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Genomics of cancer progression and heterogeneity

Guest Editors: Elaine R. Mardis and Samuel Aparicio

Recent advances, such as single-cell sequencing technologies and new algorithmic methods, are allowing us to study cancer genomics at a depth and breadth that was not previously possible.

Genome Biology highlights the importance of this field with a special collection covering all aspects of cancer progression and heterogeneity, including methodological advances to study cancer evolution and clonality, insights into tumor heterogeneity, discussions on personalized genomics and ethics of cancer data sharing, and more.

  1. Content type: METHOD

    Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building meth...

    Authors: Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef-Haghighi, Robert B West and Serafim Batzoglou

    Citation: Genome Biology 2015 16:91

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  2. Content type: Research

    Melanoma is the most fatal skin cancer displaying a high degree of molecular heterogeneity. Phenotype switching is a mechanism that contributes to melanoma heterogeneity by altering transcription profiles for ...

    Authors: Phil F Cheng, Olga Shakhova, Daniel S Widmer, Ossia M Eichhoff, Daniel Zingg, Sandra C Frommel, Benedetta Belloni, Marieke IG Raaijmakers, Simone M Goldinger, Raffaella Santoro, Silvio Hemmi, Lukas Sommer, Reinhard Dummer and Mitchell P Levesque

    Citation: Genome Biology 2015 16:42

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  3. Content type: Research

    An essential question in cancer is why individuals with the same disease have different clinical outcomes. Progress toward a more personalized medicine in cancer patients requires taking into account the under...

    Authors: Andrés Castellanos-Martín, Sonia Castillo-Lluva, María del Mar Sáez-Freire, Adrián Blanco-Gómez, Lourdes Hontecillas-Prieto, Carmen Patino-Alonso, Purificación Galindo-Villardon, Luis Pérez del Villar, Carmen Martín-Seisdedos, María Isidoro-Garcia, María del Mar Abad-Hernández, Juan Jesús Cruz-Hernández, César Augusto Rodríguez-Sánchez, Rogelio González-Sarmiento, Diego Alonso-López, Javier De Las Rivas…

    Citation: Genome Biology 2015 16:40

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  4. Content type: METHOD

    Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more ...

    Authors: Amit G Deshwar, Shankar Vembu, Christina K Yung, Gun Ho Jang, Lincoln Stein and Quaid Morris

    Citation: Genome Biology 2015 16:35

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  5. Content type: Research

    Colorectal cancer with metastases limited to the liver (liver-limited mCRC) is a distinct clinical subset characterized by possible cure with surgery. We performed high-depth sequencing of over 750 cancer-asso...

    Authors: Iain Beehuat Tan, Simeen Malik, Kalpana Ramnarayanan, John R McPherson, Dan Liang Ho, Yuka Suzuki, Sarah Boonhsui Ng, Su Yan, Kiat Hon Lim, Dennis Koh, Chew Min Hoe, Chung Yip Chan, Rachel Ten, Brian KP Goh, Alexander YF Chung, Joanna Tan…

    Citation: Genome Biology 2015 16:32

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  6. Content type: Research

    The extent of intratumoral mutational heterogeneity remains unclear in gliomas, the most common primary brain tumors, especially with respect to point mutation. To address this, we applied single molecule mole...

    Authors: Akash Kumar, Evan A Boyle, Mari Tokita, Andrei M Mikheev, Michelle C Sanger, Emily Girard, John R Silber, Luis F Gonzalez-Cuyar, Joseph B Hiatt, Andrew Adey, Choli Lee, Jacob O Kitzman, Donald E Born, Daniel L Silbergeld, James M Olson, Robert C Rostomily…

    Citation: Genome Biology 2014 15:530

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  7. Content type: Method

    Many cancer genes form mutation hotspots that disrupt their functional domains or active sites, leading to gain- or loss-of-function. We propose a mutation set enrichment analysis (MSEA) implemented by two nov...

