482. (doi:10.1038/ng.2814) (PMID:24162739) (PMCID:PMC3839851)

Tarpey, P. S. et al. (2013) Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Nature Genetics, 45(8), pp. 923-926. (doi:10.1038/ng.2668) (PMID:23770606) (PMCID:PMC3743157)

Voet, T. et al. (2013) Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Research, 41(12), pp. 6119-6138. (doi:10.1093/nar/gkt345) (PMID:23630320) (PMCID:PMC3695511)

Schulte, I. et al. (2012) Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. BMC Genomics, 13(1), 719. (doi:10.1186/1471-2164-13-719) (PMID:23260012) (PMCID:PMC3548764)

McBride, D. J. et al. (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. Journal of Pathology, 227(4), pp. 446-455. (doi:10.1002/path.4042) (PMID:22514011) (PMCID:PMC3428857)

Persson, M. et al. (2012) Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma. Genes, Chromosomes and Cancer, 51(8), pp. 805-817. (doi:10.1002/gcc.21965) (PMID:22505352)

Nik-Zainal, S. et al. (2012) Mutational processes molding the genomes of 21 breast cancers. Cell, 149(5), pp. 979-993. (doi:10.1016/j.cell.2012.04.024) (PMID:22608084) (PMCID:PMC3414841)

Nik-Zainal, S. et al. (2012) The life history of 21 breast cancers. Cell, 149(5), pp. 994-1007. (doi:10.1016/j.cell.2012.04.023) (PMID:22608083) (PMCID:PMC3428864)

Ng, C. K.Y. et al. (2012) The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer. Journal of Pathology, 226(5), pp. 703-712. (doi:10.1002/path.3980) (PMID:22183581)

Cooke, S. L. and Brenton, J. D. (2011) Evolution of platinum resistance in high-grade serous ovarian cancer. Lancet Oncology, 12(12), pp. 1169-1174. (doi:10.1016/S1470-2045(11)70123-1) (PMID:21742554)

Cooke, S.L. , Temple, J., MacArthur, S., Zahra, M.A., Tan, L.T., Crawford, R.A.F., Ng, C.K.Y., Jimenez-Linan, M., Sala, E. and Brenton, J.D. (2011) Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer. British Journal of Cancer, 104(2), pp. 361-368. (doi:10.1038/sj.bjc.6605971) (PMID:21063398) (PMCID:PMC3031882)

Cooke, S.L. , Ng, C.K.Y., Melnyk, N., Garcia, M.J., Hardcastle, T., Temple, J., Langdon, S., Huntsman, D. and Brenton, J.D. (2010) Genomic analysis of genetic heterogeneity and evolution in high-grade serous ovarian carcinoma. Oncogene, 29, pp. 4905-4913. (doi:10.1038/onc.2010.245) (PMID:20581869) (PMCID:PMC2933510)

Schrader, K. A. et al. (2009) The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors. PLoS ONE, 4(11), e7988. (doi:10.1371/journal.pone.0007988) (PMID:19956657) (PMCID:PMC2777318)

Cooke, S. L. , Pole, J. C.M., Chin, S.-F., Ellis, I. O., Caldas, C. and Edwards, P. A.W. (2008) High-resolution array CGH clarifies events occurring on 8p in carcinogenesis. BMC Cancer, 8, 288. (doi:10.1186/1471-2407-8-288) (PMID:18840272) (PMCID:PMC2576333)

Howarth, K.D. et al. (2008) Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene, 27, pp. 3345-3359. (doi:10.1038/sj.onc.1210993) (PMID:18084325) (PMCID:PMC2423006)

Cooke, S. L. , Northup, J. K., Champaige, N. L., Zinser, W., Edwards, P. A.W., Lockhart, L. H. and Velagaleti, G. V.N. (2008) Molecular cytogenetic characterization of a unique and complex de novo 8p rearrangement. American Journal of Medical Genetics: Part A, 146A(9), pp. 1166-1172. (doi:10.1002/ajmg.a.32248) (PMID:18302246)

Wakefield, L., Robinson, J., Long, H., Ibbitt, J. C., Cooke, S. , Hurst, H. C. and Sim, E. (2008) Arylamine N-acetyltransferase 1 expression in breast cancer cell lines: A potential marker in estrogen receptor-positive tumors. Genes, Chromosomes and Cancer, 47(2), pp. 118-126. (doi:10.1002/gcc.20512) (PMID:17973251)

Paterson, A. L. et al. (2007) Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event. Genes, Chromosomes and Cancer, 46(5), pp. 427-439. (doi:10.1002/gcc.20424) (PMID:17285574)

Pole, J.C.M., Courtay-Cahen, C., Garcia, M.J., Blood, K.A., Cooke, S.L. , Alsop, A.E., Tse, D.M.L., Caldas, C. and Edwards, P.A.W. (2006) High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation. Oncogene, 25, pp. 5693-5706. (doi:10.1038/sj.onc.1209570) (PMID:16636668)

Book Sections

Cooke, S. and Campbell, P. (2012) Circulating DNA and next-generation sequencing. In: Schlag, P.-M. and Senn, H.-J. (eds.) Minimal Residual Disease and Circulating Tumor Cells in Breast Cancer. Series: Recent results in cancer research (195). Springer. ISBN 9783642281600

This list was generated on Thu Dec 5 18:54:08 2019 GMT.