Advanced Sequencing: Publications

  • Abbosh, C; Birkbak, NJ; Wilson, GA; Jamal-Hanjani, M; Constantin, T; Salari, R; Quesne, JL; Moore, DA; Veeriah, S; Rosenthal, R; Marafioti, T; Kirkizlar, E; Watkins, TBK; McGranahan, N; Ward, S; Martinson, L; Riley, J; Fraioli, F; Bakir, MA; Grönroos, E; Zambrana, F; Endozo, R; Bi, WL; Fennessy, FM; Sponer, N; Johnson, D; Laycock, J; Shafi, S; Czyzewska-Khan, J; Rowan, A; Chambers, T; Matthews, N; Turajlic, S; Hiley, C; Lee, SM; Forster, MD; Ahmad, T; Falzon, M; Borg, E; Lawrence, D; Hayward, M; Kolvekar, S; Panagiotopoulos, N; Janes, SM; Thakrar, R; Ahmed, A; Blackhall, F; Summers, Y; Hafez, D; Naik, A; Ganguly, A; Kareht, S; Shah, R; Joseph, L; Quinn, AM; Crosbie, P; Naidu, B; Middleton, G; Langman, G; Trotter, S; Nicolson, M; Remmen, H; Kerr, K; Chetty, M; Gomersall, L; Fennell, DA; Nakas, A; Rathinam, S; Anand, G; Khan, S; Russell, P; Ezhil, V; Ismail, B; Irvin-sellers, M; Prakash, V; Lester, JF; Kornaszewska, M; Attanoos, R; Adams, H; Davies, H; Oukrif, D; Akarca, AU; Hartley, JA; Lowe, HL; Lock, S; Iles, N; Bell, H; Ngai, Y; Elgar, G; Szallasi, Z; Schwarz, RF; Herrero, J; Stewart, A; Quezada, SA; Van Loo, P; Dive, C; Lin, CJ; Rabinowitz, M; Aerts, HJWL; Hackshaw, A; Shaw, JA; Zimmermann, BG; The TRACERx Consortium; The PEACE Consortium and Swanton, C (2017)
    Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.
    Nature 545, 446-451 PubMed abstract
  • Coda, DM; Gaarenstroom, T; East, P; Patel, H; Miller, DSJ; Lobley, A; Matthews, N; Stewart, A and Hill, CS (2017)
    Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling.
    eLife 6, e22474 PubMed abstract
  • Crockford, A; Zalmas, LP; Grönroos, E; Dewhurst, SM; McGranahan, N; Cuomo, ME; Encheva, V; Snijders, AP; Begum, J; Purewal, S; Cerveira, J; Patel, H; Renshaw, MJ and Swanton, C (2017)
    Cyclin D mediates tolerance of genome-doubling in cancers with functional p53.
    Annals of Oncology 28, 149-156 PubMed abstract
  • Desai, R; Frazier, AE; Durigon, R; Patel, H; Jones, AW; Dalla Rosa, I; Lake, NJ; Compton, AG; Mountford, HS; Tucker, EJ; Mitchell, ALR; Jackson, D; Sesay, A; Di Re, M; van den Heuvel, LP; Burke, D; Francis, D; Lunke, S; McGillivray, G; Mandelstam, S; Mochel, F; Keren, B; Jardel, C; Turner, AM; Ian Andrews, P; Smeitink, J; Spelbrink, JN; Heales, SJ; Kohda, M; Ohtake, A; Murayama, K; Okazaki, Y; Lombès, A; Holt, IJ; Thorburn, DR and Spinazzola, A (2017)
    ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
    Brain 140, 1595-1610 PubMed abstract
  • Egawa, N; Wang, Q; Griffin, HM; Murakami, I; Jackson, D; Mahmood, R and Doorbar, J (2017)
    HPV16 and 18 genome amplification show different E4-dependence, with 16E4 enhancing E1 nuclear accumulation and replicative efficiency via its cell cycle arrest and kinase activation functions.
    PLOS Pathogens 13, e1006282 PubMed abstract
  • Entwistle, LJ; Pelly, VS; Coomes, SM; Kannan, Y; Perez-Lloret, J; Czieso, S; Silva dos Santos, M; MacRae, JI; Collinson, L; Sesay, A; Nikolov, N; Metidji, A; Helmby, H; Hui, DY and Wilson, MS (2017)
    Epithelial-cell-derived phospholipase A2 group 1B is an endogenous anthelmintic.
