Now showing items 1-17 of 17

    • canSAR: an integrated cancer public translational research and drug discovery resource. 

      Halling-Brown, MD; Bulusu, KC; Patel, M; Tym, JE; Al-Lazikani, B (2012-01)
      canSAR is a fully integrated cancer research and drug discovery resource developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification ...
    • canSAR: updated cancer research and drug discovery knowledgebase. 

      Bulusu, KC; Tym, JE; Coker, EA; Schierz, AC; Al-Lazikani, B (2014-01)
      canSAR (http://cansar.icr.ac.uk) is a public integrative cancer-focused knowledgebase for the support of cancer translational research and drug discovery. Through the integration of biological, pharmacological, chemical, ...
    • ELM: the status of the 2010 eukaryotic linear motif resource. 

      Gould, CM; Diella, F; Via, A; Puntervoll, P; Gemünd, C; Chabanis-Davidson, S; Michael, S; Sayadi, A; Bryne, JC; Chica, C; Seiler, M; Davey, NE; Haslam, N; Weatheritt, RJ; Budd, A; Hughes, T; Pas, J; Rychlewski, L; Travé, G; Aasland, R; Helmer-Citterich, M; Linding, R; Gibson, TJ (2010-01)
      Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. ...
    • GENCODE reference annotation for the human and mouse genomes. 

      Frankish, A; Diekhans, M; Ferreira, A-M; Johnson, R; Jungreis, I; Loveland, J; Mudge, JM; Sisu, C; Wright, J; Armstrong, J; Barnes, I; Berry, A; Bignell, A; Carbonell Sala, S; Chrast, J; Cunningham, F; Di Domenico, T; Donaldson, S; Fiddes, IT; García Girón, C; Gonzalez, JM; Grego, T; Hardy, M; Hourlier, T; Hunt, T; Izuogu, OG; Lagarde, J; Martin, FJ; Martínez, L; Mohanan, S; Muir, P; Navarro, FCP; Parker, A; Pei, B; Pozo, F; Ruffier, M; Schmitt, BM; Stapleton, E; Suner, M-M; Sycheva, I; Uszczynska-Ratajczak, B; Xu, J; Yates, A; Zerbino, D; Zhang, Y; Aken, B; Choudhary, JS; Gerstein, M; Guigó, R; Hubbard, TJP; Kellis, M; Paten, B; Reymond, A; Tress, ML; Flicek, P (2019-01)
      The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 ...
    • Generation and characterisation of two D2A1 mammary cancer sublines to model spontaneous and experimental metastasis in a syngeneic BALB/c host. 

      Jungwirth, U; van Weverwijk, A; Melake, MJ; Chambers, AF; Gao, Q; Fivaz, M; Isacke, CM (2018-01-18)
      Studying the complex mechanisms underlying breast cancer metastasis and therapy response necessitates relevant in vivo models, particularly syngeneic models with an intact immune system. Two syngeneic spontaneously metastatic ...
    • Genetic correlation between multiple myeloma and chronic lymphocytic leukaemia provides evidence for shared aetiology. 

      Went, M; Sud, A; Speedy, H; Sunter, NJ; Försti, A; Law, PJ; Johnson, DC; Mirabella, F; Holroyd, A; Li, N; Orlando, G; Weinhold, N; van Duin, M; Chen, B; Mitchell, JS; Mansouri, L; Juliusson, G; Smedby, KE; Jayne, S; Majid, A; Dearden, C; Allsup, DJ; Bailey, JR; Pratt, G; Pepper, C; Fegan, C; Rosenquist, R; Kuiper, R; Stephens, OW; Bertsch, U; Broderick, P; Einsele, H; Gregory, WM; Hillengass, J; Hoffmann, P; Jackson, GH; Jöckel, K-H; Nickel, J; Nöthen, MM; da Silva Filho, MI; Thomsen, H; Walker, BA; Broyl, A; Davies, FE; Hansson, M; Goldschmidt, H; Dyer, MJS; Kaiser, M; Sonneveld, P; Morgan, GJ; Hemminki, K; Nilsson, B; Catovsky, D; Allan, JM; Houlston, RS (2018-12-21)
      The clustering of different types of B-cell malignancies in families raises the possibility of shared aetiology. To examine this, we performed cross-trait linkage disequilibrium (LD)-score regression of multiple myeloma ...
    • Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. 

