Now showing items 1-20 of 32

    • Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. 

      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, Z; 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; CRUK-ICGC Prostate Group; 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; Eeles, R; Cooper, CS; Brewer, DS (2017-09-25)
      A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively ...
    • CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation. 

      Whiffin, N; Walsh, R; Govind, R; Edwards, M; Ahmad, M; Zhang, X; Tayal, U; Buchan, R; Midwinter, W; Wilk, AE; Najgebauer, H; Francis, C; Wilkinson, S; Monk, T; Brett, L; O'Regan, DP; Prasad, SK; Morris-Rosendahl, DJ; Barton, PJR; Edwards, E; Ware, JS; Cook, SA (2018-10)
      PURPOSE:Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier ( ...
    • Circulating tumor DNA-From bench to bedside. 

      Lim, JSJ; Janku, F; Yap, TA (2017-05)
      In the era of personalized medicine, tumor sampling is paramount to enable the assessment of actionable molecular aberrations to help rationalize and guide treatment decisions. Longitudinal tracking of such aberrations may ...
    • Combinatorial drug therapy for cancer in the post-genomic era. 

      Al-Lazikani, B; Banerji, U; Workman, P (2012-07-10)
      Over the past decade, whole genome sequencing and other 'omics' technologies have defined pathogenic driver mutations to which tumor cells are addicted. Such addictions, synthetic lethalities and other tumor vulnerabilities ...
    • Comprehensive translocation and clonality detection in lymphoproliferative disorders by next-generation sequencing. 

      Wren, D; Walker, BA; Brüggemann, M; Catherwood, MA; Pott, C; Stamatopoulos, K; Langerak, AW; Gonzalez, D; EuroClonality-NGS consortium (2017-02)
    • CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. 

      Münz, M; Ruark, E; Renwick, A; Ramsay, E; Clarke, M; Mahamdallie, S; Cloke, V; Seal, S; Strydom, A; Lunter, G; Rahman, N (2015-07-28)
      Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision ...
    • Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis. 

      Morfopoulou, S; Mee, ET; Connaughton, SM; Brown, JR; Gilmour, K; Chong, WKK; Duprex, WP; Ferguson, D; Hubank, M; Hutchinson, C; Kaliakatsos, M; McQuaid, S; Paine, S; Plagnol, V; Ruis, C; Virasami, A; Zhan, H; Jacques, TS; Schepelmann, S; Qasim, W; Breuer, J (2017-01)
      Routine childhood vaccination against measles, mumps and rubella has virtually abolished virus-related morbidity and mortality. Notwithstanding this, we describe here devastating neurological complications associated with ...
    • Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach. 

      Pender, A; Garcia-Murillas, I; Rana, S; Cutts, RJ; Kelly, G; Fenwick, K; Kozarewa, I; Gonzalez de Castro, D; Bhosle, J; O'Brien, M; Turner, NC; Popat, S; Downward, J (2015-01)
      Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection ...
    • FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment. 

      Wilkins, A; Chauhan, R; Rust, A; Pearson, A; Daley, F; Manodoro, F; Fenwick, K; Bliss, J; Yarnold, J; Somaiah, N (2018-08)
      BACKGROUND:Bio-banked formalin-fixed paraffin-embedded (FFPE) tissues provide an excellent opportunity for translational genomic research. Historically matched blood has not always been collected as a source of germline ...
    • Gene Copy Number Estimation from Targeted Next-Generation Sequencing of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification. 

      Seed, G; Yuan, W; Mateo, J; Carreira, S; Bertan, C; Lambros, M; Boysen, G; Ferraldeschi, R; Miranda, S; Figueiredo, I; Riisnaes, R; Crespo, M; Rodrigues, DN; Talevich, E; Robinson, DR; Kunju, LP; Wu, Y-M; Lonigro, R; Sandhu, S; Chinnaiyan, AM; de Bono, JS (2017-10)
      Purpose: Precise detection of copy number aberrations (CNA) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next-generation sequencing (NGS) is inexpensive, ...
    • A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. 

      Vijayakrishnan, J; Kumar, R; Henrion, MYR; Moorman, AV; Rachakonda, PS; Hosen, I; da Silva Filho, MI; Holroyd, A; Dobbins, SE; Koehler, R; Thomsen, H; Irving, JA; Allan, JM; Lightfoot, T; Roman, E; Kinsey, SE; Sheridan, E; Thompson, PD; Hoffmann, P; Nöthen, MM; Heilmann-Heimbach, S; Jöckel, KH; Greaves, M; Harrison, CJ; Bartram, CR; Schrappe, M; Stanulla, M; Hemminki, K; Houlston, RS (2017-03)
      Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype ...
    • High throughput sequencing in acute lymphoblastic leukemia reveals clonal architecture of central nervous system and bone marrow compartments. 

