☆ 4.5 Editorial Material

3-methylcytosine in cancer: an underappreciated methyl lesion?

EPIGENOMICS (2016)

Journal

EPIGENOMICS

Volume 8, Issue 4, Pages 451-454

Publisher

FUTURE MEDICINE LTD

DOI: 10.2217/epi.15.121

Keywords

3-methylcytosine; AlkB homolog; biomarker; cancer; cisplatin; DNA; DNA methylation; ifosfamide; methyl methanesulphonate; resistance; temozolomide

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Genetics & Heredity

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Lau, Georgina Long, Hilda A. Pickett, Antonia L. Pritchard, Gulietta M. Pupo, Robyn P. M. Saw, Sarah-Jane Schramm, Catherine A. Shang, Ping Shang, Andrew J. Spillane, Jonathan R. Stretch, Varsha Tembe, John F. Thompson, Ricardo E. Vilain, James S. Wilmott, Jean Y. Yang, Nicholas K. Hayward, Graham J. Mann, Richard A. Scolyer, John Bartlett, Prashant Bavi, Dianne E. Chadwick, Michelle Chan-Seng-Yue, Sean Cleary, Ashton A. Connor, Karolina Czajka, Robert E. Denroche, Neesha C. Dhani, Jenna Eagles, Steven Gallinger, Robert C. Grant, David Hedley, Michael A. Hollingsworth, Gun Ho Jang, Jeremy Johns, Sangeetha Kalimuthu, Sheng-Ben Liang, Ilinca Lungu, Xuemei Luo, Faridah Mbabaali, Treasa A. McPherson, Jessica K. Miller, Malcolm J. Moore, Faiyaz Notta, Danielle Pasternack, Gloria M. Petersen, Michael H. A. Roehrl, Michelle Sam, Iris Selander, Stefano Serra, Sagedeh Shahabi, Sarah P. Thayer, Lee E. Timms, Gavin W. Wilson, Julie M. Wilson, Bradly G. Wouters, John D. McPherson, Timothy A. 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Hooijer, Jocelyne Jacquemier, Se Jin Jang, Jon G. Jonasson, Jos Jonkers, Hyung-Yong Kim, Tari A. King, Stian Knappskog, Gu Kong, Savitri Krishnamurthy, Sunil R. Lakhani, Anita Langerod, Denis Larsimont, Hee Jin Lee, Jeong-Yeon Lee, Ming Ta Michael Lee, Ole Christian Lingjaerde, Gaetan MacGrogan, John W. M. Martens, Sarah O'Meara, Iris Pauporte, Sarah Pinder, Xavier Pivot, Elena Provenzano, Colin A. Purdie, Manasa Ramakrishna, Kamna Ramakrishnan, Jorge Reis-Filho, Andrea L. Richardson, Markus Ringner, Javier Bartolome Rodriguez, F. German Rodriguez-Gonzalez, Gilles Romieu, Roberto Salgado, Torill Sauer, Rebecca Shepherd, Anieta M. Sieuwerts, Peter T. Simpson, Marcel Smid, Christos Sotiriou, Paul N. Span, Olafur Andri Stefansson, Alasdair Stenhouse, Henk G. Stunnenberg, Fred Sweep, Benita Kiat Tee Tan, Gilles Thomas, Alastair M. Thompson, Stefania Tommasi, Isabelle Treilleux, Andrew Tutt, Naoto T. Ueno, Steven Van Laere, Gert G. Van den Eynden, Peter Vermeulen, Alain Viari, Anne Vincent-Salomon, Bernice H. Wong, Lucy Yates, Xueqing Zou, Carolien H. M. van Deurzen, Marc J. van de Vijver, Laura van't Veer, Ole Ammerpohl, Sietse Aukema, Anke K. Bergmann, Stephan H. Bernhart, Arndt Borkhardt, Christoph Borst, Birgit Burkhardt, Alexander Claviez, Maria Elisabeth Goebler, Andrea Haake, Siegfried Haas, Martin Hansmann, Jessica Hoell, Michael Hummel, Dennis Karsch, Wolfram Klapper, Michael Kneba, Markus Kreuz, Dieter Kube, Ralf Kueppers, Dido Lenze, Markus Loeffler, Cristina Lopez, Luisa Mantovani-Loeffler, Peter Moeller, German Ott, Bernhard Radlwimmer, Julia Richter, Marius Rohde, Philip C. Rosenstiel, Andreas Rosenwald, Markus B. Schilhabel, Stefan Schreiber, Peter F. Stadler, Peter Staib, Stephan Stilgenbauer, Stephanie