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International Journal of Oncology
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Print ISSN: 1019-6439 Online ISSN: 1791-2423
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International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

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International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

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Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

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Article

Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories

  • Authors:
    • Pedro Mendez
    • Jennifer Dang
    • James Wansoo Kim
    • Sharon Lee
    • Jun-Hee Yoon
    • Thomas Kim
    • Charles J. Sailey
    • David M. Jablons
    • Il-Jin Kim
  • View Affiliations / Copyright

    Affiliations: Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94115, USA, CureSeq Inc., Brisbane, CA 94005, USA
  • Pages: 235-242
    |
    Published online on: April 25, 2016
       https://doi.org/10.3892/ijo.2016.3497
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Abstract

Next-generation sequencing (NGS) has led to breakthroughs for genetic and genomic analyses and personalized medicine approaches for many diseases. More and more clinical laboratories are using NGS as a genetic screening tool for providing mutation information that is used to select the best treatment regimens for cancer patients. However, several obstacles prevent the routine implementation of NGS technology into the clinical molecular diagnosis setting: the sophisticated sample preparation process, high cost, time-consuming data analyses, as well as the reproducibility and accuracy of interpretation. To systematically evaluate the performance and quality of targeted NGS cancer panel analyses in clinical laboratories, we performed three different tests: i) laboratory-to-laboratory accuracy test, ii) intra-laboratory precision validation, and iii) limit of detection test, using formalin-fixed, paraffin-embedded cancer tissue specimens, cell lines and mutation positive DNA. A laboratory-to-laboratory accuracy test performed using 51 samples showed 100% sensitivity and 99.97% specificity. For the intra-laboratory precision test, 100% reproducibility was observed. For the limit of detection test, KRAS mutations from samples diluted from 70 to 2% of mutant allele frequencies were detected correctly. We believe that the present study demonstrated the feasibility of clinical implementation of a targeted NGS cancer panel analysis for personalized medicine.
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Copy and paste a formatted citation
Spandidos Publications style
Mendez P, Dang J, Kim JW, Lee S, Yoon J, Kim T, Sailey CJ, Jablons DM and Kim I: Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories. Int J Oncol 49: 235-242, 2016.
APA
Mendez, P., Dang, J., Kim, J.W., Lee, S., Yoon, J., Kim, T. ... Kim, I. (2016). Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories. International Journal of Oncology, 49, 235-242. https://doi.org/10.3892/ijo.2016.3497
MLA
Mendez, P., Dang, J., Kim, J. W., Lee, S., Yoon, J., Kim, T., Sailey, C. J., Jablons, D. M., Kim, I."Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories". International Journal of Oncology 49.1 (2016): 235-242.
Chicago
Mendez, P., Dang, J., Kim, J. W., Lee, S., Yoon, J., Kim, T., Sailey, C. J., Jablons, D. M., Kim, I."Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories". International Journal of Oncology 49, no. 1 (2016): 235-242. https://doi.org/10.3892/ijo.2016.3497
Copy and paste a formatted citation
x
Spandidos Publications style
Mendez P, Dang J, Kim JW, Lee S, Yoon J, Kim T, Sailey CJ, Jablons DM and Kim I: Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories. Int J Oncol 49: 235-242, 2016.
APA
Mendez, P., Dang, J., Kim, J.W., Lee, S., Yoon, J., Kim, T. ... Kim, I. (2016). Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories. International Journal of Oncology, 49, 235-242. https://doi.org/10.3892/ijo.2016.3497
MLA
Mendez, P., Dang, J., Kim, J. W., Lee, S., Yoon, J., Kim, T., Sailey, C. J., Jablons, D. M., Kim, I."Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories". International Journal of Oncology 49.1 (2016): 235-242.
Chicago
Mendez, P., Dang, J., Kim, J. W., Lee, S., Yoon, J., Kim, T., Sailey, C. J., Jablons, D. M., Kim, I."Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories". International Journal of Oncology 49, no. 1 (2016): 235-242. https://doi.org/10.3892/ijo.2016.3497
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