Clinical actionability enhanced through deep targeted sequencing of solid tumors

Ken Chen, Funda Meric-Bernstam, Hao Zhao, Qingxiu Zhang, Nader Ezzeddine, Lin Ya Tang, Yuan Qi, Yong Mao, Tenghui Chen, Zechen Chong, Wanding Zhou, Xiaofeng Zheng, Amber Johnson, Kenneth D. Aldape, Mark J. Routbort, Rajyalakshmi Luthra, Scott Kopetz, Michael A. Davies, John De Groot, Stacy MoulderRavi Vinod, Carol J. Farhangfar, Kenna Mills Shaw, John Mendelsohn, Gordon B. Mills, Agda Karina Eterovic

    Research output: Contribution to journalArticle

    68 Scopus citations

    Abstract

    BACKGROUND: Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is present and whether it may affect clinical decision-making. To study this question, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples. METHODS: We assayed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer-related genes. Mutations, indels, and copy number data were reported. RESULTS: We obtained a 1000-fold mean sequencing depth and identified 4794 nonsynonymous mutations in the samples analyzed, of which 15.2% were present at <10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) otherwise would have been unactionable. In addition, acquiring ultrahigh depth also ensured a low false discovery rate (<2.2%) from FFPE samples. CONCLUSIONS: Our results were as accurate as a commercially available CLIA-compliant hotspot panel but allowed the detection of a higher number of mutations in actionable genes. Our study reveals the critical importance of acquiring and utilizing high sequencing depth in profiling clinical tumor samples and presents a very useful platform for implementing routine sequencing in a cancer care institution.

    Original languageEnglish (US)
    Pages (from-to)544-553
    Number of pages10
    JournalClinical chemistry
    Volume61
    Issue number3
    DOIs
    StatePublished - Mar 1 2015

    ASJC Scopus subject areas

    • Clinical Biochemistry
    • Biochemistry, medical

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  • Cite this

    Chen, K., Meric-Bernstam, F., Zhao, H., Zhang, Q., Ezzeddine, N., Tang, L. Y., Qi, Y., Mao, Y., Chen, T., Chong, Z., Zhou, W., Zheng, X., Johnson, A., Aldape, K. D., Routbort, M. J., Luthra, R., Kopetz, S., Davies, M. A., De Groot, J., ... Eterovic, A. K. (2015). Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clinical chemistry, 61(3), 544-553. https://doi.org/10.1373/clinchem.2014.231100