    Cell Host & Microbe 22, 484-493.e485 PubMed abstract
  • Esnault, C; Gualdrini, F; Horswell, S; Kelly, G; Stewart, A; East, P; Matthews, N and Treisman, R (2017)
    ERK-induced activation of TCF family of SRF cofactors initiates a chromatin modification cascade associated with transcription.
    Molecular Cell 65, 1081-1095 e1085 PubMed abstract
  • Jamal-Hanjani, M; Wilson, GA; McGranahan, N; Birkbak, NJ; Watkins, TBK; Veeriah, S; Shafi, S; Johnson, DH; Mitter, R; Rosenthal, R; Salm, M; Horswell, S; Escudero, M; Matthews, N; Rowan, A; Chambers, T; Moore, DA; Turajlic, S; Xu, H; Lee, S-M; Forster, MD; Ahmad, T; Hiley, CT; Abbosh, C; Falzon, M; Borg, E; Marafioti, T; Lawrence, D; Hayward, M; Kolvekar, S; Panagiotopoulos, N; Janes, SM; Thakrar, R; Ahmed, A; Blackhall, F; Summers, Y; Shah, R; Joseph, L; Quinn, AM; Crosbie, PA; Naidu, B; Middleton, G; Langman, G; Trotter, S; Nicolson, M; Remmen, H; Kerr, K; Chetty, M; Gomersall, L; Fennell, DA; Nakas, A; Rathinam, S; Anand, G; Khan, S; Russell, P; Ezhil, V; Ismail, B; Irvin-Sellers, M; Prakash, V; Lester, JF; Kornaszewska, M; Attanoos, R; Adams, H; Davies, H; Dentro, S; Taniere, P; O'Sullivan, B; Lowe, HL; Hartley, JA; Iles, N; Bell, H; Ngai, Y; Shaw, JA; Herrero, J; Szallasi, Z; Schwarz, RF; Stewart, A; Quezada, SA; Le Quesne, J; Van Loo, P; Dive, C; Hackshaw, A; Swanton, C and The TRACERx Consortium (2017)
    Tracking the evolution of non-small-cell lung cancer.
    New England Journal of Medicine 376, 2109-2121 PubMed abstract
  • López-Garcia, C; Sansregret, L; Domingo, E; McGranahan, N; Hobor, S; Birkbak, NJ; Horswell, S; Grönroos, E; Favero, F; Rowan, AJ; Matthews, N; Begum, S; Phillimore, B; Burrell, R; Oukrif, D; Spencer-Dene, B; Kovac, M; Stamp, G; Stewart, A; Danielsen, H; Novelli, M; Tomlinson, I and Swanton, C (2017)
    BCL9L dysfunction impairs caspase-2 expression permitting aneuploidy tolerance in colorectal cancer.
    Cancer Cell 31, 79-93 PubMed abstract
  • Passaro, D; Di Tullio, A; Abarrategi, A; Rouault-Pierre, K; Foster, K; Ariza-McNaughton, L; Montaner, B; Chakravarty, P; Bhaw, L; Diana, G; Lassailly, F; Gribben, J and Bonnet, D (2017)
    Increased vascular permeability in the bone marrow microenvironment contributes to disease progression and drug response in acute myeloid leukemia.
    Cancer Cell 32, 324-341 e326 PubMed abstract
  • Sangrithi, MN; Royo, H; Mahadevaiah, SK; Ojarikre, O; Bhaw, L; Sesay, A; Peters, AHFM; Stadler, M and Turner, JMA (2017)
    Non-canonical and sexually dimorphic X dosage compensation states in the mouse and human germline.
    Developmental Cell 40, 289-301 PubMed abstract
  • Blaas, L; Pucci, F; Messal, HA; Andersson, AB; Ruiz, EJ; Gerling, M; Douagi, I; Spencer-Dene, B; Musch, A; Mitter, R; Bhaw, L; Stone, R; Bornhorst, D; Sesay, AK; Jonkers, J; Stamp, G; Malanchi, I; Toftgård, R and Behrens, A (2016)
    Lgr6 labels a rare population of mammary gland progenitor cells that are able to originate luminal mammary tumours.
    Nature Cell Biology 18, 1346-1356 PubMed abstract
  • Gualdrini, F; Esnault, C; Horswell, S; Stewart, A; Matthews, N and Treisman, R (2016)
    SRF co-factors control the balance between cell proliferation and contractility.