    Authors: Peilin Jia, Quan Wang, Qingxia Chen, Katherine E Hutchinson, William Pao and Zhongming Zhao

    Citation: Genome Biology 2014 15:489

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  8. Content type: Method

    Intra-tumor heterogeneity concerns the existence of genetically different subclones within the same tumor. Single sample quantification of heterogeneity relies on precise determination of chromosomal copy numb...

    Authors: Ingrid M Lönnstedt, Franco Caramia, Jason Li, Debora Fumagalli, Roberto Salgado, Andrew Rowan, Max Salm, Nnennaya Kanu, Peter Savas, Stuart Horswell, Stephan Gade, Sibylle Loibl, Patrick Neven, Christos Sotiriou, Charles Swanton, Sherene Loi…

    Citation: Genome Biology 2014 15:470

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  9. Content type: Method

    We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation...

    Authors: Sheng Li, Francine Garrett-Bakelman, Alexander E Perl, Selina M Luger, Chao Zhang, Bik L To, Ian D Lewis, Anna L Brown, Richard J D’Andrea, M Elizabeth Ross, Ross Levine, Martin Carroll, Ari Melnick and Christopher E Mason

    Citation: Genome Biology 2014 15:472

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  10. Content type: Research

    The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aber...

    Authors: Hinke F van Thuijl, Ilari Scheinin, Daoud Sie, Agusti Alentorn, Hendrik F van Essen, Martijn Cordes, Ruth Fleischeuer, Anja M Gijtenbeek, Guus Beute, Wimar A van den Brink, Gerrit A Meijer, Miek Havenith, Ahmed Idbaih, Khê Hoang-Xuan, Karima Mokhtari, Roel GW Verhaak…

    Citation: Genome Biology 2014 15:471

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  11. Content type: Opinion

    Rapid technological development has created an urgent need for improved evaluation of algorithms for the analysis of cancer genomics data. We outline how challenge-based assessment may help fill this gap by le...

    Authors: Paul C Boutros, Adam A Margolin, Joshua M Stuart, Andrea Califano and Gustavo Stolovitzky

    Citation: Genome Biology 2014 15:462

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  12. Content type: Research

    Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are neoplastic disorders of hematopoietic stem cells. DNA methyltransferase inhibitors, 5-azacytidine and 5-aza-2′-deoxycytidine (decitabine), be...

    Authors: Kirstin Lund, John J Cole, Nathan D VanderKraats, Tony McBryan, Nikolay A Pchelintsev, William Clark, Mhairi Copland, John R Edwards and Peter D Adams

    Citation: Genome Biology 2014 15:406

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  13. Content type: Research

    Mismatch repair deficient colorectal adenomas are composed of transformed cells that descend from a common founder and progressively accumulate genomic alterations. The proliferation history of these tumors is...

    Authors: Anna De Grassi, Fabio Iannelli, Matteo Cereda, Sara Volorio, Valentina Melocchi, Alessandra Viel, Gianluca Basso, Luigi Laghi, Michele Caselle and Francesca D Ciccarelli

    Citation: Genome Biology 2014 15:437

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  14. Content type: Review

    Enumeration and molecular characterization of circulating tumor cells isolated from peripheral blood of patients with cancer can aid selection of targeted therapy for patients, monitoring of response to therap...

    Authors: Joaquin Mateo, Marco Gerlinger, Daniel Nava Rodrigues and Johann S de Bono

    Citation: Genome Biology 2014 15:448

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  15. Content type: Review

    The study of single cancer cells has transformed from qualitative microscopic images to quantitative genomic datasets. This paradigm shift has been fueled by the development of single-cell sequencing technolog...

    Authors: Nicholas E Navin

    Citation: Genome Biology 2014 15:452

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  16. Content type: Research

    IntClust is a classification of breast cancer comprising 10 subtypes based on molecular drivers identified through the integration of genomic and transcriptomic data from 1,000 breast tumors and validated in a...

    Authors: H Raza Ali, Oscar M Rueda, Suet-Feung Chin, Christina Curtis, Mark J Dunning, Samuel AJR Aparicio and Carlos Caldas

    Citation: Genome Biology 2014 15:431

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  17. Content type: Research

    Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti...

