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Handbook of Biomarkers and Precision Medicine
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Table of Contents

Preface Maria Freire

  1. What is a Biomarker and their Role in Drug Development?

  2. Definitions and conceptual framework of Biomarkers in Precision Medicine Claudio Carini, Mark D Fidock, Alain J van Gool In search of predictive biomarkers in cancer immunotherapy: Establishment of collaborative network for the validation process Giuseppe Masucci, Paola A Ascierto, Lisa Villabona Integrating personalized medicine in the healthcare: Payers and reimbursements Dominic Galante, Marylou Buyse Regulatory strategies to accelerate the implementation of biomarkers and companion diagnostics (CDX) F Owen Fields
  3. Biomarkers in Preclinical Sciences
  4. Lost in Translation - the challenges with the use of animal models in translational research
    Attila Seyhan,Claudio Carini Application of pharmacokinetic and pharmacodynamic modelling of biomarkers of efficacy in Translational research Neil Benson The DIAMONDS platform: Providing Decision Support for Toxicological Assessment based on Integration of Structural, Toxicological and Biomarker information Rob H Stierum, E Dinant Kroese, Jack TWE Vogels, Harrie Buist, Danyel GJ Jennen, Eugene P van Someren Predicting the (non)clinical toxicity of novel drug targets: an in silico perspective
    Jennifer Venhorst, Lars Verschuren, Annemette V Thougaard, Jorrit J Hornberg, Tanja Rouhani Rankouhi Unwanted Immunogenicity Responses to Biotherapeuitcs Shobha Purushothama, Boris Gorovits Biomarker use for advanced screening of drug-induced kidney injury Martijn J Wilmer, Frans GM Russel Soluble biomarkers for Cardiotoxicity Amy Pointon and Nick Edmunds

  5. Biomarkers in Translational Medicine
  6. Lost in Translation- Bridging the Pre-Clinical and Clinical Worlds Concepts, Examples, and Successes and Failure in Translational Medicine Attila Seyhan and Claudio Carini Necessary Characterization of Biomarkers to be "Fit for Purpose" Suso Platero Crucial role of high quality biosamples in biomarker development Cornelia Stumptner, Karine Sargsyan, Penelope Kungl, Kurt Zatloukal Informatics solution for biomarker discovery and personalized medicine in clinical care
    Jan Willem Boiten, Rita Azevedo, Marinel Cavelaars, Andre Dekker, Remond JA Fijneman, Arnoud van der Maas, Morris Swertz, Jeroen AN Belien, Gerrit A Meijer Systems Biology Approaches to Identify New Biomarkers Lars Kuepfer, Andreas Schuppert The need for global collaboration in translational medicine Florence Bietrix, Antoni L Andreu, Giovanni Migliaccio, Anton E Ussi

  7. Biomarker-informed Clinical Trials
  8. Overview of biomarker discovery and statistical considerations Overview of classical design in biomarker informed clinical trials Bo Huang, Jing Wang, Robert A. Beckman, Sandeep Menon and Weidong Zhang Novel biomarker guided clinical trials design: A practical view Bo Huang, Jing Wang, Robert A. Beckman, Sandeep Menon and Weidong Zhang Outsourcing Biomarker Clinical Trials: Advantages and Disadvantages Robert Holt Case studies for biomarker based clinical trials Bo Huang, Jing Wang, Robert A. Beckman, Sandeep Menon and Weidong Zhang Informational designs and potential applications to Rare Disease Robert Beckman, Cong Chen

  9. The road ahead: Identification of the hurdles and solutions to the implementation of Precision Medicine in healthcare
  10. Paving a new era in patient centric care through innovations in Precision Medicine Mark Fidock, Glen Hughes, Alain J van Gool, Claudio Carini Integrating Molecular Testing into Early Stage Clinical Applications
    JonathanIWilde Ectopic gene deregulations and chromosome conformations: integrating novel molecular testing into clinical applications, from leukemias to gliomas" Francis Hector Grand, Matthew Salter, Ewan Hunter, Alexandre Akoulitchev Challenges and Opportunities of Next Generation Sequencing Companion Diagnostics Benoit Destenaves Implementing companion diagnostics Martina Kaufmann Publishing biomedical research findings - what are the odds? Andreas Scherer Computational Biology: Modeling from Molecule to Disease and Personalized Medicine Nina Kusch, Lisa Turnhoff, Andreas Schuppert Expectations for Quality Control: Challenges with multi-plex assays John L Allinson

