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Table of Contents

December 2016

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Cancer Genomics: Large-Scale Projects Translate into Therapeutic Advances
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The cancer field has been transformed over recent years by advances in the genomics field, both in terms of technological developments, but also in relation to the wealth of data that has been created by several high profile large consortia sequencing projects, such as The Cancer Genome Atlas (TCGA). In this month's Editorial, Dr. Elaine Mardis and Dr. Marc Ladanyi, the Guest Editors of December's Special Issue on "Translating the Cancer Genome," highlight some key papers that appear in this issue of PLOS Medicine, and emphasize how these studies have advanced cancer detection and therapies, and will drive further developments.

Image Credit: qimono, Pixabay

Editorial

Cancer Genomics: Large-Scale Projects Translate into Therapeutic Advances

Elaine R. Mardis, Marc Ladanyi

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002209

Perspectives

Precision Cancer Diagnostics: Tracking Genomic Evolution in Clinical Trials

Francisco Beca, Andrew H. Beck

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002177

Related Articles

  1. Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine

Sequencing Strategies to Guide Decision Making in Cancer Treatment

James T. Topham, Marco A. Marra

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002189

Immunotherapy in the Precision Medicine Era: Melanoma and Beyond

Mack Y. Su, David E. Fisher

PLOS Medicine: published December 13, 2016 | https://doi.org/10.1371/journal.pmed.1002196

Overcoming Steroid Resistance in T Cell Acute Lymphoblastic Leukemia

Steven Goossens, Pieter Van Vlierberghe

PLOS Medicine: published December 20, 2016 | https://doi.org/10.1371/journal.pmed.1002208

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  1. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

Blood-Based Analysis of Circulating Cell-Free DNA and Tumor Cells for Early Cancer Detection

Klaus Pantel

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002205

Research Articles

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine

Gerald Goh, Ramona Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock-Ah Im, Sung-Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen R. Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002136

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  1. Precision Cancer Diagnostics: Tracking Genomic Evolution in Clinical Trials

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study

Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A. Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J. Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T. Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E. Caporaso, Mitchell H. Gail, Angela C. Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J. Chanock, Maria Teresa Landi

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002162

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

Katherine A. Hoadley, Marni B. Siegel, Krishna L. Kanchi, Christopher A. Miller, Li Ding, Wei Zhao, Xiaping He, Joel S. Parker, Michael C. Wendl, Robert S. Fulton, Ryan T. Demeter, Richard K. Wilson, Lisa A. Carey, Charles M. Perou, Elaine R. Mardis

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002174

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  1. Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis

Brian J. Reon, Jordan Anaya, Ying Zhang, James Mandell, Benjamin Purow, Roger Abounader, Anindya Dutta

PLOS Medicine: published December 6, 2016 | https://doi.org/10.1371/journal.pmed.1002192

Predictors of Chemosensitivity in Triple Negative Breast Cancer: An Integrated Genomic Analysis

Tingting Jiang, Weiwei Shi, Vikram B. Wali, Lőrinc S. Pongor, Charles Li, Rosanna Lau, Balázs Győrffy, Richard P. Lifton, William F. Symmans, Lajos Pusztai, Christos Hatzis

PLOS Medicine: published December 13, 2016 | https://doi.org/10.1371/journal.pmed.1002193

Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study

H. Raza Ali, Leon Chlon, Paul D. P. Pharoah, Florian Markowetz, Carlos Caldas

PLOS Medicine: published December 13, 2016 | https://doi.org/10.1371/journal.pmed.1002194

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study

Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A. Smith, Cydney Nielsen, Eva Giné, Adele Telenius, Daisuke Ennishi, Andrew Mungall, Richard Moore, Ryan D. Morin, Nathalie A. Johnson, Laurie H. Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M. Connors, David W. Scott, Christian Steidl, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah

PLOS Medicine: published December 13, 2016 | https://doi.org/10.1371/journal.pmed.1002197

Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study

Christine A. Parkinson, Davina Gale, Anna M. Piskorz, Heather Biggs, Charlotte Hodgkin, Helen Addley, Sue Freeman, Penelope Moyle, Evis Sala, Karen Sayal, Karen Hosking, Ioannis Gounaris, Mercedes Jimenez-Linan, Helena M. Earl, Wendi Qian, Nitzan Rosenfeld, James D. Brenton

PLOS Medicine: published December 20, 2016 | https://doi.org/10.1371/journal.pmed.1002198

IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

Yunlei Li, Jessica G. C. A. M. Buijs-Gladdines, Kirsten Canté-Barrett, Andrew P. Stubbs, Eric M. Vroegindeweij, Willem K. Smits, Ronald van Marion, Winand N. M. Dinjens, Martin Horstmann, Roland P. Kuiper, Rogier C. Buijsman, Guido J. R. Zaman, Peter J. van der Spek, Rob Pieters, Jules P. P. Meijerink

PLOS Medicine: published December 20, 2016 | https://doi.org/10.1371/journal.pmed.1002200

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Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

Nicolas Pécuchet, Eleonora Zonta, Audrey Didelot, Pierre Combe, Constance Thibault, Laure Gibault, Camille Lours, Yves Rozenholc, Valérie Taly, Pierre Laurent-Puig, Hélène Blons, Elizabeth Fabre

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002199

Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis

Celine Lefebvre, Thomas Bachelot, Thomas Filleron, Marion Pedrero, Mario Campone, Jean-Charles Soria, Christophe Massard, Christelle Lévy, Monica Arnedos, Magali Lacroix-Triki, Julie Garrabey, Yannick Boursin, Marc Deloger, Yu Fu, Frédéric Commo, Véronique Scott, Ludovic Lacroix, Maria Vittoria Dieci, Maud Kamal, Véronique Diéras, Anthony Gonçalves, Jean-Marc Ferrerro, Gilles Romieu, Laurence Vanlemmens, Marie-Ange Mouret Reynier, Jean-Christophe Théry, Fanny Le Du, Séverine Guiu, Florence Dalenc, Gilles Clapisson, Hervé Bonnefoi, Marta Jimenez, Christophe Le Tourneau, Fabrice André

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002201

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”

Peter Savas, Zhi Ling Teo, Christophe Lefevre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A. Francis, Heather A. Thorne, Maria Joao Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen Fox, David D. Bowtell, Sarah-Jane Dawson, Terence P. Speed, Charles Swanton, Sherene Loi

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002204

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  1. Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study

Navya Nair, Olga Camacho-Vanegas, Dmitry Rykunov, Matthew Dashkoff, Sandra Catalina Camacho, Cassie A. Schumacher, Jonathan C. Irish, Timothy T. Harkins, Elijah Freeman, Isaac Garcia, Elena Pereira, Sviatoslav Kendall, Rachel Belfer, Tamara Kalir, Robert Sebra, Boris Reva, Peter Dottino, John A. Martignetti

PLOS Medicine: published December 27, 2016 | https://doi.org/10.1371/journal.pmed.1002206