      Zeng, C; Guo, X; Long, J; Kuchenbaecker, KB; Droit, A; Michailidou, K; Ghoussaini, M; Kar, S; Freeman, A; Hopper, JL; Milne, RL; Bolla, MK; Wang, Q; Dennis, J; Agata, S; Ahmed, S; Aittomäki, K; Andrulis, IL; Anton-Culver, H; Antonenkova, NN; Arason, A; Arndt, V; Arun, BK; Arver, B; Bacot, F; Barrowdale, D; Baynes, C; Beeghly-Fadiel, A; Benitez, J; Bermisheva, M; Blomqvist, C; Blot, WJ; Bogdanova, NV; Bojesen, SE; Bonanni, B; Borresen-Dale, A-L; Brand, JS; Brauch, H; Brennan, P; Brenner, H; Broeks, A; Brüning, T; Burwinkel, B; Buys, SS; Cai, Q; Caldes, T; Campbell, I; Carpenter, J; Chang-Claude, J; Choi, J-Y; Claes, KBM; Clarke, C; Cox, A; Cross, SS; Czene, K; Daly, MB; de la Hoya, M; De Leeneer, K; Devilee, P; Diez, O; Domchek, SM; Doody, M; Dorfling, CM; Dörk, T; Dos-Santos-Silva, I; Dumont, M; Dwek, M; Dworniczak, B; Egan, K; Eilber, U; Einbeigi, Z; Ejlertsen, B; Ellis, S; Frost, D; Lalloo, F; EMBRACE; Fasching, PA; Figueroa, J; Flyger, H; Friedlander, M; Friedman, E; Gambino, G; Gao, Y-T; Garber, J; García-Closas, M; Gehrig, A; Damiola, F; Lesueur, F; Mazoyer, S; Stoppa-Lyonnet, D; behalf of GEMO Study Collaborators; Giles, GG; Godwin, AK; Goldgar, DE; González-Neira, A; Greene, MH; Guénel, P; Haeberle, L; Haiman, CA; Hallberg, E; Hamann, U; Hansen, TVO; Hart, S; Hartikainen, JM; Hartman, M; Hassan, N; Healey, S; Hogervorst, FBL; Verhoef, S; HEBON; Hendricks, CB; Hillemanns, P; Hollestelle, A; Hulick, PJ; Hunter, DJ; Imyanitov, EN; Isaacs, C; Ito, H; Jakubowska, A; Janavicius, R; Jaworska-Bieniek, K; Jensen, UB; John, EM; Joly Beauparlant, C; Jones, M; Kabisch, M; Kang, D; Karlan, BY; Kauppila, S; Kerin, MJ; Khan, S; Khusnutdinova, E; Knight, JA; Konstantopoulou, I; Kraft, P; Kwong, A; Laitman, Y; Lambrechts, D; Lazaro, C; Le Marchand, L; Lee, CN; Lee, MH; Lester, J; Li, J; Liljegren, A; Lindblom, A; Lophatananon, A; Lubinski, J; Mai, PL; Mannermaa, A; Manoukian, S; Margolin, S; Marme, F; Matsuo, K; McGuffog, L; Meindl, A; Menegaux, F; Montagna, M; Muir, K; Mulligan, AM; Nathanson, KL; Neuhausen, SL; Nevanlinna, H; Newcomb, PA; Nord, S; Nussbaum, RL; Offit, K; Olah, E; Olopade, OI; Olswold, C; Osorio, A; Papi, L; Park-Simon, T-W; Paulsson-Karlsson, Y; Peeters, S; Peissel, B; Peterlongo, P; Peto, J; Pfeiler, G; Phelan, CM; Presneau, N; Radice, P; Rahman, N; Ramus, SJ; Rashid, MU; Rennert, G; Rhiem, K; Rudolph, A; Salani, R; Sangrajrang, S; Sawyer, EJ; Schmidt, MK; Schmutzler, RK; Schoemaker, MJ; Schürmann, P; Seynaeve, C; Shen, C-Y; Shrubsole, MJ; Shu, X-O; Sigurdson, A; Singer, CF; Slager, S; Soucy, P; Southey, M; Steinemann, D; Swerdlow, A; Szabo, CI; Tchatchou, S; Teixeira, MR; Teo, SH; Terry, MB; Tessier, DC; Teulé, A; Thomassen, M; Tihomirova, L; Tischkowitz, M; Toland, AE; Tung, N; Turnbull, C; van den Ouweland, AMW; van Rensburg, EJ; Ven den Berg, D; Vijai, J; Wang-Gohrke, S; Weitzel, JN; Whittemore, AS; Winqvist, R; Wong, TY; Wu, AH; Yannoukakos, D; Yu, J-C; Pharoah, PDP; Hall, P; Chenevix-Trench, G; KConFab; AOCS Investigators; Dunning, AM; Simard, J; Couch, FJ; Antoniou, AC; Easton, DF; Zheng, W (2016-06-21)
      BACKGROUND:Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD:We performed a fine-scale ...
    • Identification of recurrent noncoding mutations in B-cell lymphoma using capture Hi-C. 