    Molecular Cell 64, 1048-1061 PubMed abstract
  • Kantidakis, T; Saponaro, M; Mitter, R; Horswell, S; Kranz, A; Boeing, S; Aygün, O; Kelly, GP; Matthews, N; Stewart, A; Stewart, AF and Svejstrup, JQ (2016)
    Mutation of cancer driver MLL2 results in transcription stress and genome instability.
    Genes & Development 30, 408-420 PubMed abstract
  • Morales Torres, C; Biran, A; Burney, MJ; Patel, H; Henser-Brownhill, T; Cohen, A-HS; Li, Y; Ben-Hamo, R; Nye, E; Spencer-Dene, B; Chakravarty, P; Efroni, S; Matthews, N; Misteli, T; Meshorer, E and Scaffidi, P (2016)
    The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity.
    Science 353, aaf1644 PubMed abstract
  • Cheng, TMK; Heeger, S; Chaleil, RAG; Matthews, N; Stewart, A; Wright, J; Lim, C; Bates, PA and Uhlmann, F (2015)
    A simple biophysical model emulates budding yeast chromosome condensation.
    eLife 4, e05565 PubMed abstract
  • Ehrensberger, AH; Franchini, D-M; East, P; George, R; Matthews, N; Maslen, SL and Svejstrup, JQ (2015)
    Retention of the native epigenome in purified mammalian chromatin.
    PLOS ONE 10, e0133246 PubMed abstract
  • Godin-Heymann, N; Brabetz, S; Murillo, MM; Saponaro, M; Santos, CR; Lobley, A; East, P; Chakravarty, P; Matthews, N; Kelly, G; Jordan, S; Castellano, E and Downward, J (2015)
    Tumour-suppression function of KLF12 through regulation of anoikis.
    Oncogene 35, 3324-3334 PubMed abstract
  • Hunt, LE; Noyvert, B; Bhaw-Rosun, L; Sesay, AK; Paternoster, L; Nohr, EA; Davey Smith, G; Tommerup, N; Sørensen, TIA and Elgar, G (2015)
    Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5.
    Genome Medicine 7, 126 PubMed abstract
  • Kanu, N; Grönroos, E; Martinez, P; Burrell, RA; Yi Goh, X; Bartkova, J; Maya-Mendoza, A; Mistrik, M; Rowan, AJ; Patel, H; Rabinowitz, A; East, P; Wilson, G; Santos, CR; McGranahan, N; Gulati, S; Gerlinger, M; Birkbak, NJ; Joshi, T; Alexandrov, LB; Stratton, MR; Powles, T; Matthews, N; Bates, PA; Stewart, A; Szallasi, Z; Larkin, J; Bartek, J and Swanton, C (2015)
    SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.
    Oncogene 34, 5699-5708 PubMed abstract
  • Kovac, M; Navas, C; Horswell, S; Salm, M; Bardella, C; Rowan, A; Stares, M; Castro-Giner, F; Fisher, R; de Bruin, EC; Kovacova, M; Gorman, M; Makino, S; Williams, J; Jaeger, E; Jones, A; Howarth, K; Larkin, J; Pickering, L; Gore, M; Nicol, DL; Hazell, S; Stamp, G; O'Brien, T; Challacombe, B; Matthews, N; Phillimore, B; Begum, S; Rabinowitz, A; Varela, I; Chandra, A; Horsfield, C; Polson, A; Tran, M; Bhatt, R; Terracciano, L; Eppenberger-Castori, S; Protheroe, A; Maher, E; El Bahrawy, M; Fleming, S; Ratcliffe, P; Heinimann, K; Swanton, C and Tomlinson, I (2015)
    Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution.
    Nature Communications 6, 6336 PubMed abstract
  • Murugaesu, N; Wilson, GA; Birkbak, NJ; Watkins, TBK; McGranahan, N; Kumar, S; Abbassi-Ghadi, N; Salm, M; Mitter, R; Horswell, S; Rowan, A; Phillimore, B; Biggs, J; Begum, S; Matthews, N; Hochhauser, D; Hanna, GB and Swanton, C (2015)
    Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy.
    Cancer Discovery 5, 821-831 PubMed abstract
  • Chandler, H; Patel, H; Palermo, R; Brookes, S; Matthews, N and Peters, G (2014)
    Role of polycomb group proteins in the DNA damage response--a reassessment.
    PLOS ONE 9, e102968 PubMed abstract
  • Collart, C; Owens, NDL; Bhaw-Rosun, L; Cooper, B; De Domenico, E; Patrushev, I; Sesay, AK; Smith, JN; Smith, JC and Gilchrist, MJ (2014)
    High-resolution analysis of gene activity during the Xenopus mid-blastula transition.
