Prof Andy Lynch

Prof Andy Lynch
Professor of Statistics in Bioscience



data source: symbiosis

Research Overview from research@st-andrews

Recent publications listed in research@st-andrews
Mitchell, TJ, Turajlic, S, Rowan, A, Nicol, D, Farmery, JHR, O’Brien, T, Martincorena, I, Tarpey, P, Angelopoulos, N, Yates, LR, Butler, AP, Raine, K, Stewart, GD, Challacombe, B, Fernando, A, Lopez, JI, Hazell, S, Chandra, A, Chowdhury, S, Rudman, S, Soultati, A, Stamp, G, Fotiadis, N, Pickering, L, Au, L, Spain, L, Lynch, J, Stares, M, Teague, J, Maura, F, Wedge, DC, Horswell, S, Chambers, T, Litchfield, K, Xu, H, Stewart, A, Elaidi, R, Oudard, S, McGranahan, N, Csabai, I, Gore, M, Futreal, PA, Larkin, J, Lynch, AG, Szallasi, Z, Swanton, C & Campbell, PJ 2018, 'Timing the landmark events in the evolution of clear cell renal cell cancer: TRACERx renal' Cell, vol 173, no. 3, e17, pp. 611-623. DOI: 10.1016/j.cell.2018.02.020
Wedge, DC, Gundem, G, Mitchell, T, Woodstock, DJ, Martincorena, I, Ghori, M, Zamora, J, Butler, A, Whitaker, H, Kote-Jarai, Z, Alexandrov, LB, Van Loo, P, Massie, CE, Dentro, S, Warren, AY, Verrill, C, Berney, DM, Dennis, N, Merson, S, Hawkins, S, Howat, W, Lu, Y-J, Lambert, A, Kay, J, Kremeyer, B, Karaszi, K, Luxton, H, Camacho, N, Marsden, L, Edwards, S, Matthews, L, Bo, V, Leongamornlert, D, McLaren, S, Ng, A, Yu, Y, Zhang, H, Dadaev, T, Thomas, S, Easton, DF, Ahmed, M, Bancroft, E, Fisher, C, Livni, N, Nicol, D, Tavaré, S, Gill, P, Greenman, C, Khoo, V, CAMCAP study group, The TCGA consortium & Lynch, A 2018, 'Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets' Nature Genetics. DOI: 10.1038/s41588-018-0086-z
Smeets, E, Lynch, AG, Prekovic, S, Van den Broeck, T, Moris, L, Helsen, C, Joniau, S, Claessens, F & Massie, CE 2018, 'The role of TET-mediated DNA hydroxymethylation in prostate cancer' Molecular and Cellular Endocrinology, vol 462, no. A, pp. 41-55. DOI: 10.1016/j.mce.2017.08.021
Camacho, N, Van Loo, P, Edwards, S, Kay, JD, Matthews, L, Haase, K, Clark, J, Dennis, N, Thomas, S, Kremeyer, B, Zamora, J, Butler, AP, Gundem, G, Merson, S, Luxton, H, Hawkins, S, Ghori, M, Marsden, L, Lambert, A, Karaszi, K, Pelvender, G, Massie, CE, Kote-Jarai, ZS, Raine, K, Jones, D, Howat, WJ, Hazell, S, Livni, N, Fisher, C, Ogden, C, Kumar, P, Thompson, A, Nicol, D, Mayer, E, Dudderidge, T, Yu, Y, Zhang, H, Shah, NC, Gnanapragasam, VJ, Group, TCRUK-ICGCP, Isaacs, W, Visakorpi, T, Hamdy, F, Berney, D, Verrill, C, Warren, AY, Wedge, DC, Lynch, AG, Foster, CS, Lu, YJ, Bova, GS, Whitaker, HC, McDermott, U, Neal, DE, Eeles, R, Cooper, CS & Brewer, DS 2017, 'Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data' PLoS Genetics, vol 13, no. 9, e1007001. DOI: 10.1371/journal.pgen.1007001
Asim, M, Tarish, F, Zecchini, HI, Sanjiv, K, Gelali, E, Massie, CE, Baridi, A, Warren, AY, Zhao, W, Ogris, C, McDuffus, L-A, Mascalchi, P, Shaw, G, Dev, H, Wadhwa, K, Wijnhoven, P, Forment, JV, Lyons, SR, Lynch, AG, O'Neill, C, Zecchini, VR, Rennie, PS, Baniahmad, A, Tavaré, S, Mills, IG, Galanty, Y, Crosetto, N, Schultz, N, Neal, D & Helleday, T 2017, 'Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer' Nature Communications, vol 8, 374. DOI: 10.1038/s41467-017-00393-y