      Cornish, AJ; Hoang, PH; Dobbins, SE; Law, PJ; Chubb, D; Orlando, G; Houlston, RS (2019-01)
      The identification of driver mutations is fundamental to understanding oncogenesis. Although genes frequently mutated in B-cell lymphoma have been identified, the search for driver mutations has largely focused on the ...
    • Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis. 

      Turajlic, S; Litchfield, K; Xu, H; Rosenthal, R; McGranahan, N; Reading, JL; Wong, YNS; Rowan, A; Kanu, N; Al Bakir, M; Chambers, T; Salgado, R; Savas, P; Loi, S; Birkbak, NJ; Sansregret, L; Gore, M; Larkin, J; Quezada, SA; Swanton, C (2017-08)
      BACKGROUND:The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the ...
    • MicroRNA and gene co-expression networks characterize biological and clinical behavior of rhabdomyosarcomas. 

      Missiaglia, E; Shepherd, CJ; Aladowicz, E; Olmos, D; Selfe, J; Pierron, G; Delattre, O; Walters, Z; Shipley, J (2017-01)
      Rhabdomyosarcomas (RMS) in children and adolescents are heterogeneous sarcomas broadly defined by skeletal muscle features and the presence/absence of PAX3/7-FOXO1 fusion genes. MicroRNAs are small non-coding RNAs that ...
    • Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations. 

