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Precision cancer medicine

Guest editors: Michael Berger and Eliezer Van Allen

Genome Medicine is pleased to present a special issue on Precision Cancer Medicine. It explores how genomics is providing a detailed understanding of cancer and how next generation sequencing can aid diagnosis and guide the development of targeted therapies.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest editors declare no competing interests.

  1. Method

    Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

    The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative...

    Zeynep Kalender Atak, Hana Imrichova, Dmitry Svetlichnyy, Gert Hulselmans, Valerie Christiaens, Joke Reumers, Hugo Ceulemans and Stein Aerts

    Genome Medicine 2017 9:80

    Published on: 30 August 2017

  2. Software

    PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

    The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical dia...

    Kenneth D. Doig, Andrew Fellowes, Anthony H. Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A. Doyle, Ella R. Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T. Papenfuss and Stephen B. Fox

    Genome Medicine 2017 9:38

    Published on: 24 April 2017

  3. Research

    Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

    High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immuno...

    Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Laurie Gay, Siraj M. Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S. Lieber…

    Genome Medicine 2017 9:34

    Published on: 19 April 2017

  4. Research

    Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance

    Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblas...

    David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins and Walter Kolch

    Genome Medicine 2017 9:15

    Published on: 10 February 2017

  5. Research

    Longitudinal analysis of treatment-induced genomic alterations in gliomas

    Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, an...

    E. Zeynep Erson-Omay, Octavian Henegariu, S. Bülent Omay, Akdes Serin Harmancı, Mark W. Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E. Clark, Caner Çağlar, Mehmet Bakırcıoğlu, M. Necmettin Pamir, Viviane Tabar, Alexander O. Vortmeyer, Kaya Bilguvar…

    Genome Medicine 2017 9:12

    Published on: 2 February 2017

  6. Method

    3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets

    Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an indicator of functional impact. We extend such ana...

    Jianjiong Gao, Matthew T. Chang, Hannah C. Johnsen, Sizhi Paul Gao, Brooke E. Sylvester, Selcuk Onur Sumer, Hongxin Zhang, David B. Solit, Barry S. Taylor, Nikolaus Schultz and Chris Sander

    Genome Medicine 2017 9:4

    Published on: 23 January 2017

  7. Research

    Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

    Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has b...

    Jennifer A. Oberg, Julia L. Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N. Sireci, Susan J. Hsiao, Andrew T. Turk, Filemon S. Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J. Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J. Andrews, James H. Garvin…

    Genome Medicine 2016 8:133

    Published on: 23 December 2016

  8. Research

    Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine

    Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been li...

    Masayuki Nagahashi, Toshifumi Wakai, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Ryoma Yagi, Nobuaki Sato, Yuko Kitagawa, Hiroyuki Uetake, Kazuhiro Yoshida, Eiji Oki, Shin-ei Kudo, Hiroshi Izutsu, Keisuke Kodama…

    Genome Medicine 2016 8:136

    Published on: 22 December 2016

  9. Opinion

    Looking beyond the cancer cell for effective drug combinations

    Combinations of therapies are being actively pursued to expand therapeutic options and deal with cancer’s pervasive resistance to treatment. Research efforts to discover effective combination treatments have f...

    Jonathan R. Dry, Mi Yang and Julio Saez-Rodriguez

    Genome Medicine 2016 8:125

    Published on: 25 November 2016

  10. Research

    Somatic cancer variant curation and harmonization through consensus minimum variant level data

    To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (C...

    Deborah I. Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J. Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F. Davis, Reece K. Hart, Christine Micheel, Meredith Weaver, Eliezer M. Van Allen, Donald W. Parsons, Howard L. McLeod, Michael S. Watson, Sharon E. Plon…

    Genome Medicine 2016 8:117

    Published on: 4 November 2016

  11. Research

    A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma

    Precision medicine approaches are ideally suited for rare tumors where comprehensive characterization may have diagnostic, prognostic, and therapeutic value. We describe the clinical case and molecular charact...

    Filemon S. Dela Cruz, Daniel Diolaiti, Andrew T. Turk, Allison R. Rainey, Alberto Ambesi-Impiombato, Stuart J. Andrews, Mahesh M. Mansukhani, Peter L. Nagy, Mariano J. Alvarez, Andrea Califano, Farhad Forouhar, Beata Modzelewski, Chelsey M. Mitchell, Darrell J. Yamashiro, Lianna J. Marks, Julia L. Glade Bender…

    Genome Medicine 2016 8:116

    Published on: 31 October 2016

  12. Review

    Approaches to modernize the combination drug development paradigm

    Recent advances in genomic sequencing and omics-based capabilities are uncovering tremendous therapeutic opportunities and rapidly transforming the field of cancer medicine. Molecularly targeted agents aim to ...

    Daphne Day and Lillian L. Siu

    Genome Medicine 2016 8:115

    Published on: 28 October 2016

  13. Method

    Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer

    Homologous recombination (HR) is the primary pathway for repairing double-strand DNA breaks implicating in the development of cancer. RNAi-based knockdowns of BRCA1 and RAD51 in this pathway have been performed t...

    Yue Wang, Kenneth M. K. Mark, Matthew H. Ung, Arminja Kettenbach, Todd Miller, Wei Xu, Wenqing Cheng, Tian Xia and Chao Cheng

    Genome Medicine 2016 8:114

    Published on: 27 October 2016

  14. Review

    Integrating cancer genomic data into electronic health records

    The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10–15 years. At the same time, new technologies and the electronic health record (EHR) in pa...

    Jeremy L. Warner, Sandeep K. Jain and Mia A. Levy

    Genome Medicine 2016 8:113

    Published on: 26 October 2016

  15. Research

    Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial

    The clinical utility of molecular profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical ...

    Tracy L. Stockley, Amit M. Oza, Hal K. Berman, Natasha B. Leighl, Jennifer J. Knox, Frances A. Shepherd, Eric X. Chen, Monika K. Krzyzanowska, Neesha Dhani, Anthony M. Joshua, Ming-Sound Tsao, Stefano Serra, Blaise Clarke, Michael H. Roehrl, Tong Zhang, Mahadeo A. Sukhai…

    Genome Medicine 2016 8:109

    Published on: 25 October 2016

  16. Research

    Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways

    In high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations but...

    Tushar Tomar, Steven de Jong, Nicolette G. Alkema, Rieks L. Hoekman, Gert Jan Meersma, Harry G. Klip, Ate GJ van der Zee and G. Bea A. Wisman

    Genome Medicine 2016 8:107

    Published on: 20 October 2016

  17. Software

    Rational design of cancer gene panels with OncoPaD

    Profiling the somatic mutations of genes which may inform about tumor evolution, prognostics and treatment is becoming a standard tool in clinical oncology. Commercially available cancer gene panels rely on ma...

    Carlota Rubio-Perez, Jordi Deu-Pons, David Tamborero, Nuria Lopez-Bigas and Abel Gonzalez-Perez

    Genome Medicine 2016 8:98

    Published on: 3 October 2016

  18. Research

    The multi-omic landscape of transcription factor inactivation in cancer

    Hypermethylation of transcription factor promoters bivalently marked in stem cells is a cancer hallmark. However, the biological significance of this observation for carcinogenesis is unclear given that most o...

    Andrew E. Teschendorff, Shijie C. Zheng, Andy Feber, Zhen Yang, Stephan Beck and Martin Widschwendter

    Genome Medicine 2016 8:89

    Published on: 25 August 2016

  19. Research

    Cancer network activity associated with therapeutic response and synergism

    Cancer patients often show no or only modest benefit from a given therapy. This major problem in oncology is generally attributed to the lack of specific predictive biomarkers, yet a global measure of cancer c...

    Jordi Serra-Musach, Francesca Mateo, Eva Capdevila-Busquets, Gorka Ruiz de Garibay, Xiaohu Zhang, Raj Guha, Craig J. Thomas, Judit Grueso, Alberto Villanueva, Samira Jaeger, Holger Heyn, Miguel Vizoso, Hector Pérez, Alex Cordero, Eva Gonzalez-Suarez, Manel Esteller…

    Genome Medicine 2016 8:88

    Published on: 24 August 2016