  11. Lessons from the past and pioneers of the future
  12. Development of Mariviroc and the Companion Diagnostic HIV Tropism Assay Elna van der Ryst, James Demarest, Jayvant Heera, Mike Westby,Charles Knisch Case studies: Infertility and Anti-Mullerian Hormone Martin Hund, Joan-Carles Arce Factor Xa: Case Study Boris Gorovits Delivering Companion Diagnostics for Complex Biomarkers: The BRCA Companion Diagnostic Story for LYNPARZATM (Olaparib) Maria C M Orr and Simon P Dearden Delivering the personalized medicine promise: best practice recommendations for designing biomarker development processes Karen KY Lam, Mary Zacour, Ji-Young V Kim, Zsuzsanna Hollander, Rhonda Wideman, Raymond T Ng, Scott J Tebbutt, Bruce M McManus Development, Launch and Adoption of a Pharmacodiagnostic: Planning Versus Reacting for Pharmaceutical Companies Mike Montalto, George Green Biomarker Consortia to drive BM discovery and clinical applications in the UK - lessons learned from RA-MAP John Isaacs, Sarah Brockbank, Ayako Pedersen Andrew Cope Measuring the Success of US biomarker Consortia Menetski Joseph The value of public-private partnerships in the Netherlands Hanna L Groen, Nico LU van Meeteren
  13. Paving a new era of personalized medicine: Emerging technologies
  14. A new era of personalized medicine: emerging technologies - functional proteomics, companion diagnostics and precision cancer medicine Michela Perani, Peter Parker The impact of epigenetics on the future of personalized medicine Jane Mellor Incorporating predictive imaging biomarkers in clinical trials for personalised healthcare John C Waterton Innovation in Metabonomics to improve personalized healthcare Nelma Pertega-Gomez and Massimo Loda Ultra-sensitive immunoassays to detect low abundant protein biomarkers Paul Wheeler Glycomics as an innovative approach for personalized medicine Stefanie Holst, Nurulamin Abu Bakar, Monique van Scherpenzeel, Manfred Wuhrer, Dirk J Lefeber miRNA as novel biomarkers of health and disease Laura Garcia Bermejo Targeted proteomics for absolute quantification of protein biomarkers in serum and tissues
    Coskun Guzel, Christoph Stingl, Frank Klont, Roel Tans, Esther Willems, Rainer Bischoff, Alain J van Gool, Theo M Luider, the Biomarker Development Center Consortium Integrated omics for tissue-based mapping of the human proteome Cecilia Lindskog Proteogenomics and multi-omics data integration for personalized medicine Peter Horvatovich, Corry-Anke Brandsma, Frank Suits, Rainer Bischoff, Victor Guryev Sequencing Approaches for Personalized Cancer Therapy Selection in Pathology Wendy de Leng, Manon Huibers, John Hinrichs, Edwin Cuppen, Stefan Willems Mass spectrometry imaging: enabling comprehensive spatial analysis of molecular biomarkers in tissue for personalized medicine Tiffany Porta, Steven WM Olde Damink, Ron MA Heeren Insights for personalized medicine from the gut microbiome: Lesson learned from celiac disease Gloria Serena, Anna Sapone, Alessio Fasano