Sungalee, Monika Szczepanowski, Umut H. Toprak, Lorenz H. P. Truemper, Rabea Wagener, Thorsten Zenz, Volker Hovestadt, Christof von Kalle, Marcel Kool, Andrey Korshunov, Pablo Landgraf, Hans Lehrach, Paul A. Northcott, Stefan M. Pfister, Guido Reifenberger, Hans-Joerg Warnatz, Stephan Wolf, Marie-Laure Yaspo, Yassen Assenov, Clarissa Gerhauser, Sarah Minner, Thorsten Schlomm, Ronald Simon, Guido Sauter, Holger Sueltmann, Nidhan K. Biswas, Arindam Maitra, Partha P. Majumder, Rajiv Sarin, Stefano Barbi, Giada Bonizzato, Cinzia Cantu, Angelo P. Dei Tos, Matteo Fassan, Sonia Grimaldi, Claudio Luchini, Giuseppe Malleo, Giovanni Marchegiani, Michele Milella, Salvatore Paiella, Antonio Pea, Paolo Pederzoli, Andrea Ruzzenente, Roberto Salvia, Nicola Sperandio, Yasuhito Arai, Natsuko Hama, Nobuyoshi Hiraoka, Fumie Hosoda, Hiromi Nakamura, Hidenori Ojima, Takuji Okusaka, Yasushi Totoki, Tomoko Urushidate, Masashi Fukayama, Shumpei Ishikawa, Hitoshi Katai, Hiroto Katoh, Daisuke Komura, Hirofumi Rokutan, Mihoko Saito-Adachi, Akihiro Suzuki, Hirokazu Taniguchi, Kenji Tatsuno, Tetsuo Ushiku, Shinichi Yachida, Shogo Yamamoto, Hiroshi Aikata, Koji Arihiro, Shun-ichi Ariizumi, Kazuaki Chayama, Mayuko Furuta, Kunihito Gotoh, Shinya Hayami, Satoshi Hirano, Yoshiiku Kawakami, Kazuhiro Maejima, Toru Nakamura, Kaoru Nakano, Hideki Ohdan, Aya Sasaki-Oku, Hiroko Tanaka, Masaki Ueno, Masakazu Yamamoto, Hiroki Yamaue, Su Pin Choo, Ioana Cutcutache, Narong Khuntikeo, Choon Kiat Ong, Chawalit Pairojkul, Irinel Popescu, Keun Soo Ahn, Marta Aymerich, Armando Lopez-Guillermo, Carlos Lopez-Otin, Xose S. Puente, Elias Campo, Fernanda Amary, Daniel Baumhoer, Sam Behjati, Bodil Bjerkehagen, P. A. Futreal, Ola Myklebost, Nischalan Pillay, Patrick Tarpey, Roberto Tirabosco, Olga Zaikova, Adrienne M. Flanagan, Jacqueline Boultwood, David T. Bowen, Mario Cazzola, Anthony R. Green, Eva Hellstrom-Lindberg, Luca Malcovati, Jyoti Nangalia, Elli Papaemmanuil, Paresh Vyas, Yeng Ang, Hugh Barr, Duncan Beardsmore, Matthew Eldridge, James Gossage, Nicola Grehan, George B. Hanna, Stephen J. Hayes, Ted R. Hupp, David Khoo, Jesper Lagergren, Laurence B. Lovat, Shona MacRae, Maria O'Donovan, J. Robert O'Neill, Simon L. Parsons, Shaun R. Preston, Sonia Puig, Tom Roques, Grant Sanders, Sharmila Sothi, Simon Tavare, Olga Tucker, Richard Turkington, Timothy J. Underwood, Ian Welch, Rebecca C. Fitzgerald, Daniel M. Berney, Johann S. De Bono, Declan Cahill, Niedzica Camacho, Nening M. Dennis, Tim Dudderidge, Sandra E. Edwards, Cyril Fisher, Christopher S. Foster, Mohammed Ghori, Pelvender Gill, Vincent J. Gnanapragasam, Gunes Gundem, Freddie C. Hamdy, Steve Hawkins, Steven Hazell, William Howat, William B. Isaacs, Katalin Karaszi, Jonathan D. Kay, Vincent Khoo, Zsofia Kote-Jarai, Barbara Kremeyer, Pardeep Kumar, Adam Lambert, Daniel A. Leongamornlert, Naomi Livni, Yong-Jie Lu, Hayley J. Luxton, Luke Marsden, Charlie E. Massie, Lucy Matthews, Erik Mayer, Ultan McDermott, Sue Merson, David E. Neal, Anthony Ng, David Nicol, Christopher Ogden, Edward W. Rowe, Nimish C. Shah, Sarah Thomas, Alan Thompson, Clare Verrill, Tapio Visakorpi, Anne Y. Warren, Hayley C. Whitaker, Hongwei Zhang, Nicholas van As, Rosalind A. Eeles, Adam Abeshouse, Nishant Agrawal, Rehan Akbani, Hikmat Al Ahmadie, Monique Albert, Kenneth