      Rebbeck, TR; Friebel, TM; Friedman, E; Hamann, U; Huo, D; Kwong, A; Olah, E; Olopade, OI; Solano, AR; Teo, S-H; Thomassen, M; Weitzel, JN; Chan, TL; Couch, FJ; Goldgar, DE; Kruse, TA; Palmero, EI; Park, SK; Torres, D; van Rensburg, EJ; McGuffog, L; Parsons, MT; Leslie, G; Aalfs, CM; Abugattas, J; Adlard, J; Agata, S; Aittomäki, K; Andrews, L; Andrulis, IL; Arason, A; Arnold, N; Arun, BK; Asseryanis, E; Auerbach, L; Azzollini, J; Balmaña, J; Barile, M; Barkardottir, RB; Barrowdale, D; Benitez, J; Berger, A; Berger, R; Blanco, AM; Blazer, KR; Blok, MJ; Bonadona, V; Bonanni, B; Bradbury, AR; Brewer, C; Buecher, B; Buys, SS; Caldes, T; Caliebe, A; Caligo, MA; Campbell, I; Caputo, SM; Chiquette, J; Chung, WK; Claes, KBM; Collée, JM; Cook, J; Davidson, R; de la Hoya, M; De Leeneer, K; de Pauw, A; Delnatte, C; Diez, O; Ding, YC; Ditsch, N; Domchek, SM; Dorfling, CM; Velazquez, C; Dworniczak, B; Eason, J; Easton, DF; Eeles, R; Ehrencrona, H; Ejlertsen, B; EMBRACE; Engel, C; Engert, S; Evans, DG; Faivre, L; Feliubadaló, L; Ferrer, SF; Foretova, L; Fowler, J; Frost, D; Galvão, HCR; Ganz, PA; Garber, J; Gauthier-Villars, M; Gehrig, A; GEMO Study Collaborators; Gerdes, A-M; Gesta, P; Giannini, G; Giraud, S; Glendon, G; Godwin, AK; Greene, MH; Gronwald, J; Gutierrez-Barrera, A; Hahnen, E; Hauke, J; HEBON; Henderson, A; Hentschel, J; Hogervorst, FBL; Honisch, E; Imyanitov, EN; Isaacs, C; Izatt, L; Izquierdo, A; Jakubowska, A; James, P; Janavicius, R; Jensen, UB; John, EM; Vijai, J; Kaczmarek, K; Karlan, BY; Kast, K; Investigators, K; Kim, S-W; Konstantopoulou, I; Korach, J; Laitman, Y; Lasa, A; Lasset, C; Lázaro, C; Lee, A; Lee, MH; Lester, J; Lesueur, F; Liljegren, A; Lindor, NM; Longy, M; Loud, JT; Lu, KH; Lubinski, J; Machackova, E; Manoukian, S; Mari, V; Martínez-Bouzas, C; Matrai, Z; Mebirouk, N; Meijers-Heijboer, HEJ; Meindl, A; Mensenkamp, AR; Mickys, U; Miller, A; Montagna, M; Moysich, KB; Mulligan, AM; Musinsky, J; Neuhausen, SL; Nevanlinna, H; Ngeow, J; Nguyen, HP; Niederacher, D; Nielsen, HR; Nielsen, FC; Nussbaum, RL; Offit, K; Öfverholm, A; Ong, K-R; Osorio, A; Papi, L; Papp, J; Pasini, B; Pedersen, IS; Peixoto, A; Peruga, N; Peterlongo, P; Pohl, E; Pradhan, N; Prajzendanc, K; Prieur, F; Pujol, P; Radice, P; Ramus, SJ; Rantala, J; Rashid, MU; Rhiem, K; Robson, M; Rodriguez, GC; Rogers, MT; Rudaitis, V; Schmidt, AY; Schmutzler, RK; Senter, L; Shah, PD; Sharma, P; Side, LE; Simard, J; Singer, CF; Skytte, A-B; Slavin, TP; Snape, K; Sobol, H; Southey, M; Steele, L; Steinemann, D; Sukiennicki, G; Sutter, C; Szabo, CI; Tan, YY; Teixeira, MR; Terry, MB; Teulé, A; Thomas, A; Thull, DL; Tischkowitz, M; Tognazzo, S; Toland, AE; Topka, S; Trainer, AH; Tung, N; van Asperen, CJ; van der Hout, AH; van der Kolk, LE; van der Luijt, RB; Van Heetvelde, M; Varesco, L; Varon-Mateeva, R; Vega, A; Villarreal-Garza, C; von Wachenfeldt, A; Walker, L; Wang-Gohrke, S; Wappenschmidt, B; Weber, BHF; Yannoukakos, D; Yoon, S-Y; Zanzottera, C; Zidan, J; Zorn, KK; Hutten Selkirk, CG; Hulick, PJ; Chenevix-Trench, G; Spurdle, AB; Antoniou, AC; Nathanson, KL (2018-05)
      The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of ...
    • A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies. 

      Nyamundanda, G; Poudel, P; Patil, Y; Sadanandam, A (2017-09-07)
      Genome projects now generate large-scale data often produced at various time points by different laboratories using multiple platforms. This increases the potential for batch effects. Currently there are several batch ...
    • p.Val804Met, the Most Frequent Pathogenic Mutation in RET, Confers a Very Low Lifetime Risk of Medullary Thyroid Cancer. 