  15. The next frontiers of therapeutic target areas: Autoimmunity, inflammation, respiratory, metabolic, cardiovascular and neurological diseases
  16. Precision Mucosal Sampling and Biomarkers in Allergic Rhinitis and Asthma Ashillesh Jha, Ryan S Thwaites, Nehmat Singh, Trevor Hansel Stratified medicine in autoimmune diseases John A Reynolds, Ian Bruce Biomarkers of Systemic Lupus Erythematosus Hiroshi Kato, Andras Perl Advances in cardiovascular Diagnostics - Use of cardiac biomarkers in clinical research and care of the patient Mark Effron and Zahoor Khan Biomarkers for psychiatric disease: an overview Roy Perlis Progressing towards precision psychiatry: current challenges in applying biomarkers in psychiatry
    Victor L Kallen, Brisa S Fernandes Identification of Biomarkers for the diagnosis, prediction and progression of Alzheimer's Disease Bennett P Greenwood, Vladimir Tolstikov, Paula P Narain, Jeremy Chaufty, Viatcheslav R Akmaev, Vivek Vishnudas, Stephane Gesta, Rangaprasad Sarangarajan, Niven R Narain, Mike Kiebish Biomarkers in Lung Cancer George Santis, Richard Lee and Crispin T Hiley

  17. Lessons Learned: What have we learned and what is the next challenge?
Translational science in modern pharmaceutical R&D: the influence of organizational structures on successes and failures Peter MA Groenen Biomarkers Qualification and Companion Diagnostics- Failure and Success of regulatory Process Federico Goodsaid Not all Biomarkers Are Worthwhile: An Unsuccessful Use and Pitfalls to Avoid Abdel Halim Research Reproducibility: The Case for Standards Leonard P Freedman, Raymond H Cypess Can Big Data Analytics Recapitulate Biology? A Survey of Multi-omics Data Integration Approaches
Armit Singh, Casey P Shannon, Kim-Anh Le Cao, and Scott J Tebbutt Can healthcare be made more affordable by the use of biomarkers? Rene L Sluiter, Wietske Kievit, Gert Jan van der Wilt Omics driven medicine for democratizating healthcare delivery and health economics Mike Kiebish, Viatcheslav R Akmaev, Vivek Vishnudas, Stephane Gesta, Rangaprasad Sarangarajan, Niven R

