Chapter 17. Standard Operating Procedures in Clinical Gene Expression Biomarker Panel Development

  1. Andreas Scherer Founder/CEO of Spheromics
  1. Khurram Shahzad1,
  2. Anshu Sinha2,
  3. Farhana Latif3 and
  4. Mario C Deng3

Published Online: 2 NOV 2009

DOI: 10.1002/9780470685983.ch17

Batch Effects and Noise in Microarray Experiments: Sources and Solutions

Batch Effects and Noise in Microarray Experiments: Sources and Solutions

How to Cite

Shahzad, K., Sinha, A., Latif, F. and Deng, M. C. (2009) Standard Operating Procedures in Clinical Gene Expression Biomarker Panel Development, in Batch Effects and Noise in Microarray Experiments: Sources and Solutions (ed A. Scherer), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470685983.ch17

Editor Information

  1. Spheromics, Kontiolahti, Finland

Author Information

  1. 1

    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA

  2. 2

    Department of Biomedical Informatics, Columbia University, New York, NY, USA

  3. 3

    Department of Medicine, Columbia University, New York, NY, USA

Publication History

  1. Published Online: 2 NOV 2009
  2. Published Print: 30 OCT 2009

ISBN Information

Print ISBN: 9780470741382

Online ISBN: 9780470685983

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Keywords:

  • systems biology;
  • genomic biomarker panel;
  • CARGO study;
  • standard operating procedures (SOPs);
  • clinical trial;
  • consensus;
  • gene discovery

Summary

The development of genomic biomarker panels in the context of personalized medicine aims to address biological variation (disease etiology, gender, etc.) while at the same time controlling technical variation (noise). Whether biomarker trials are undertaken by single clinical/laboratory units or in multicenter collaborations, technical noise can be addressed (though not completely eliminated) by the implementation of standard operating procedures (SOPs). Once agreed upon by the study members, SOPs have to become obligatory. We illustrate the usefulness of SOPs by describing the development of a genomic biomarker panel for the absence of acute cardiac allograft rejection resulting from the Cardiac Allograft Rejection Gene Expression Observational (CARGO) study. This biomarker panel is the first Food and Drug Administration-approved genomic biomarker test in the history of transplantation medicine.