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Genomics Clinical Trial Assay Development: Issues and Lessons Learned

Genomics Clinical Trial Assay Development: Issues and Lessons Learned

Genomics Clinical Trial Assay Development: Issues and Lessons Learned

  • Editor: Dr. Matthew Marton   Ken CN Chang  
  • ISBN: 978-1-63278-040-9
  • DOI: 10.4172/978-1-63278-040-9-041
  • No of Pages: 62
  • Publisher: OMICS International
  • Published On: July 2015 , Wed 08
  • Chapter 1      
    Introduction- General Considerations for Developing a Successful Clinical Assay
    Authors: Ken CN Chang, Matthew J Marton

    Most scientists in the field of assay development and validation understand that the goal of developing a successful clinical assay is to make sure that the assay is precise, accurate, sensitive, specific, and reproducible.

  • Chapter 2      
    Case Studies: Issues and Lessons Learned for Developing and Validating Genotyping Assays for SNPs in Highly Homologous Gene Regions with High Nucleotide Sequence Diversity among Different Human Populations
    Authors: Bo Wei

    Genome-Wide Association Studies (GWAS) have identified many human genetic variations that are associated with diseases susceptibility and development, as well as individual’s responses to drug treatments.

  • Chapter 3      
    Case Studies: Issues and Lessons Learned from Gene Expression Profiling Assays and Mutation Assays
    Authors: Ken CN Chang

    Microarray gene expression profiling and Next Generation Sequencing (NGS) are two technologies similar in many ways. They are both break-through scientific innovations, use chip or flow cell technologies, and generate large amount of data that require some level of bioinformatics pipeline to interpret the data.

  • Chapter 4      
    Making a Gold Standard Assay Even Better: Lessons Learned in Rt-qPCR
    Authors: Miho Kibukawa

    Reverse Transcription (RT) followed by real time Polymerase Chain Reaction (qPCR) constitutes a powerful platform for clinical and diagnostic applications.

  • Chapter 5      
    Outsourcing Clinical Biomarker Assays - Will the Pendulum Swing Back?
    Authors: Matthew J Marton

    Partnering with external companies for clinical assay development and validation or clinical sample analysis has become common.

  • Chapter 6      
    General Considerations for Analytical Validation of Next Generation Sequencing- Based Assays
    Authors: Saumya Pant, Matthew J Marton

    Next Generation Sequencing (NGS) - based assays offer efficiency of scale via the ability to query multiple regions of the genome as well as the capacity to barcode samples uniquely to multiplex samples in a single run to achieve efficiency of cost and Turnaround Time (TAT).

  • Chapter 7      
    Lessons Learned in Lung, Breast and Colorectal Cancer Companion Diagnostics and Future Perspectives
    Authors: Mary J Savage, Deepti Aurora-Garg, Kenneth Emancipator, Marisa Dolled-Filhart

    Understanding the network of intra- and extra-cellular disease pathways in cancer biology has led to more successful, targeted oncology therapies.

  • Dr. Matthew Marton

    Merck Research Laboratories, Molecular Biomarkers and Diagnostics, Rahway, New Jersey, United States of America

    Matthew Marton is Director of Genomics in Merck, Sharp and Dohme’s Translational Molecular Biomarker Laboratory, where his team has deployed predictive biomarkers as patient enrichment assays on multiple technology platforms in over a dozen Merck clinical studies. His current work focuses on the companion diagnostic strategy for novel genomic assays as molecular diagnostics, and he is a contributor to several CLSI documents involving molecular diagnostic testing in oncology. Prior work at Merck focused on technology/ method development and biomarker discovery, with an emphasis on quality control of molecular profiling assays. Earlier in his career, Dr. Marton worked with Drs. Stephen Friend and Leland Hartwell at the Seattle Project, a drug discovery think tank, which led to the founding of Rosetta Inpharmatics, a biotechnology company that was acquired by Merck in 2001. At Rosetta and subsequently at Merck, he led scientific efforts to create a GLP-like high throughput functional genomics laboratory. Dr. Marton completed postdoctoral training at the NIH and holds a PhD from Princeton University and a Certificate in Biomedical Regulatory Affairs from the University of Washington. He currently holds the Regulatory Affairs Certification (RAC) from the Regulatory Affairs Professional Society (RAPS).

  • Ken CN Chang

    Molecular Biomarkers and Diagnostics, Merck & Co. Inc., Rahway, New Jersey, United States of America

    Ken CN Chang is the Scientific and Clinical Biomarker Development Lead at Merck & Co. since 2011. He holds a Ph.D. degree in Medicinal Chemistry and Pharmacology from State University of New York at Stony Brook, and completed more than 3 years of postdoctoral research at the Department of Pharmacology, Yale University School of Medicine. Prior to Merck, he worked at Wyeth Research and Pfizer Inc. for more than 17 years as principal investigator/drug discovery team leader in various disease areas, and as genomics and cellbased assay core lab manager. His research interests and expertise include DNA structure conformation, DNA replication and repair mechanisms, chemical carcinogenesis and mutagenesis, anti-cancer/anti-viral drug discovery, target identification/target validation using gene expression profiling technologies, as well as clinical biomarker assay development and validation.

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