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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.

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  1. Cancers have long been recognized to be not only genetically but also epigenetically distinct from their tissues of origin. Although genetic alterations underlying oncogene upregulation have been well studied,...

    Authors: Jianzhong Su, Yung-Hsin Huang, Xiaodong Cui, Xinyu Wang, Xiaotian Zhang, Yong Lei, Jianfeng Xu, Xueqiu Lin, Kaifu Chen, Jie Lv, Margaret A. Goodell and Wei Li
    Citation: Genome Biology 2018 19:108
    Content type: Research Published on:

  2. Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progres...

    Authors: Clemency Jolly and Peter Van Loo
    Citation: Genome Biology 2018 19:95
    Content type: Review Published on:

  3. Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and n...

    Authors: Lorena Verduci, Maria Ferraiuolo, Andrea Sacconi, Federica Ganci, Jlenia Vitale, Teresa Colombo, Paola Paci, Sabrina Strano, Giuseppe Macino, Nikolaus Rajewsky and Giovanni Blandino
    Citation: Genome Biology 2017 18:237
    Content type: Research Published on:

  4. Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylatio...

    Authors: Yuting Chen, Martin Widschwendter and Andrew E. Teschendorff
    Citation: Genome Biology 2017 18:236
    Content type: Research Published on:

  5. Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt th...

    Authors: Sören Müller, Gary Kohanbash, S. John Liu, Beatriz Alvarado, Diego Carrera, Aparna Bhaduri, Payal B. Watchmaker, Garima Yagnik, Elizabeth Di Lullo, Martina Malatesta, Nduka M. Amankulor, Arnold R. Kriegstein, Daniel A. Lim, Manish Aghi, Hideho Okada and Aaron Diaz
    Citation: Genome Biology 2017 18:234
    Content type: Research Published on:

  8. It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and s...

    Authors: Oskar Marín-Béjar, Aina M. Mas, Jovanna González, Dannys Martinez, Alejandro Athie, Xabier Morales, Mikel Galduroz, Ivan Raimondi, Elena Grossi, Shuling Guo, Ana Rouzaut, Igor Ulitsky and Maite Huarte
    Citation: Genome Biology 2017 18:202
    Content type: Research Published on:

  9. Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically...

    Authors: Song Liu, Yuwen Liu, Qin Zhang, Jiayu Wu, Junbo Liang, Shan Yu, Gong-Hong Wei, Kevin P. White and Xiaoyue Wang
    Citation: Genome Biology 2017 18:194
    Content type: Research Published on:

  10. 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
    Content type: Research Published on:

  12. 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
    Content type: Method Published on:

  13. 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
    Content type: Method Published on:

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

  14. 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
    Content type: Method Published on:

  15. 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
    Content type: Research Published on:

  16. 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
    Content type: Research Highlight Published on:

  17. 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
    Content type: Method Published on:

  18. 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
    Content type: Method Published on:

  19. 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
    Content type: METHOD Published on:

  20. 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
    Content type: METHOD Published on:

  21. 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
    Content type: Research Highlight Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: METHOD Published on:

  26. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

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

  29. 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
    Content type: Method Published on:

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

  30. 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
    Content type: Research Highlight Published on:

  31. 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
    Content type: Research Published on:

  34. 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
    Content type: Method Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Highlight Published on:

  37. 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
    Content type: Research Published on:

  38. 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
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  40. 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
    Content type: Research Published on:

  42. 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
    Content type: Method Published on:

  43. 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
    Content type: Research Published on:

  44. 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
    Content type: Research Published on:

  45. 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
    Content type: Research Highlight Published on:

  46. 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
    Content type: Research Published on:

  47. 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
    Content type: Research Published on:

  48. 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
    Content type: METHOD Published on:

  49. 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
    Content type: Research Published on: