Now showing items 1-11 of 11

    • Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer. 

      Lote, H; Spiteri, I; Ermini, L; Vatsiou, A; Roy, A; McDonald, A; Maka, N; Balsitis, M; Bose, N; Simbolo, M; Mafficini, A; Lampis, A; Hahne, JC; Trevisani, F; Eltahir, Z; Mentrasti, G; Findlay, C; Kalkman, EAJ; Punta, M; Werner, B; Lise, S; Aktipis, A; Maley, C; Greaves, M; Braconi, C; White, J; Fassan, M; Scarpa, A; Sottoriva, A; Valeri, N
      Background: Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but ...
    • Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer. 

      Lote, H; Spiteri, I; Ermini, L; Vatsiou, A; Roy, A; McDonald, A; Maka, N; Balsitis, M; Bose, N; Simbolo, M; Mafficini, A; Lampis, A; Hahne, JC; Trevisani, F; Eltahir, Z; Mentrasti, G; Findlay, C; Kalkman, EAJ; Punta, M; Werner, B; Lise, S; Aktipis, A; Maley, C; Greaves, M; Braconi, C; White, J; Fassan, M; Scarpa, A; Sottoriva, A; Valeri, N (2017-06)
      Background Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but ...
    • Clinical <i>BRCA1/2</i> Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance. 

      Pettitt, SJ; Frankum, JR; Punta, M; Lise, S; Alexander, J; Chen, Y; Yap, TA; Haider, S; Tutt, ANJ; Lord, CJ (2020-10)
      Reversion mutations in <i>BRCA1</i> or <i>BRCA2</i> are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, and analyzed more than 300 ...
    • Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer. 

      von Loga, K; Woolston, A; Punta, M; Barber, LJ; Griffiths, B; Semiannikova, M; Spain, G; Challoner, B; Fenwick, K; Simon, R; Marx, A; Sauter, G; Lise, S; Matthews, N; Gerlinger, M (2020-01-16)
      Mismatch repair deficient (dMMR) gastro-oesophageal adenocarcinomas (GOAs) show better outcomes than their MMR-proficient counterparts and high immunotherapy sensitivity. The hypermutator-phenotype of dMMR tumours theoretically ...
    • Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer. 

      Woolston, A; Khan, K; Spain, G; Barber, LJ; Griffiths, B; Gonzalez-Exposito, R; Hornsteiner, L; Punta, M; Patil, Y; Newey, A; Mansukhani, S; Davies, MN; Furness, A; Sclafani, F; Peckitt, C; Jiménez, M; Kouvelakis, K; Ranftl, R; Begum, R; Rana, I; Thomas, J; Bryant, A; Quezada, S; Wotherspoon, A; Khan, N; Fotiadis, N; Marafioti, T; Powles, T; Lise, S; Calvo, F; Guettler, S; von Loga, K; Rao, S; Watkins, D; Starling, N; Chau, I; Sadanandam, A; Cunningham, D; Gerlinger, M (2019-07)
      Despite biomarker stratification, the anti-EGFR antibody cetuximab is only effective against a subgroup of colorectal cancers (CRCs). This genomic and transcriptomic analysis of the cetuximab resistance landscape in 35 RAS ...
    • <i>In Vivo</i> Modeling of Chemoresistant Neuroblastoma Provides New Insights into Chemorefractory Disease and Metastasis. 

      Yogev, O; Almeida, GS; Barker, KT; George, SL; Kwok, C; Campbell, J; Zarowiecki, M; Kleftogiannis, D; Smith, LM; Hallsworth, A; Berry, P; Möcklinghoff, T; Webber, HT; Danielson, LS; Buttery, B; Calton, EA; da Costa, BM; Poon, E; Jamin, Y; Lise, S; Veal, GJ; Sebire, N; Robinson, SP; Anderson, J; Chesler, L (2019-10)
      Neuroblastoma is a pediatric cancer that is frequently metastatic and resistant to conventional treatment. In part, a lack of natively metastatic, chemoresistant <i>in vivo</i> models has limited our insight into the ...
    • Identification of single nucleotide variants using position-specific error estimation in deep sequencing data 

      Kleftogiannis, D; Punta, M; Jayaram, A; Sandhu, S; Wong, S; Gasi Tandefelt, D; Conteduca, V; Wetterskog, D; Attard, G; Lise, S (2018-11-23)
      <h4>Background</h4> 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 ...
    • 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. ...
    • Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. 

      Heindl, A; Khan, AM; Rodrigues, DN; Eason, K; Sadanandam, A; Orbegoso, C; Punta, M; Sottoriva, A; Lise, S; Banerjee, S; Yuan, Y (2018-09-25)
      How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial statistical analyses in 514 high grade serous ovarian samples to ...
    • The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer. 

      Barry, P; Vatsiou, A; Spiteri, I; Nichol, D; Cresswell, GD; Acar, A; Trahearn, N; Hrebien, S; Garcia-Murillas, I; Chkhaidze, K; Ermini, L; Huntingford, IS; Cottom, H; Zabaglo, L; Koelble, K; Khalique, S; Rusby, JE; Muscara, F; Dowsett, M; Maley, CC; Natrajan, R; Yuan, Y; Schiavon, G; Turner, N; Sottoriva, A (2018-10)
      <b>Purpose:</b> The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our ...
    • Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing. 

      Mansukhani, S; Barber, LJ; Kleftogiannis, D; Moorcraft, SY; Davidson, M; Woolston, A; Proszek, PZ; Griffiths, B; Fenwick, K; Herman, B; Matthews, N; O'Leary, B; Hulkki, S; Gonzalez De Castro, D; Patel, A; Wotherspoon, A; Okachi, A; Rana, I; Begum, R; Davies, MN; Powles, T; von Loga, K; Hubank, M; Turner, N; Watkins, D; Chau, I; Cunningham, D; Lise, S; Starling, N; Gerlinger, M (2018-11)
      Background Circulating free DNA sequencing (cfDNA-Seq) can portray cancer genome landscapes, but highly sensitive and specific technologies are necessary to accurately detect mutations with often low variant frequencies.Methods ...