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Cancer Genomics

Genome Biology Collection

cancer genomics © Ewing et al., Genome Biology (2013)Cancer is a disease of the genome, arising from various types of genomic changes that alter the behaviour of cells. A number of genomic and post-genomic studies have been conducted to provide insight into the molecular mechanisms underlying the development of cancer. In this Genome Biology collection, we showcase recent efforts to provide a comprehensive perspective on cancer, including tumor initiation, metastasis, and drug resistance.

  1. Content type: Research

    Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characteriz...

    Authors: Amin Emad, Junmei Cairns, Krishna R. Kalari, Liewei Wang and Saurabh Sinha

    Citation: Genome Biology 2017 18:153

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  2. Content type: Method

    Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

    Authors: Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp and Sohrab P. Shah

    Citation: Genome Biology 2017 18:140

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    The Correction to this article has been published in Genome Biology 2017 18:188

  3. Content type: Method

    We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

    Authors: Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

    Citation: Genome Biology 2017 18:141

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  4. Content type: Method

    Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, i...

    Authors: Louise Harewood, Kamal Kishore, Matthew D. Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V. Peter Collins and Peter Fraser

    Citation: Genome Biology 2017 18:125

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  5. Content type: Research

    Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

    Authors: Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

    Citation: Genome Biology 2017 18:98

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  6. Content type: Research Highlight

    Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

    Authors: Gabriel J. Sandoval and William C. Hahn

    Citation: Genome Biology 2017 18:95

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  7. Content type: Method

    Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues...

    Authors: Grace O. Silva, Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou and Mengjie Chen

    Citation: Genome Biology 2017 18:66

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  8. Content type: Method

    We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously inf...

    Authors: Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang, Frank Alber, Fengzhu Sun, Steven M. Dubinett, Wenyuan Li and Xianghong Jasmine Zhou

    Citation: Genome Biology 2017 18:53

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  9. Content type: METHOD

    Next-generation sequencing (NGS) of bulk tumour tissue can identify constituent cell populations in cancers and measure their abundance. This requires computational deconvolution of allelic counts from somatic...

    Authors: Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté and Sohrab P. Shah

    Citation: Genome Biology 2017 18:44

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  10. Content type: METHOD

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most me...

    Authors: Ines de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A. J. Ponder, Kerstin B. Meyer and Florian Markowetz

    Citation: Genome Biology 2017 18:39

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  11. Content type: Research Highlight

    Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of...

    Authors: Toni Celià-Terrassa and Yibin Kang

    Citation: Genome Biology 2017 18:31

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  12. Content type: Research

    Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is dif...

    Authors: Ulrike M. Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa Kathiria, William J. Greenleaf and Howard Y. Chang

    Citation: Genome Biology 2017 18:15

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  13. Content type: Research

    Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...

    Authors: Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W. Nichols, Manju Aron, Kimberly D. Siegmund, Osamu Ukimura, Monish Aron, ‬Mariana Stern, Parkash Gill, John D. Carpten, Torben F. Ørntoft, Karina D. Sørensen, Daniel J. Weisenberger…

    Citation: Genome Biology 2017 18:3

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  14. Content type: METHOD

    In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration...

    Authors: Sander Canisius, John W. M. Martens and Lodewyk F. A. Wessels

    Citation: Genome Biology 2016 17:261

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  15. Content type: Research

    Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. Th...

    Authors: Jonas Demeulemeester, Parveen Kumar, Elen K. Møller, Silje Nord, David C. Wedge, April Peterson, Randi R. Mathiesen, Renathe Fjelldal, Masoud Zamani Esteki, Koen Theunis, Elia Fernandez Gallardo, A. Jason Grundstad, Elin Borgen, Lars O. Baumbusch, Anne-Lise Børresen-Dale, Kevin P. White…

    Citation: Genome Biology 2016 17:250

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  16. Content type: Research

    Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the express...

    Authors: Yasin Şenbabaoğlu, Ron S. Gejman, Andrew G. Winer, Ming Liu, Eliezer M. Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J. Manley, Danny N. Khalil, Samuel D. Kaffenberger, Yingbei Chen…

    Citation: Genome Biology 2016 17:231

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    The Erratum to this article has been published in Genome Biology 2017 18:46

  17. Content type: Method

    We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneo...