Yates, LR, Knappskog, S, Wedge, D, Farmery, JHR, Gonzalez, S, Martincorena, I, Alexandrov, LB, Van Loo, P, Haugland, HK, Lilleng, PK, Gundem, G, Gerstung, M, Pappaemmanuil, E, Gazinska, P, Bhosle, SG, Jones, D, Raine, K, Mudie, L, Latimer, C, Sawyer, E, Desmedt, C, Sotiriou, C, Stratton, MR, Sieuwerts, AM, Lynch, AG, Martens, JW, Richardson, AL, Tutt, A, Lønning, PE & Campbell, PJ 2017, 'Genomic evolution of breast cancer metastasis and relapse' Cancer Cell, vol 32, no. 2, e7, pp. 169-184. DOI: 10.1016/j.ccell.2017.07.005
Janowitz, T, Williams, EH, Marshall, A, Ainsworth, N, Thomas, PB, Sammut, SJ, Shepherd, S, White, J, Mark, PB, Lynch, AG, Jodrell, DI, Tavaré, S & Earl, H 2017, 'New model for estimating glomerular filtration rate in patients with cancer' Journal of Clinical Oncology, vol 35, no. 24, pp. 2798-2805. DOI: 10.1200/JCO.2017.72.7578
Noorani, A, Bornschein, J, Lynch, AG, Secrier, M, Achilleos, A, Eldridge, M, Bower, L, Weaver, JMJ, Crawte, J, Ong, C-A, Shannon, N, MacRae, S, Grehan, N, Nutzinger, B, O'Donovan, M, Hardwick, R, Tavaré, S, Fitzgerald, RC & on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium 2017, 'A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy' Genome Research, vol 27, no. 6, pp. 902-912. DOI: 10.1101/gr.214296.116
Luca, B-A, Brewer, DS, Edwards, DR, Edwards, S, Whitaker, HC, Merson, S, Dennis, N, Cooper, RA, Hazell, S, Warren, AY, Eeles, R, Lynch, AG, Ross-Adams, H, Lamb, AD, Neal, DE, Sethia, K, Mills, RD, Ball, RY, Curley, H, Clark, J, Moulton, V & Cooper, CS 2017, 'DESNT: a poor prognosis category of human prostate cancer' European Urology Focus, vol In press. DOI: 10.1016/j.euf.2017.01.016
Dunning, MJ, Vowler, SL, Lalonde, E, Ross-Adams, H, Boutros, P, Mills, IG, Lynch, AG & Lamb, AD 2017, 'Mining human prostate cancer datasets: the “camcAPP” shiny app' EBioMedicine, vol 17, pp. 5-6. DOI: 10.1016/j.ebiom.2017.02.022
Thomas, BC, Kay, JD, Menon, S, Vowler, SL, Dawson, SN, Bucklow, LJ, Luxton, HJ, Johnston, T, Massie, CE, Pugh, M, Warren, AY, Barker, P, Burling, K, Lynch, AG, George, A, Burge, J, Corcoran, M, Stearn, S, Lamb, AD, Sharma, NL, Shaw, GL, Neal, DE & Whitaker, HC 2016, 'Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel' Endocrine-Related Cancer, vol 23, no. 10, pp. 797-812. DOI: 10.1530/ERC-16-0287
Behjati, S, Gundem, G, Wedge, DC, Roberts, ND, Tarpey, PS, Cooke, SL, Van Loo, P, Alexandrov, LB, Ramakrishna, M, Davies, H, Nik-Zainal, S, Hardy, C, Latimer, C, Raine, KM, Stebbings, L, Menzies, A, Jones, D, Shepherd, R, Butler, AP, Teague, JW, Jorgensen, M, Khatri, B, Pillay, N, Shlien, A, Futreal, PA, Badie, C, McDermott, U, Bova, GS, Richardson, AL, Flanagan, AM, Stratton, MR, Campbell, PJ & ICGC Prostate Group 2016, 'Mutational signatures of ionizing radiation in second malignancies' Nature Communications, vol 7, 12605. DOI: 10.1038/ncomms12605