    Development 141, 1927-1939 PubMed abstract
  • de Bruin, EC; McGranahan, N; Mitter, R; Salm, M; Wedge, DC; Yates, L; Jamal-Hanjani, M; Shafi, S; Murugaesu, N; Rowan, AJ; Grönroos, E; Muhammad, MA; Horswell, S; Gerlinger, M; Varela, I; Jones, D; Marshall, J; Voet, T; Van Loo, P; Rassl, DM; Rintoul, RC; Janes, SM; Lee, S-M; Forster, M; Ahmad, T; Lawrence, D; Falzon, M; Capitanio, A; Harkins, TT; Lee, CC; Tom, W; Teefe, E; Chen, S-C; Begum, S; Rabinowitz, A; Phillimore, B; Spencer-Dene, B; Stamp, G; Szallasi, Z; Matthews, N; Stewart, A; Campbell, P and Swanton, C (2014)
    Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.
    Science 346, 251-256 PubMed abstract
  • Deddouche, S; Goubau, D; Rehwinkel, J; Chakravarty, P; Begum, S; Maillard, PV; Borg, A; Matthews, N; Feng, Q; van Kuppeveld, FJM and Reis e Sousa, C (2014)
    Identification of an LGP2-associated MDA5 agonist in picornavirus-infected cells.
    eLife 3, e01535 PubMed abstract
  • Esnault, C; Stewart, A; Gualdrini, F; East, P; Horswell, S; Matthews, N and Treisman, R (2014)
    Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts.
    Genes & Development 28, 943-958 PubMed abstract
  • Fisher, R; Horswell, S; Rowan, A; Salm, MP; de Bruin, EC; Gulati, S; McGranahan, N; Stares, M; Gerlinger, M; Varela, I; Crockford, A; Favero, F; Quidville, V; André, F; Navas, C; Grönroos, E; Nicol, D; Hazell, S; Hrouda, D; O'Brien, T; Matthews, N; Phillimore, B; Begum, S; Rabinowitz, A; Biggs, J; Bates, PA; McDonald, NQ; Stamp, G; Spencer-Dene, B; Hsieh, JJ; Xu, J; Pickering, L; Gore, M; Larkin, J and Swanton, C (2014)
    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
    Genome Biology 15, 433 PubMed abstract
  • Gerlinger, M; Horswell, S; Larkin, J; Rowan, AJ; Salm, MP; Varela, I; Fisher, R; McGranahan, N; Matthews, N; Santos, CR; Martinez, P; Phillimore, B; Begum, S; Rabinowitz, A; Spencer-Dene, B; Gulati, S; Bates, PA; Stamp, G; Pickering, L; Gore, M; Nicol, DL; Hazell, S; Futreal, PA; Stewart, A and Swanton, C (2014)
    Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.
    Nature Genetics 46, 225-233 PubMed abstract
  • Jamal-Hanjani, M; Hackshaw, A; Ngai, Y; Shaw, J; Dive, C; Quezada, S; Middleton, G; de Bruin, E; Le Quesne, J; Shafi, S; Falzon, M; Horswell, S; Blackhall, F; Khan, I; Janes, S; Nicolson, M; Lawrence, D; Forster, M; Fennell, D; Lee, S-M; Lester, J; Kerr, K; Muller, S; Iles, N; Smith, S; Murugaesu, N; Mitter, R; Salm, M; Stuart, A; Matthews, N; Adams, H; Ahmad, T; Attanoos, R; Bennett, J; Birkbak, NJ; Booton, R; Brady, G; Buchan, K; Capitano, A; Chetty, M; Cobbold, M; Crosbie, P; Davies, H; Denison, A; Djearman, M; Goldman, J; Haswell, T; Joseph, L; Kornaszewska, M; Krebs, M; Langman, G; MacKenzie, M; Millar, J; Morgan, B; Naidu, B; Nonaka, D; Peggs, K; Pritchard, C; Remmen, H; Rowan, A; Shah, R; Smith, E; Summers, Y; Taylor, M; Veeriah, S; Waller, D; Wilcox, B; Wilcox, M; Woolhouse, I; McGranahan, N and Swanton, C (2014)
    Tracking genomic cancer evolution for precision medicine: the lung TRACERx study.