    Authors: Etienne Becht, Nicolas A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Biology 2016 17:218

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    The Erratum to this article has been published in Genome Biology 2016 17:249

  18. Content type: Research Highlight

    A new mitotic clock and mathematical approach that incorporates DNA methylation biology common among human cell types provides a new tool for cancer epigenetics research.

    Authors: Brock C. Christensen and Karl T. Kelsey

    Citation: Genome Biology 2016 17:216

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  19. Content type: Research

    Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be...

    Authors: Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, R. David Leslie, Shijie C. Zheng, Martin Widschwendter, Stephan Beck and Andrew E. Teschendorff

    Citation: Genome Biology 2016 17:205

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  20. Content type: Method

    We show that variability in general levels of drug sensitivity in pre-clinical cancer models confounds biomarker discovery. However, using a very large panel of cell lines, each treated with many drugs, we cou...

    Authors: Paul Geeleher, Nancy J. Cox and R. Stephanie Huang

    Citation: Genome Biology 2016 17:190

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  21. Content type: Research

    The APOBEC3 family of cytidine deaminases mutate the cancer genome in a range of cancer types. Although many studies have documented the downstream effects of APOBEC3 activity through next-generation sequencin...

    Authors: Nnennaya Kanu, Maria Antonietta Cerone, Gerald Goh, Lykourgos-Panagiotis Zalmas, Jirina Bartkova, Michelle Dietzen, Nicholas McGranahan, Rebecca Rogers, Emily K. Law, Irina Gromova, Maik Kschischo, Michael I. Walton, Olivia W. Rossanese, Jiri Bartek, Reuben S. Harris, Subramanian Venkatesan…

    Citation: Genome Biology 2016 17:185

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  22. Content type: Research

    Understanding the interactions between tumor and the host immune system is critical to finding prognostic biomarkers, reducing drug resistance, and developing new therapies. Novel computational methods are nee...

    Authors: Bo Li, Eric Severson, Jean-Christophe Pignon, Haoquan Zhao, Taiwen Li, Jesse Novak, Peng Jiang, Hui Shen, Jon C. Aster, Scott Rodig, Sabina Signoretti, Jun S. Liu and X. Shirley Liu

    Citation: Genome Biology 2016 17:174

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  23. Content type: Research Highlight

    Understanding a tumor’s complex cellular heterogeneity will be crucial for the development of better treatment strategies. A new study suggests a novel method for the in silico dissociation of solid tumors and...

    Authors: Dvir Aran and Atul J. Butte

    Citation: Genome Biology 2016 17:175

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  24. Content type: Research

    Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular...

    Authors: David M. Nelson, Farah Jaber-Hijazi, John J. Cole, Neil A. Robertson, Jeffrey S. Pawlikowski, Kevin T. Norris, Steven W. Criscione, Nikolay A. Pchelintsev, Desiree Piscitello, Nicholas Stong, Taranjit Singh Rai, Tony McBryan, Gabriel L. Otte, Colin Nixon, William Clark, Harold Riethman…

    Citation: Genome Biology 2016 17:158

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  25. Content type: Research

    Chronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly pro...

    Authors: Dvir Aran, Audrey Lasry, Adar Zinger, Moshe Biton, Eli Pikarsky, Asaf Hellman, Atul J. Butte and Yinon Ben-Neriah

    Citation: Genome Biology 2016 17:145

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  26. Content type: Research

    Altered metabolism is a hallmark of cancer. However, the role of genomic changes in metabolic genes driving the tumour metabolic shift remains to be elucidated. Here, we have investigated the genomic and trans...

    Authors: Syed Haider, Alan McIntyre, Ruud G. P. M. van Stiphout, Laura M. Winchester, Simon Wigfield, Adrian L. Harris and Francesca M. Buffa

    Citation: Genome Biology 2016 17:140

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  27. Content type: Method

    Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here w...