About the Author

Claudio Carini, MD, PhD, FRCPath, has been involved in the application of biomarkers in precision medicine for the past 18 years. He is currently appointed as H. Faculty in the Department of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine at King's College, School of Medicine, London. He is a member of the F-NIH Biomarkers Consortium Steering Committees for Cancer, Inflammation & Immunity, and Neuroscience. He is also a senior member of the Scientific Advisory Boards for several biotechnology companies and a member of the New York Academy of Sciences. Claudio was formerly the Global Head of Clinical Immunology and Biomarkers at Pfizer Inc., where he led precision medicine activities across multiple therapeutic areas and facilitated international collaborations with prestigious academic institutions. He also held senior roles in pharmaceutical companies (Wyeth, Novartis, and Roche) and faculty positions at Harvard and Johns Hopkins Medical School. He is a strong believer of open innovation networks, and in his roles he has been collaborating extensively with different stakeholders to speed up the clinical application of scientific research through public-private partnerships. He has served in several national and international scientific boards: F-NIH Inflammation/Immunity; MRC, Inflammation/ Immunology Initiative-Rheumatoid Arthritis Consortium; MRC, "Stratified Medicine, SLE Consortium; IMI, ABIRISK, EU/EFPIA"; The PML Consortium. Claudio has over 200 publications in national and international peer-reviewed journals. He has also co-edited three books in the field of Biomarkers and Precision Medicine: Biomarkers in Drug Development: A Handbook of Practice Application and Strategy, (2010), Clinical and Statistical Considerations in Personalized Medicine, (2014), and Handbook of Biomarkers & Precision Medicine (2019 in press). Mark D. Fidock, PhD, is Vice President of Precision Medicine Laboratories within the IMED Biotech Unit, AstraZeneca, Cambridge, UK. He received his PhD from the University of East Anglia, UK, in Molecular Pharmacology. Mark is a trained molecular biologist/pharmacologist and gained extensive experience in drug development early in his career while at Pfizer Ltd, Sandwich, UK. He supported the development and approval of four new therapies and provided leadership for the Biomarker and Translational Medicine activities across multiple therapeutic areas. Mark joined AstraZeneca in 2013, appointed to the role of Head of Precision Medicine Laboratories and a member of the Precision Medicine and Genomics Leadership Team. He has overall accountability for all clinical testing activities that enables diagnostic development and regulatory approval. Mark leads a global multidisciplinary team providing strategy and direction in the development of Companion Diagnostic tests linked to targeted therapeutics across Oncology; Respiratory; and Cardiovascular, Renal, & Metabolism. These laboratory tests are deployed across both early- and late-phase clinical trials with the intent for global regulatory approval. By 2019 Mark had achieved >25 regulatory approved companion diagnostic tests across 3 major markets (USA, EU and Japan) linked to 4 AstraZeneca targeted therapies. Mark has a passion for innovative diagnostic science, driving research such as the use of artificial intelligence across tissue and molecular diagnostics to enable approaches that improve clinical testing outcomes with the ambition to change clinical care pathways. Mark has published more than 30 peer-reviewed articles in scientific journals and an active editor of the Journal of Precision Medicine. As an internationally recognized expert in Precision Medicine he holds an honorary position at the University of Cambridge and a member of the Institute of Translational and Stratified Medicine, Plymouth, scientific advisory board. Alain J. van Gool, PhD, is a professor of Personalized Healthcare and heads the Translational Metabolic Laboratory at the Radboud university medical center, Nijmegen Netherlands, with a strong passion in the application of biomarkers in translational medicine and personalized healthcare. Being trained as biochemist and molecular biologist, Alain worked at pharmaceutical industry (Organon, Schering-Plough, MSD), academia, applied research institutes, and university medical centers in EU, USA, and Singapore. He has been leading technology-based laboratories, cross-functional expert teams, therapeutic project teams, and public-private consortia, many of which were focused on the discovery, development, and implementation of translational biomarkers in a variety of therapeutic areas. His technical expertise resides most strongly in molecular profiling through x-omics, analytical biomarker development, and applications in translational scientific research. Alain is a strong believer of public-private partnerships and thrives to work with specialists to translate research findings to applications. With that background, he currently also acts as Strategic Advisor to the Executive Board of Radboudumc, coordinates the Radboudumc Technology Centers, is Scientific Lead Technologies of DTL (the Dutch Techcenter for Life Sciences), is Chair Biomarker Platform of EATRIS (the European infrastructure for Translational Medicine), is co-initiator of Health-RI (the Netherlands Personalized Medicine and Health Research Infrastructure), and project leader and PI of the Netherlands X-omics Initiative, thus contributing to the organization and coordination of local, national, and European technology infrastructures. Alain has published 40 peer-reviewed articles in scientific journals and is a frequently invited keynote speaker at scientific conferences and public events. Complementing his daily work, he enjoys contributing as translational biomarker scientist to editorial boards of scientific journals, funding agencies, and scientific advisory boards of start-up enterpreneurs, multinational companies, diagnostic organizations, public-private consortia, and conference organizers.

Reviews

"This handbook is hardcover and was published at CRC Press / Taylor and Francis Group in 2019. From the first time I opened it, I could notice that the printing and quality of paper is exceptional. The handbook has 631 pages and very nicely coloured figures, schemes and drawings, that are very easily understandable and very helpful in processing the text of the handbook. The field of biomarkers is approached in this book in a scholastic manner, starting from the first discovery and use of biomarkers to the regulatory approaches in the field of precision medicine, passing from preclinical studies, translational medicine, clinical trials, and implementation in practice. Several case-studies are presented related to HIV diagnosis, infertility, coagulation, BRCA identification, but also case-studies related to biomarker-based clinical trials... This handbook is complete, exact, succinct and unique, and gathers information from different perspectives, useful to different players from the field of biomarkers in precision medicine, making it a an excellent tool for learning. First of all, I would recommend this handbook to researchers from the medical and connected fields. It could help the development of this engaging field of personalized care due to highly accurate and relevant data presented by the authors. Secondly, I would recommend it to medical doctors from all specialties since it offers a deep and comprehensive approach into a field that only a few decades ago was hardly recognized and since the practice of medicine in most specialties during the following years will, for sure, include a personalized approach to
patients. Both these addressees, researchers and medical practitioners, can make a difference. Least but not last, I would say that even residents and medical students would benefit from the comprehensive approach that this book provides."
- Costela Serban, ISCB December 2019

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