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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. Content type: Research

    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

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  2. Content type: Research

    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

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  3. Content type: Research

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. 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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  7. 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

  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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

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