Aldape, Adrian Ally, Elizabeth L. Appelbaum, Joshua Armenia, Sylvia Asa, J. Todd Auman, Miruna Balasundaram, Saianand Balu, Jill Barnholtz-Sloan, Oliver F. Bathe, Stephen B. Baylin, Christopher Benz, Andrew Berchuck, Mario Berrios, Darell Bigner, Michael Birrer, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Marcus Bosenberg, Reanne Bowlby, Jeffrey Boyd, Russell R. Broaddus, Malcolm Brock, Denise Brooks, Susan Bullman, Samantha J. Caesar-Johnson, Thomas E. Carey, Rebecca Carlsen, Robert Cerfolio, Vishal S. Chandan, Hsiao-Wei Chen, Andrew D. Cherniack, Jeremy Chien, Juok Cho, Eric Chuah, Carrie Cibulskis, Leslie Cope, Matthew G. Cordes, Erin Curley, Bogdan Czerniak, Ludmila Danilova, Ian J. Davis, Timothy Defreitas, John A. Demchok, Noreen Dhalla, Rajiv Dhir, HarshaVardhan Doddapaneni, Adel El-Naggar, Ina Felau, Martin L. Ferguson, Gaetano Finocchiaro, Kwun M. Fong, Scott Frazer, William Friedman, Catrina C. Fronick, Lucinda A. Fulton, Stacey B. Gabriel, Jianjiong Gao, Nils Gehlenborg, Jeffrey E. Gershenwald, Ronald Ghossein, Nasra H. Giama, Richard A. Gibbs, Carmen Gomez, Ramaswamy Govindan, D. Neil Hayes, Apurva M. Hegde, David Heiman, Zachary Heins, Austin J. Hepperla, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Ralph H. Hruban, Jianhong Hu, Mei Huang, David Huntsman, Jason Huse, Christine A. Iacobuzio Donahue, Michael Ittmann, Joy C. Jayaseelan, Stuart R. Jefferys, Corbin D. Jones, Steven J. M. Jones, Hartmut Juhl, Koo Jeong Kang, Beth Karlan, Katayoon Kasaian, Electron Kebebew, Hark Kyun Kim, Viktoriya Korchina, Ritika Kundra, Phillip H. Lai, Eric Lander, Xuan Le, Darlene Lee, Douglas A. Levine, Lora Lewis, Tim Ley, Haiyan Irene Li, Pei Lin, W. M. Linehan, Fei Fei Liu, Yiling Lu, Lisa Lype, Yussanne Ma, Dennis T. Maglinte, Elaine R. Mardis, Jeffrey Marks, Marco A. Marra, Thomas J. Matthew, Michael Mayo, Karen McCune, Samuel R. Meier, Shaowu Meng, Piotr A. Mieczkowski, Tom Mikkelsen, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Carl Morrison, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, David Mutch, Donna M. Muzny, Jerome Myers, Yulia Newton, Michael S. Noble, Peter O'Donnell, Brian Patrick O'Neill, Angelica Ochoa, Joong-Won Park, Joel S. Parker, Harvey Pass, Alessandro Pastore, Nathan A. Pennell, Charles M. Perou, Nicholas Petrelli, Olga Potapova, Janet S. Rader, Suresh Ramalingam, W. Kimryn Rathmell, Victor Reuter, Sheila M. Reynolds, Matthew Ringel, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Charles Saller, Francisco Sanchez-Vega, Dirk Schadendorf, Jacqueline E. Schein, Heather K. Schmidt, Nikolaus Schultz, Raja Seethala, Yasin Senbabaoglu, Troy Shelton, Yan Shi, Juliann Shih, Ilya Shmulevich, Craig Shriver, Sabina Signoretti, Janae Simons, Samuel Singer, Payal Sipahimalani, Tara J. Skelly, Karen Smith McCune, Nicholas D. Socci, Matthew G. Soloway, Anil K. Sood, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, R. Houston Thompson, Leigh B. Thorne, Ming Tsao, Christopher Umbricht, David J. Van Den Berg, Erwin G. Van Meir, Umadevi Veluvolu, Douglas Voet, Linghua Wang, Paul Weinberger, Daniel J. Weisenberger, Dennis Wigle, Matthew D. Wilkerson, Richard K. Wilson, Boris Winterhoff, Maciej Wiznerowicz, Tina Wong, Winghing Wong, Liu Xi, Christina Yau, Hailei Zhang, Hongxin Zhang, Jiashan Zhang