    Authors: Loris Mularoni, Radhakrishnan Sabarinathan, Jordi Deu-Pons, Abel Gonzalez-Perez and Núria López-Bigas

    Citation: Genome Biology 2016 17:128

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  28. Content type: Research

    Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses ...

    Authors: Bruna R. Correa, Patricia Rosa de Araujo, Mei Qiao, Suzanne C. Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro A. F. Galante and Luiz O. F. Penalva

    Citation: Genome Biology 2016 17:125

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  29. Content type: Research

    Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accel...

    Authors: Bjorn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubsky, Diana C. J. Spierings, Tristan V. de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S. J. M. de Bont, Anke van den Berg, Victor Guryev, Peter M. Lansdorp, Maria Colomé-Tatché and Floris Foijer

    Citation: Genome Biology 2016 17:115

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  30. Content type: Research Highlight

    Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical ...

    Authors: Alexander Davis and Nicholas E. Navin

    Citation: Genome Biology 2016 17:113

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  31. Content type: Research

    Soluble protein and lipid mediators play essential roles in the tumor environment, but their cellular origins, targets, and clinical relevance are only partially known. We have addressed this question for the ...

    Authors: Silke Reinartz, Florian Finkernagel, Till Adhikary, Verena Rohnalter, Tim Schumann, Yvonne Schober, W. Andreas Nockher, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller-Brüsselbach and Rolf Müller

    Citation: Genome Biology 2016 17:108

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  32. Content type: Research

    Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome o...

    Authors: Bernadett Szikriszt, Ádám Póti, Orsolya Pipek, Marcin Krzystanek, Nnennaya Kanu, János Molnár, Dezső Ribli, Zoltán Szeltner, Gábor E. Tusnády, István Csabai, Zoltan Szallasi, Charles Swanton and Dávid Szüts

    Citation: Genome Biology 2016 17:99

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  33. Content type: METHOD

    Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary hist...

    Authors: Katharina Jahn, Jack Kuipers and Niko Beerenwinkel

    Citation: Genome Biology 2016 17:86

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  34. Content type: Research

    Intratumoral heterogeneity hampers the success of marker-based anticancer treatment because the targeted therapy may eliminate a specific subpopulation of tumor cells while leaving others unharmed. Accordingly...

    Authors: Kyu-Tae Kim, Hye Won Lee, Hae-Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Shin, Hyunho Kim, Yoojin Shin, Do-Hyun Nam, Byong Chang Jeong, David G. Kirsch, Kyeung Min Joo and Woong-Yang Park

    Citation: Genome Biology 2016 17:80

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  35. Content type: Research

    Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined str...

    Authors: Alessandro Ori, Murat Iskar, Katarzyna Buczak, Panagiotis Kastritis, Luca Parca, Amparo Andrés-Pons, Stephan Singer, Peer Bork and Martin Beck

    Citation: Genome Biology 2016 17:47

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  36. Content type: Software

    Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the...

    Authors: Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S. Taylor and Charles Swanton

    Citation: Genome Biology 2016 17:31

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  37. Content type: Research

    Although the chemopreventive effects of aspirin have been extensively investigated, the roles of many cell components, such as long non-coding RNAs, in these effects are still not completely understood.

    Authors: Haiyan Guo, Jun Liu, Qiwen Ben, Yuehong Qu, Man Li, Ying Wang, Wantao Chen and Jianjun Zhang

    Citation: Genome Biology 2016 17:24

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  38. Content type: Research

    The androgen receptor (AR) is a pivotal drug target for the treatment of prostate cancer, including its lethal castration-resistant (CRPC) form. All current non-steroidal AR antagonists, such as hydroxyflutami...

    Authors: Nada Lallous, Stanislav V. Volik, Shannon Awrey, Eric Leblanc, Ronnie Tse, Josef Murillo, Kriti Singh, Arun A. Azad, Alexander W. Wyatt, Stephane LeBihan, Kim N. Chi, Martin E. Gleave, Paul S. Rennie, Colin C. Collins and Artem Cherkasov

    Citation: Genome Biology 2016 17:10

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