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Next-generation sequencing in the clinic

Nature Biotechnology volume 31, pages 990–992 (2013)Cite this article

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Pools of cell lines carrying a variety of known mutations are used to validate the performance of a cancer diagnostic test based on next-generation sequencing.

As next-generation sequencing (NGS) of tumor cells becomes more sophisticated, it is likely to inform all aspects of cancer management, from diagnostic testing to treatment and drug discovery. In this issue, Frampton et al.1 describe a comprehensive NGS assay applicable to clinical samples that identifies single-base substitutions, copy-number variations and focal amplifications in 287 cancer-related genes, fusion events involving 19 frequently rearranged genes and 3,549 single-nucleotide polymorphisms in other locations throughout the genome—all within a single sequencing run. Validating the analytic performance of such a test is challenging because it assays so many nucleotide positions in the genome (∼1.5 Mb in total). The authors therefore use 53 cell lines to create reference materials for assessing the sensitivity and specificity of variant detection. Finally, they apply their test to >2,000 clinical cases. The overall approach of the study—including assay design, creation of reference materials and validation—serves as a model for the development of future clinical NGS tests.

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Figure 1: Clinical sequencing test protocol and validation.

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Authors and Affiliations

  1. Jason Y. Park is at the Department of Pathology, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, Texas, USA, and the Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,

    Jason Y Park

  2. Larry J. Kricka is at the Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania, USA.,

    Larry J Kricka

  3. Department of Cancer Biology, Paolo Fortina is at the Cancer Genomics Laboratory, Kimmel Cancer Center, Thomas Jefferson University, Jefferson Medical College, Philadelphia, Pennsylvania, USA.,

    Paolo Fortina

Authors
  1. Jason Y Park
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  2. Larry J Kricka
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  3. Paolo Fortina
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Correspondence to Jason Y Park.

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The authors declare no competing financial interests.

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Park, J., Kricka, L. & Fortina, P. Next-generation sequencing in the clinic. Nat Biotechnol 31, 990–992 (2013). https://doi.org/10.1038/nbt.2743

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