      Loveday, C; Josephs, K; Chubb, D; Gunning, A; Izatt, L; Tischkowitz, M; Ellard, S; Turnbull, C (2018-11)
      Context:To date, penetrance figures for medullary thyroid cancer (MTC) for variants in rearranged during transfection (RET) have been estimated from families ascertained because of the presence of MTC. Objective:To gain ...
    • The predicted impact of coding single nucleotide polymorphisms database. 

      Rudd, MF; Williams, RD; Webb, EL; Schmidt, S; Sellick, GS; Houlston, RS (2005-11)
      Nonsynonymous single nucleotide polymorphisms (nsSNP) have the potential to affect the structure or function of expressed proteins and are, therefore, likely to represent modifiers of inherited susceptibility. We have ...
    • Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer. 

      Orlando, G; Law, PJ; Cornish, AJ; Dobbins, SE; Chubb, D; Broderick, P; Litchfield, K; Hariri, F; Pastinen, T; Osborne, CS; Taipale, J; Houlston, RS (2018-10)
      Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1-6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the ...
    • Protein-altering germline mutations implicate novel genes related to lung cancer development. 

      Ji, X; Mukherjee, S; Landi, MT; Bosse, Y; Joubert, P; Zhu, D; Gorlov, I; Xiao, X; Han, Y; Gorlova, O; Hung, RJ; Brhane, Y; Carreras-Torres, R; Christiani, DC; Caporaso, N; Johansson, M; Liu, G; Bojesen, SE; Le Marchand, L; Albanes, D; Bickeböller, H; Aldrich, MC; Bush, WS; Tardon, A; Rennert, G; Chen, C; Byun, J; Dragnev, KH; Field, JK; Kiemeney, LF; Lazarus, P; Zienolddiny, S; Lam, S; Schabath, MB; Andrew, AS; Bertazzi, PA; Pesatori, AC; Diao, N; Su, L; Song, L; Zhang, R; Leighl, N; Johansen, JS; Mellemgaard, A; Saliba, W; Haiman, C; Wilkens, L; Fernandez-Somoano, A; Fernandez-Tardon, G; Heijden, EHFMVD; Kim, JH; Davies, MPA; Marcus, MW; Brunnström, H; Manjer, J; Melander, O; Muller, DC; Overvad, K; Trichopoulou, A; Tumino, R; Goodman, GE; Cox, A; Taylor, F; Woll, P; Wichmann, E; Muley, T; Risch, A; Rosenberger, A; Grankvist, K; Johansson, M; Shepherd, F; Tsao, M-S; Arnold, SM; Haura, EB; Bolca, C; Holcatova, I; Janout, V; Kontic, M; Lissowska, J; Mukeria, A; Ognjanovic, S; Orlowski, TM; Scelo, G; Swiatkowska, B; Zaridze, D; Bakke, P; Skaug, V; Butler, LM; Offit, K; Srinivasan, P; Bandlamudi, C; Hellmann, MD; Solit, DB; Robson, ME; Rudin, CM; Stadler, ZK; Taylor, BS; Berger, MF; Houlston, R; McLaughlin, J; Stevens, V; Nickle, DC; Obeidat, M; Timens, W; Artigas, MS; Shete, S; Brenner, H; Chanock, S; Brennan, P; McKay, JD; Amos, CI (2020-05-11)
      Few germline mutations are known to affect lung cancer risk. We performed analyses of rare variants from 39,146 individuals of European ancestry and investigated gene expression levels in 7,773 samples. We find a large-effect ...
    • Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23-gene panel with utility for non-invasive diagnosis and risk stratification. 

      Ward, DG; Gordon, NS; Boucher, RH; Pirrie, SJ; Baxter, L; Ott, S; Silcock, L; Whalley, CM; Stockton, JD; Beggs, AD; Griffiths, M; Abbotts, B; Ijakipour, H; Latheef, FN; Robinson, RA; White, AJ; James, ND; Zeegers, MP; Cheng, KK; Bryan, RT (2019-09)
      OBJECTIVES:To develop a focused panel of somatic mutations (SMs) present in the majority of urothelial bladder cancers (UBCs), to investigate the diagnostic and prognostic utility of this panel, and to compare the ...