    Authors: A Rose Brannon, Efsevia Vakiani, Brooke E Sylvester, Sasinya N Scott, Gregory McDermott, Ronak H Shah, Krishan Kania, Agnes Viale, Dayna M Oschwald, Vladimir Vacic, Anne-Katrin Emde, Andrea Cercek, Rona Yaeger, Nancy E Kemeny, Leonard B Saltz, Jinru Shia…

    Citation: Genome Biology 2014 15:454

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  18. Content type: Research

    Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolutio...

    Authors: Lincoln D Nadauld, Sarah Garcia, Georges Natsoulis, John M Bell, Laura Miotke, Erik S Hopmans, Hua Xu, Reetesh K Pai, Curt Palm, John F Regan, Hao Chen, Patrick Flaherty, Akifumi Ootani, Nancy R Zhang, James M Ford, Calvin J Kuo…

    Citation: Genome Biology 2014 15:428

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  19. Content type: Review

    The presence of multiple subclones within tumors mandates understanding of longitudinal and spatial subclonal dynamics. Resolving the spatial and temporal heterogeneity of subclones with cancer driver events m...

    Authors: Crispin Hiley, Elza C de Bruin, Nicholas McGranahan and Charles Swanton

    Citation: Genome Biology 2014 15:453

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  20. Content type: Research

    Genomic analysis of multi-focal renal cell carcinomas from an individual with a germline VHL mutation offers a unique opportunity to study tumor evolution.

    Authors: Rosalie Fisher, Stuart Horswell, Andrew Rowan, Maximilian P Salm, Elza C de Bruin, Sakshi Gulati, Nicholas McGranahan, Mark Stares, Marco Gerlinger, Ignacio Varela, Andrew Crockford, Francesco Favero, Virginie Quidville, Fabrice André, Carolina Navas, Eva Grönroos…

    Citation: Genome Biology 2014 15:433

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  21. Content type: Opinion

    Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate...

    Authors: Benjamin M Good, Benjamin J Ainscough, Josh F McMichael, Andrew I Su and Obi L Griffith

    Citation: Genome Biology 2014 15:438

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  22. Content type: Method

    Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somat...

    Authors: Yi Qiao, Aaron R Quinlan, Amir A Jazaeri, Roeland GW Verhaak, David A Wheeler and Gabor T Marth

    Citation: Genome Biology 2014 15:443

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  23. Content type: Research

    Genomic analyses of hundreds of prostate tumors have defined a diverse landscape of mutations and genome rearrangements, but the transcriptomic effect of this complexity is less well understood, particularly a...

    Authors: Alexander W Wyatt, Fan Mo, Kendric Wang, Brian McConeghy, Sonal Brahmbhatt, Lina Jong, Devon M Mitchell, Rebecca L Johnston, Anne Haegert, Estelle Li, Janet Liew, Jake Yeung, Raunak Shrestha, Anna V Lapuk, Andrew McPherson, Robert Shukin…

    Citation: Genome Biology 2014 15:426

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  24. Content type: METHOD

    As molecular profiling data continue to accumulate, the design of integrative computational analyses that can provide insights into the dynamic aspects of cancer progression becomes feasible. Here, we present ...

    Authors: Yijun Sun, Jin Yao, Norma J Nowak and Steve Goodison

    Citation: Genome Biology 2014 15:440

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  25. Content type: Method

    Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of ...

    Authors: Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan-Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin and Francesca Demichelis

    Citation: Genome Biology 2014 15:439

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    The Erratum to this article has been published in Genome Biology 2017 18:80

  26. Content type: Software

    Molecular analysis has revealed extensive intra-tumor heterogeneity in human cancer samples, but cannot identify cell-to-cell variations within the tissue microenvironment. In contrast, in situ analysis can ident...