Garcia, E, Hayden, A, Birts, C, Britton, E, Cowie, A, Pickard, K, Mellone, M, Choh, C, Derouet, M, Duriez, P, Noble, F, White, MJ, Primrose, JN, Strefford, JC, Rose-Zerilli, M, Thomas, GJ, Ang, Y, Sharrocks, AD, Fitzgerald, RC, Underwood, TJ & & the OCCAMS consortium 2016, 'Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1' Scientific Reports, vol 6, 32417. DOI: 10.1038/srep32417
Secrier, M, Li, X, de Silva, N, Eldridge, MD, Contino, G, Bornschein, J, MacRae, S, Grehan, N, O'Donovan, M, Miremadi, A, Yang, T-P, Bower, L, Chettouh, H, Crawte, J, Galeano-Dalmau, N, Grabowska, A, Saunders, J, Underwood, T, Waddell, N, Barbour, AP, Nutzinger, B, Achilleos, A, Edwards, PAW, Lynch, AG, Tavaré, S, Fitzgerald, RC & Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium 2016, 'Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance' Nature Genetics, vol 48, no. 10, pp. 1131-41. DOI: 10.1038/ng.3659
Shaw, GL, Whitaker, H, Corcoran, M, Dunning, MJ, Luxton, H, Kay, J, Massie, CE, Miller, JL, Lamb, AD, Ross-Adams, H, Russell, R, Nelson, AW, Eldridge, MD, Lynch, AG, Ramos-Montoya, A, Mills, IG, Taylor, AE, Arlt, W, Shah, N, Warren, AY & Neal, DE 2016, 'The early effects of rapid androgen deprivation on human prostate cancer' European Urology, vol 70, no. 2, pp. 214-218. DOI: 10.1016/j.eururo.2015.10.042
Contino, G, Eldridge, MD, Secrier, M, Bower, L, Elliott, RF, Weaver, J, Lynch, AG, Edwards, PAW & Fitzgerald, RC 2016, 'Whole-genome sequencing of nine esophageal adenocarcinoma cell lines' F1000Research, vol 5, 1336. DOI: 10.12688/F1000RESEARCH.7033.1
Asim, M, Massie, CE, Orafidiya, F, Pértega-Gomes, N, Warren, AY, Esmaeili, M, Selth, LA, Zecchini, HI, Luko, K, Qureshi, A, Baridi, A, Menon, S, Madhu, B, Escriu, C, Lyons, S, Vowler, SL, Zecchini, VR, Shaw, G, Hessenkemper, W, Russell, R, Mohammed, H, Stefanos, N, Lynch, AG, Grigorenko, E, D’Santos, C, Taylor, C, Lamb, A, Sriranjan, R, Yang, J, Stark, R, Dehm, SM, Rennie, PS, Carroll, JS, Griffiths, JR, Tavaré, S, Mills, IG, McEwan, IJ, Baniahmad, A, Tilley, WD & Neal, DE 2016, 'Cholinekinase alpha as an androgen receptor chaperone and prostate cancer therapeutic target' Journal of the National Cancer Institute, vol 108, no. 5, djv371. DOI: 10.1093/jnci/djv371
Andrews, DJ, Lynch, AG & Tavaré, S 2016, Using Methylation Patterns for Reconstructing Cell Division Dynamics: Assessing Validation Experiments. in Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications. Elsevier Inc., pp. 3-15. DOI: 10.1016/B978-0-12-804203-8.00001-8
Alioto, TS, Buchhalter, I, Derdak, S, Hutter, B, Eldridge, MD, Hovig, E, Heisler, LE, Beck, TA, Simpson, JT, Tonon, L, Sertier, A-S, Patch, A-M, Jaeger, N, Ginsbach, P, Drews, R, Paramasivam, N, Kabbe, R, Chotewutmontri, S, Diessl, N, Previti, C, Schmidt, S, Brors, B, Feuerbach, L, Heinold, M, Groebner, S, Korshunov, A, Tarpey, PS, Butler, AP, Hinton, J, Jones, D, Menzies, A, Raine, K, Shepherd, R, Stebbings, L, Teague, JW, Ribeca, P, Giner, FC, Beltran, S, Raineri, E, Dabad, M, Heath, SC, Gut, M, Denroche, RE, Harding, NJ, Yamaguchi, TN, Fujimoto, A, Nakagawa, H, Quesada, C, Valdes-Mas, R, Nakken, S, Vodak, D, Bower, L, Lynch, AG, Anderson, CL, Waddell, N, Pearson, JV, Grimmond, SM, Peto, M, Spellman, P, He, M, Kandoth, C, Lee, S, Zhang, J, Letourneau, L, Ma, S, Seth, S, Torrents, D, Xi, L, Wheeler, DA, Lopez-Otin, C, Campo, E, Campbell, PJ, Boutros, PC, Puente, XS, Gerhard, DS, Pfister, SM, McPherson, JD, Hudson, TJ, Schlesner, M, Lichter, P, Eils, R, Jones, DTW & Gut, IG 2015, 'A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing' Nature Communications, vol 6, 10001. DOI: 10.1038/ncomms10001
Ross-Adams, H, Lamb, AD, Dunning, MJ, Halim, S, Lindberg, J, Massie, CM, Egevad, LA, Russell, R, Ramos-Montoya, A, Vowler, SL, Sharma, NL, Kay, J, Whitaker, H, Clark, J, Hurst, R, Gnanapragasam, VJ, Shah, NC, Warren, AY, Cooper, CS, Lynch, AG, Stark, R, Mills, IG, Grönberg, H, Neal, DE, Shaw, G, Hori, S, Baridi, A, Tran, M, Wadhwa, K, Nelson, A, Patel, K, Thomas, B, Luxton, H, Gnanpragasam, V, Doble, A, Kastner, C, Aho, T, Haynes, B, Partridge, W, Cromwell, E, Sangrasi, A, Burge, J, George, A, Stearn, S, Corcoran, M, Coret, H, Basnett, G, Francis, I, Whitington, T, Yuan, Y & CamCaP Study Group 2015, 'Integration of copy number and transcriptomics provides risk stratification in prostate cancer: a discovery and validation cohort study' EBioMedicine, vol 2, no. 9, pp. 1133-1144. DOI: 10.1016/j.ebiom.2015.07.017
Ross-Innes, CS, Becq, J, Warren, A, Cheetham, RK, Northen, H, O'Donovan, M, Malhotra, S, Di Pietro, M, Ivakhno, S, He, M, Weaver, JMJ, Lynch, AG, Kingsbury, Z, Ross, M, Humphray, S, Bentley, D, Fitzgerald, RC, Hayes, SJ, Ang, Y, Welch, I, Preston, S, Oakes, S, Save, V, Skipworth, R, Tucker, O, Davies, J, Crichton, C, Schusterreiter, C, Underwood, T, Noble, F, Stacey, B, Kelly, J, Byrne, J, Haydon, A, Sharland, D, Owsley, J, Barr, H, Lagergren, J, Gossage, J, Davies, A, Mason, R, Chang, F, Zylstra, J, Sanders, G, Wheatley, T, Berrisford, R, Bracey, T, Harden, C, Bunting, D, Roques, T, Nobes, J, Loo, S, Lewis, M, Cheong, E, Priest, O, Parsons, SL, Soomro, I, Kaye, P, Saunders, J, Pang, V, Welch, N, Catton, JA, Duffy, JP, Ragunath, K, Lovat, L, Haidry, R, Miah, H, Kerr, S, Eneh, V, Butawan, R, Lewis, M, Cheong, E, Kumar, B, Igali, L, Walton, S, Dann, A, Safranek, P, Hindmarsh, A, Sudjendran, V, Scott, M, Cluroe, A, Miremadi, A, Mahler-Araujo, B, Nutzinger, B, Peters, C, Abdullahi, Z, Crawte, J, MacRae, S, Noorani, A, Elliott, RF, Bower, L, Edwards, P, Tavare, S, Eldridge, M, Bornschein, J, Secrier, M, Yang, TP, O'Neill, JR, Adamczuk, K, Lao-Sirieix, P, Grehan, N, Smith, L, Lishman, S, Beardsmore, D & Dawson, S 2015, 'Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma' Nature Genetics, vol 47, no. 9, pp. 1038-1046. DOI: 10.1038/ng.3357
Paterson, AL, Weaver, JMJ, Eldridge, MD, Tavare, S, Fitzgerald, RC, Edwards, PAW & OCCAMS Consortium 2015, 'Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis' BMC Genomics, vol 16, 473. DOI: 10.1186/s12864-015-1685-z