      Bartram, J; Goulden, N; Wright, G; Adams, S; Brooks, T; Edwards, D; Inglott, S; Yousafzai, Y; Hubank, M; Halsey, C (2018-03)
    • Identification of neutral tumor evolution across cancer types. 

      Williams, MJ; Werner, B; Barnes, CP; Graham, TA; Sottoriva, A (2016-03)
      Despite extraordinary efforts to profile cancer genomes, interpreting the vast amount of genomic data in the light of cancer evolution remains challenging. Here we demonstrate that neutral tumor evolution results in a ...
    • Identification of single nucleotide variants using position-specific error estimation in deep sequencing data. 

      Kleftogiannis, D; Punta, M; Jayaram, A; Sandhu, S; Wong, SQ; Gasi Tandefelt, D; Conteduca, V; Wetterskog, D; Attard, G; Lise, S (2019-08-02)
      BACKGROUND:Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. ...
    • Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. 

      Nava Rodrigues, D; Rescigno, P; Liu, D; Yuan, W; Carreira, S; Lambros, MB; Seed, G; Mateo, J; Riisnaes, R; Mullane, S; Margolis, C; Miao, D; Miranda, S; Dolling, D; Clarke, M; Bertan, C; Crespo, M; Boysen, G; Ferreira, A; Sharp, A; Figueiredo, I; Keliher, D; Aldubayan, S; Burke, KP; Sumanasuriya, S; Fontes, MS; Bianchini, D; Zafeiriou, Z; Teixeira Mendes, LS; Mouw, K; Schweizer, MT; Pritchard, CC; Salipante, S; Taplin, M-E; Beltran, H; Rubin, MA; Cieslik, M; Robinson, D; Heath, E; Schultz, N; Armenia, J; Abida, W; Scher, H; Lord, C; D'Andrea, A; Sawyers, CL; Chinnaiyan, AM; Alimonti, A; Nelson, PS; Drake, CG; Van Allen, EM; de Bono, JS (2018-10)
      BACKGROUND:Understanding the integrated immunogenomic landscape of advanced prostate cancer (APC) could impact stratified treatment selection. METHODS:Defective mismatch repair (dMMR) status was determined by either loss ...
    • 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 ...
    • Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. 

      Garcia-Murillas, I; Schiavon, G; Weigelt, B; Ng, C; Hrebien, S; Cutts, RJ; Cheang, M; Osin, P; Nerurkar, A; Kozarewa, I; Garrido, JA; Dowsett, M; Reis-Filho, JS; Smith, IE; Turner, NC (2015-08)
      The identification of early-stage breast cancer patients at high risk of relapse would allow tailoring of adjuvant therapy approaches. We assessed whether analysis of circulating tumor DNA (ctDNA) in plasma can be used to ...
    • Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies. 

      Larson, NB; McDonnell, S; Albright, LC; Teerlink, C; Stanford, J; Ostrander, EA; Isaacs, WB; Xu, J; Cooney, KA; Lange, E; Schleutker, J; Carpten, JD; Powell, I; Bailey-Wilson, J; Cussenot, O; Cancel-Tassin, G; Giles, G; MacInnis, R; Maier, C; Whittemore, AS; Hsieh, C-L; Wiklund, F; Catalona, WJ; Foulkes, W; Mandal, D; Eeles, R; Kote-Jarai, Z; Ackerman, MJ; Olson, TM; Klein, CJ; Thibodeau, SN; Schaid, DJ (2016-09)
      Rare variants (RVs) have been shown to be significant contributors to complex disease risk. By definition, these variants have very low minor allele frequencies and traditional single-marker methods for statistical analysis ...
    • 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 ...
    • Quantification of subclonal selection in cancer from bulk sequencing data. 

      Williams, MJ; Werner, B; Heide, T; Curtis, C; Barnes, CP; Sottoriva, A; Graham, TA (2018-06)
      Subclonal architectures are prevalent across cancer types. However, the temporal evolutionary dynamics that produce tumor subclones remain unknown. Here we measure clone dynamics in human cancers by using computational ...