    Authors: Anne Trinh, Inga H Rye, Vanessa Almendro, Åslaug Helland, Hege G Russnes and Florian Markowetz

    Citation: Genome Biology 2014 15:442

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  27. Content type: Research

    Hepatocellular carcinoma (HCC) is a heterogeneous disease with high mortality rate. Recent genomic studies have identified TP53, AXIN1, and CTNNB1 as the most frequently mutated genes. Lower frequency mutations h...

    Authors: Suchit Jhunjhunwala, Zhaoshi Jiang, Eric W Stawiski, Florian Gnad, Jinfeng Liu, Oleg Mayba, Pan Du, Jingyu Diao, Stephanie Johnson, Kwong-Fai Wong, Zhibo Gao, Yingrui Li, Thomas D Wu, Sharookh B Kapadia, Zora Modrusan, Dorothy M French…

    Citation: Genome Biology 2014 15:436

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  28. Content type: Research

    Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma. DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool i...

    Authors: Thomas Fleischer, Arnoldo Frigessi, Kevin C Johnson, Hege Edvardsen, Nizar Touleimat, Jovana Klajic, Margit LH Riis, Vilde D Haakensen, Fredrik Wärnberg, Bjørn Naume, Åslaug Helland, Anne-Lise Børresen-Dale, Jörg Tost, Brock C Christensen and Vessela N Kristensen

    Citation: Genome Biology 2014 15:435

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  29. Content type: Research

    Wilms tumor is the most common pediatric renal malignancy and there is a clinical need for a molecular biomarker to assess treatment response and predict relapse. The known mutated genes in this tumor type sho...

    Authors: Jocelyn Charlton, Richard D Williams, Mark Weeks, Neil J Sebire, Sergey Popov, Gordan Vujanic, William Mifsud, Marisa Alcaide-German, Lee M Butcher, Stephan Beck and Kathy Pritchard-Jones

    Citation: Genome Biology 2014 15:434

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  30. Content type: Research

    Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, ...

    Authors: Yanwen Jiang, David Redmond, Kui Nie, Ken W Eng, Thomas Clozel, Peter Martin, Leonard HC Tan, Ari M Melnick, Wayne Tam and Olivier Elemento

    Citation: Genome Biology 2014 15:432

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  31. Content type: Research

    Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns ...

    Authors: Nicole M White, Christopher R Cabanski, Jessica M Silva-Fisher, Ha X Dang, Ramaswamy Govindan and Christopher A Maher

    Citation: Genome Biology 2014 15:429

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  32. Content type: Opinion

    Data sharing models designed to facilitate global business provide insights for improving transborder genomic data sharing. We argue that a flexible, externally endorsed, multilateral arrangement, combined wit...

    Authors: Patricia Kosseim, Edward S Dove, Carman Baggaley, Eric M Meslin, Fred H Cate, Jane Kaye, Jennifer R Harris and Bartha M Knoppers

    Citation: Genome Biology 2014 15:430

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  33. Content type: Method

    Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq dat...

    Authors: Oleg Mayba, Houston N Gilbert, Jinfeng Liu, Peter M Haverty, Suchit Jhunjhunwala, Zhaoshi Jiang, Colin Watanabe and Zemin Zhang

    Citation: Genome Biology 2014 15:405

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  34. Content type: Method

    We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differenti...

    Authors: Xiaoqi Zheng, Qian Zhao, Hua-Jun Wu, Wei Li, Haiyun Wang, Clifford A Meyer, Qian Alvin Qin, Han Xu, Chongzhi Zang, Peng Jiang, Fuqiang Li, Yong Hou, Jianxing He, Jun Wang, Jun Wang, Peng Zhang…

    Citation: Genome Biology 2014 15:419

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  35. Content type: Method

    Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted t...

    Authors: Erin N Smith, Kristen Jepsen, Mahdieh Khosroheidari, Laura Z Rassenti, Matteo D’Antonio, Emanuela M Ghia, Dennis A Carson, Catriona HM Jamieson, Thomas J Kipps and Kelly A Frazer

    Citation: Genome Biology 2014 15:420

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