NATURE (2020)

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Review Oncology

The genomics of undifferentiated sarcoma of soft tissue: Progress, challenges and opportunities

Christopher D. Steele, Nischalan Pillay

SEMINARS IN CANCER BIOLOGY (2020)

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Article Genetics & Heredity

Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs

David T. Miller, Isidro Cortes-Ciriano, Nischalan Pillay, Angela C. Hirbe, Matija Snuderl, Marilyn M. Bui, Katherine Piculell, Alyaa Al-Ibraheemi, Brendan C. Dickson, Jesse Hart, Kevin Jones, Justin T. Jordan, Raymond H. Kim, Daniel Lindsay, Yoshihiro Nishida, Nicole J. Ullrich, Xia Wang, Peter J. Park, Adrienne M. Flanagan

GENES (2020)

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Article Oncology

H3K27me3expression and methylation status in histological variants of malignant peripheral nerve sheath tumours

Iben Lyskjaer, Daniel Lindsay, Roberto Tirabosco, Christopher D. Steele, Patrick Lombard, Anna-Christina Strobl, Ana M. Rocha, Christopher Davies, Hongtao Ye, Elise Bekers, Julia Ingruber, Matt Lechner, Fernanda Amary, Nischalan Pillay, Adrienne M. Flanagan

JOURNAL OF PATHOLOGY (2020)

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Article Pathology

Sarcoma and the 100,000 Genomes Project: our experience and changes to practice

Sophie C. Prendergast, Anna-Christina Strobl, William Cross, Nischalan Pillay, Sandra J. Strauss, Hongtao Ye, Daniel Lindsay, Roberto Tirabosco, Jane Chalker, Shazia S. Mahamdallie, Alona Sosinsky, Adrienne M. Flanagan, Fernanda Amary

JOURNAL OF PATHOLOGY CLINICAL RESEARCH (2020)

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Article Multidisciplinary Sciences