    PLOS Biology 12, e1001906 PubMed abstract
  • Pemberton, H; Anderton, E; Patel, H; Brookes, S; Chandler, H; Palermo, R; Stock, J; Rodriguez-Niedenführ, M; Racek, T; de Breed, L; Stewart, A; Matthews, N and Peters, G (2014)
    Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts.
    Genome Biology 15, R23 PubMed abstract
  • Bewick, AJ; Chain, FJJ; Zimmerman, LB; Sesay, A; Gilchrist, MJ; Owens, NDL; Seifertova, E; Krylov, V; Macha, J; Tlapakova, T; Kubickova, S; Cernohorska, H; Zarsky, V and Evans, BJ (2013)
    A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis.
    Genome Biology and Evolution 5, 1087-1098 PubMed abstract
  • Cannon, JE; Place, ES; Eve, AMJ; Bradshaw, CR; Sesay, A; Morrell, NW and Smith, JC (2013)
    Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development.
    Mechanisms of Development 130, 122-131 PubMed abstract
  • Horswell, S; Matthews, N and Swanton, C (2013)
    Cancer heterogeneity and "the struggle for existence": diagnostic and analytical challenges.
    Cancer Letters 340, 220-226 PubMed abstract
  • Neves, G; Shah, MM; Liodis, P; Achimastou, A; Denaxa, M; Roalfe, G; Sesay, A; Walker, MC and Pachnis, V (2013)
    The LIM homeodomain protein Lhx6 regulates maturation of interneurons and network excitability in the mammalian cortex.
    Cerebral Cortex 23, 1811-1823 PubMed abstract
  • Sato, S; Sesay, AK and Holder, AA (2013)
    The unique structure of the apicoplast genome of the rodent malaria parasite Plasmodium chabaudi chabaudi.
    PLOS ONE 8, e61778 PubMed abstract
  • Seifertova, E; Zimmerman, LB; Gilchrist, MJ; Macha, J; Kubickova, S; Cernohorska, H; Zarsky, V; Owens, ND; Sesay, AK; Tlapakova, T and Krylov, V (2013)
    Efficient high-throughput sequencing of a laser microdissected chromosome arm.
    BMC Genomics 14, 357 PubMed abstract
  • Gerlinger, M; Rowan, AJ; Horswell, S; Larkin, J; Endesfelder, D; Gronroos, E; Martinez, P; Matthews, N; Stewart, A; Tarpey, P; Varela, I; Phillimore, B; Begum, S; McDonald, NQ; Butler, A; Jones, D; Raine, K; Latimer, C; Santos, CR; Nohadani, M; Eklund, AC; Spencer-Dene, B; Clark, G; Pickering, L; Stamp, G; Gore, M; Szallasi, Z; Downward, J; Futreal, PA and Swanton, C (2012)
    Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
    New England Journal of Medicine 366, 883-892 PubMed abstract
  • Gómez-Gaviro, MV; Scott, CE; Sesay, AK; Matheu, A; Booth, S; Galichet, C and Lovell-Badge, R (2012)
    Betacellulin promotes cell proliferation in the neural stem cell niche and stimulates neurogenesis.
    Proceedings of the National Academy of Sciences of the United States of America 109, 1317-1322 PubMed abstract
  • Kumar, MS; Hancock, DC; Molina-Arcas, M; Steckel, M; East, P; Diefenbacher, M; Armenteros-Monterroso, E; Lassailly, F; Matthews, N; Nye, E; Stamp, G; Behrens, A and Downward, J (2012)
    The GATA2 transcriptional network is requisite for RAS oncogene-driven non-small cell lung cancer.
    Cell 149, 642-655 PubMed abstract
  • McIntosh, PB; Laskey, P; Sullivan, K; Davy, C; Wang, Q; Jackson, DJ; Griffin, HM and Doorbar, J (2010)
    E1^E4-mediated keratin phosphorylation and ubiquitylation: a mechanism for keratin depletion in HPV16-infected epithelium.
    Journal of Cell Science 123, 2810-2822 PubMed abstract
  • Scott, CE; Wynn, SL; Sesay, A; Cruz, C; Cheung, M; Gaviro, M-VG; Booth, S; Gao, B; Cheah, KSE; Lovell-Badge, R and Briscoe, J (2010)
    SOX9 induces and maintains neural stem cells.
    Nature Neuroscience 13, 1181-1189 PubMed abstract

[Page last updated 1 Nov 2017]

Greg ElgarĀ 

greg.elgar@crick.ac.uk
+44 (0) 20 8816 2251