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Cancer Genomics

Genome Biology Collection

cancer genomicsCancer 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.

Image adapted from Ewing et al., Genome Biology (2013). 

  1. Method

    SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling

    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...

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

    Genome Biology 2017 18:66

    Published on: 8 April 2017

  2. Method

    CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

    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...

    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

    Genome Biology 2017 18:53

    Published on: 24 March 2017

  3. METHOD

    BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

    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...

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

    Genome Biology 2017 18:39

    Published on: 24 February 2017

  4. Research Highlight

    Mouse genomic screen reveals novel host regulator of metastasis

    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...

    Toni Celià-Terrassa and Yibin Kang

    Genome Biology 2017 18:31

    Published on: 16 February 2017

  5. Research

    Single-cell epigenomic variability reveals functional cancer heterogeneity

    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...

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

    Genome Biology 2017 18:15

    Published on: 24 January 2017

  6. Research

    Identifying aggressive prostate cancer foci using a DNA methylation classifier

    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...

    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…

    Genome Biology 2017 18:3

    Published on: 12 January 2017

  7. Research

    Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

    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...

    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…

    Genome Biology 2016 17:250

    Published on: 9 December 2016

  8. Research

    Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

    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...

    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…

    Genome Biology 2016 17:231

    Published on: 17 November 2016

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

  9. Method

    Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression

    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...

    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

    Genome Biology 2016 17:218

    Published on: 20 October 2016

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

  10. Research Highlight

    A new timepiece: an epigenetic mitotic clock

    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.

    Brock C. Christensen and Karl T. Kelsey

    Genome Biology 2016 17:216

    Published on: 19 October 2016

  11. Research

    Correlation of an epigenetic mitotic clock with cancer risk

    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...

    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

    Genome Biology 2016 17:205

    Published on: 3 October 2016

  12. Research Highlight

    DNA replication stress: a source of APOBEC3B expression in breast cancer

    APOBEC cytidine deaminases have been implicated as major contributors to the mutation burden in many cancers on the basis of their mutational signature. A new experimental study sheds light on the inciting fac...

    David W. Cescon and Benjamin Haibe-Kains

    Genome Biology 2016 17:202

    Published on: 30 September 2016

  13. Research

    DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

    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...

    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…

    Genome Biology 2016 17:185

    Published on: 15 September 2016

  14. Research Highlight

    Digitally deconvolving the tumor microenvironment

    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...

    Dvir Aran and Atul J. Butte

    Genome Biology 2016 17:175

    Published on: 22 August 2016

  15. Research

    Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

    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...

    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

    Genome Biology 2016 17:174

    Published on: 22 August 2016

  16. Research

    Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability

    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...

    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…

    Genome Biology 2016 17:158

    Published on: 25 July 2016

  17. Research

    Widespread parainflammation in human cancer

    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...

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

    Genome Biology 2016 17:145

    Published on: 8 July 2016

  18. Research

    Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia

    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...

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

    Genome Biology 2016 17:140

    Published on: 29 June 2016

  19. Research

    Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma

    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 ...

    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

    Genome Biology 2016 17:125

    Published on: 10 June 2016

  20. Research

    Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies

    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...

    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

    Genome Biology 2016 17:115

    Published on: 31 May 2016

  21. Research Highlight

    Computing tumor trees from single cells

    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 ...

    Alexander Davis and Nicholas E. Navin

    Genome Biology 2016 17:113

    Published on: 26 May 2016

  22. Research

    A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome

    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 ...

    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

    Genome Biology 2016 17:108

    Published on: 23 May 2016

  23. Research

    A comprehensive survey of the mutagenic impact of common cancer cytotoxics

    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...

    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

    Genome Biology 2016 17:99

    Published on: 9 May 2016

  24. METHOD

    Tree inference for single-cell data

    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...

    Katharina Jahn, Jack Kuipers and Niko Beerenwinkel

    Genome Biology 2016 17:86

    Published on: 5 May 2016

  25. Research

    Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma

    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...

    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

    Genome Biology 2016 17:80

    Published on: 29 April 2016

  26. Research

    Spatiotemporal variation of mammalian protein complex stoichiometries

    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...

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

    Genome Biology 2016 17:47

    Published on: 14 March 2016

  27. Software

    deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

    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...

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

    Genome Biology 2016 17:31

    Published on: 22 February 2016

  28. Research

    Functional analysis of androgen receptor mutations that confer anti-androgen resistance identified in circulating cell-free DNA from prostate cancer patients

    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...

    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

    Genome Biology 2016 17:10

    Published on: 26 January 2016

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