Somatostatin receptor 2 expression in nasopharyngeal cancer is induced by Epstein Barr virus infection: impact on prognosis, imaging and therapy

Matt Lechner, Volker H. Schartinger, Christopher D. Steele, Wen Long Nei, Marc Lucas Ooft, Liesa-Marie Schreiber, Christodoulos P. Pipinikas, Grace Tin-Yun Chung, Yuk Yu Chan, Feng Wu, Ka-Fai To, Chi Man Tsang, Wayne Pearce, Daniele Morelli, Martin Philpott, Liam Masterson, Reshma Nibhani, Graham Wells, Christopher G. Bell, Julia Koller, Susanne Delecluse, Yim Ling Yip, Jacklyn Liu, Cillian T. Forde, Martin D. Forster, Amrita Jay, Jozsef Dudas, Annika Krapp, Simon Wan, Christian Uprimny, Susanne Sprung, Johannes Haybaeck, Tim R. Fenton, Kerry Chester, Christina Thirlwell, Gary Royle, Teresa Marafioti, Rajeev Gupta, Sagung Rai Indrasari, Camelia Herdini, Mohd Afiq Mohd Slim, I. Indrawati, Liam Sutton, Renske Fles, Bing Tan, Joe Yeong, Amit Jain, Shuting Han, Haitao Wang, Kelvin S. H. Loke, Wan He, Ruilian Xu, Hongtao Jin, Zhiqiang Cheng, David Howard, Peter H. Hwang, Quynh-Thu Le, Joshua K. Tay, Robert B. West, Sai Wah Tsao, Tim Meyer, Herbert Riechelmann, Udo Oppermann, Henri-Jacques Delecluse, Stefan M. Willems, Melvin L. K. Chua, Pierre Busson, Kwok Wai Lo, Guido Wollmann, Nischalan Pillay, Bart Vanhaesebroeck, Valerie J. Lund

Summary: This study reveals that somatostatin receptor 2 is induced by the Epstein-Barr virus in nasopharyngeal carcinoma and plays a key role in the diagnosis, imaging, targeted therapies, and prognosis of the disease.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum

Shenglin Cai, Thomas Pataillot-Meakin, Akifumi Shibakawa, Ren Ren, Charlotte L. Bevan, Sylvain Ladame, Aleksandar P. Ivanov, Joshua B. Edel

Summary: The study presents a new sensing platform for miRNA detection, offering high sensitivity and specificity directly in human serum, and demonstrating monitoring of miR-141-3p and miR-375-3p in various stages of prostate cancer.

NATURE COMMUNICATIONS (2021)

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Review Cell Biology

Unravelling undifferentiated soft tissue sarcomas: insights from genomics

Shadi Hames-Fathi, Steven W. G. Nottley, Nischalan Pillay

Summary: This article reviews recent advances in the diagnosis and treatment of undifferentiated soft tissue sarcoma (USTS), including genomic sequencing, cancer evolution and heterogeneity studies, and immunotherapy. The critical role of pathologists in the diagnosis and treatment of USTS patients is emphasized.

HISTOPATHOLOGY (2022)

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Article Multidisciplinary Sciences

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

Erik N. Bergstrom, Jens Luebeck, Mia Petljak, Azhar Khandekar, Mark Barnes, Tongwu Zhang, Christopher D. Steele, Nischalan Pillay, Maria Teresa Landi, Vineet Bafna, Paul S. Mischel, Reuben S. Harris, Ludmil B. Alexandrov

Summary: This study provides a comprehensive characterization of clustered mutations and small insertions and deletions in cancer genomes. The results show that clustered mutations are enriched in driver genes and associated with differential gene expression and overall survival. Different mutational processes contribute to clustered insertions and deletions, including specific signatures in tobacco smokers and homologous-recombination-deficient cancers. APOBEC3 plays a significant role in clustered substitutions, although only a small percentage matches APOBEC3 patterns. The study also reveals the associations between the activation-induced deaminase (AID) and APOBEC3 family of deaminases with kataegis (longer strand-coordinated events).

