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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. Content type: Method

    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...

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

    Citation: Genome Medicine 2017 9:80

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  2. Content type: Software

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:38

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  3. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:34

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  4. Content type: Research

    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...

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

    Citation: Genome Medicine 2017 9:15

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  5. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2017 9:12

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  6. Content type: Method

    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...

    Authors: 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

    Citation: Genome Medicine 2017 9:4

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  7. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:133

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  8. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:136

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  9. Content type: Method

    Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are und...

    Authors: Chengliang Dong, Yunfei Guo, Hui Yang, Zeyu He, Xiaoming Liu and Kai Wang

    Citation: Genome Medicine 2016 8:135

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  10. Content type: Opinion

    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...

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

    Citation: Genome Medicine 2016 8:125

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  11. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:117

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  12. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:116

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  13. Content type: Method

    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...

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

    Citation: Genome Medicine 2016 8:114

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  14. Content type: Review

    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...

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

    Citation: Genome Medicine 2016 8:113

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  15. Content type: Research

    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 ...

    Authors: 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…

    Citation: Genome Medicine 2016 8:109

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  16. Content type: Opinion

    Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make P...

    Authors: Gabrielle Bertier, Jian Carrot-Zhang, Vassilis Ragoussis and Yann Joly

    Citation: Genome Medicine 2016 8:108

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  17. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2016 8:107

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  18. Content type: Comment

    Advances in genetic analysis have revealed new complexities in the interpretation of genetic variants. Correct assessment of a genetic variant relies on the clinical context and knowledge of the underlying bio...

    Authors: Eric Q. Konnick and Colin C. Pritchard

    Citation: Genome Medicine 2016 8:100

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  19. Content type: Software

    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...

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

    Citation: Genome Medicine 2016 8:98

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  20. Content type: Research

    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...

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

    Citation: Genome Medicine 2016 8:89

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  21. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2016 8:88

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