NATURE (2022)

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Article Microbiology

A Rapid Drug Resistance Genotyping Workflow for Mycobacterium tuberculosis, Using Targeted Isothermal Amplification and Nanopore Sequencing

Harriet D. Gliddon, Dan Frampton, Vanisha Munsamy, Jude Heaney, Thomas Pataillot-Meakin, Eleni Nastouli, Alexander S. Pym, Adrie J. C. Steyn, Deenan Pillay, Rachel A. McKendry

Summary: The study developed a workflow for rapid prediction of drug resistance in TB isolates, with low cost and high accuracy, suitable for resource-limited settings.

MICROBIOLOGY SPECTRUM (2021)

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Review Oncology

Leveraging single-cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers

Amy L. Bowes, Maxime Tarabichi, Nischalan Pillay, Peter Van Loo

Summary: This review provides an overview of current single-cell DNA sequencing technologies and their applications in studying intratumour heterogeneity (ITH) and tumour evolution. The advancements in methodological approaches have allowed for the exploration of evolutionary dynamics contributing to tumourigenesis, progression, metastasis, and therapy resistance. The use of in situ sequencing technologies and lineage tracing in both normal and malignant tissues are also discussed.

JOURNAL OF PATHOLOGY (2022)

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Review Oncology

An overview of mutational and copy number signatures in human cancer

Christopher D. Steele, Nischalan Pillay, Ludmil B. Alexandrov

Summary: The genome of each cell is constantly damaged by various processes, resulting in DNA damage and mutations. The mutational signatures of small mutational events have been extensively studied, and the focus has shifted to understanding the mutational signatures of copy number alterations (CNAs). The study of these mutational signatures has practical implications in basic science, cancer treatment, and cancer prevention.

JOURNAL OF PATHOLOGY (2022)

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Editorial Material Oncology

Recent Advances in Pathology: the 2022 Annual Review Issue of The Journal of Pathology

C. Simon Herrington, Richard Poulsom, Nischalan Pillay, Peter Bankhead, Philip J. Coates

Summary: This article introduces the importance and content of the 2022 Annual Review Issue of The Journal of Pathology, focusing on recent advances in digital pathology, mutational pattern evaluation, lineage tracing, and single cell sequencing technologies.

JOURNAL OF PATHOLOGY (2022)

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Article Multidisciplinary Sciences

Signatures of copy number alterations in human cancer

Christopher D. Steele, Ammal Abbasi, S. M. Ashiqul Islam, Amy L. Bowes, Azhar Khandekar, Kerstin Haase, Shadi Hames-Fathi, Dolapo Ajayi, Annelien Verfaillie, Pawan Dhami, Alex McLatchie, Matt Lechner, Nicholas Light, Adam Shlien, David Malkin, Andrew Feber, Paula Proszek, Tom Lesluyes, Fredrik Mertens, Adrienne M. Flanagan, Maxime Tarabichi, Peter Van Loo, Ludmil B. Alexandrov, Nischalan Pillay

Summary: Gains and losses of DNA are prevalent in cancer and contribute to cancer initiation, progression, and therapeutic resistance. A study identified 21 copy number signatures that explain 97% of the sample's copy number patterns.

NATURE (2022)

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Article Chemistry, Multidisciplinary

Detection of YAP1 and AR-V7 mRNA for Prostate Cancer Prognosis Using an ISFET Lab-On-Chip Platform

Joseph Broomfield, Melpomeni Kalofonou, Thomas Pataillot-Meakin, Sue M. Powell, Rayzel C. Fernandes, Nicolas Moser, Charlotte L. Bevan, Pantelis Georgiou

Summary: Prostate cancer is the second most common cause of male cancer-related death worldwide. Androgen deprivation therapy is the gold standard for treating advanced prostate cancer, but it often leads to castration-resistant prostate cancer. Detecting relevant biomarkers in the blood of castration-resistant patients could help personalize treatment options.

ACS SENSORS (2022)

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