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. 2017 Jun 27;8(26):41806-41814.
doi: 10.18632/oncotarget.16018.

A feasibility study of returning clinically actionable somatic genomic alterations identified in a research laboratory

Natalia Paez Arango  1 , Lauren Brusco  2 , Kenna R Mills Shaw  2 , Ken Chen  3 , Agda Karina Eterovic  4 , Vijaykumar Holla  2 , Amber Johnson  2 , Beate Litzenburger  2 , Yekaterina B Khotskaya  2 , Nora Sanchez  2 , Ann Bailey  2 , Xiaofeng Zheng  3 , Chacha Horombe  2 , Scott Kopetz  5 , Carol J Farhangfar  6 , Mark Routbort  7 , Russell Broaddus  8 , Elmer V Bernstam  9   10 , John Mendelsohn  2   11 , Gordon B Mills  2   4 , Funda Meric-Bernstam  1   2   12
Affiliations

A feasibility study of returning clinically actionable somatic genomic alterations identified in a research laboratory

Natalia Paez Arango et al. Oncotarget. .

Erratum in

Abstract

Purpose: Molecular profiling performed in the research setting usually does not benefit the patients that donate their tissues. Through a prospective protocol, we sought to determine the feasibility and utility of performing broad genomic testing in the research laboratory for discovery, and the utility of giving treating physicians access to research data, with the option of validating actionable alterations in the CLIA environment.

Experimental design: 1200 patients with advanced cancer underwent characterization of their tumors with high depth hybrid capture sequencing of 201 genes in the research setting. Tumors were also tested in the CLIA laboratory, with a standardized hotspot mutation analysis on an 11, 46 or 50 gene platform.

Results: 527 patients (44%) had at least one likely somatic mutation detected in an actionable gene using hotspot testing. With the 201 gene panel, 945 patients (79%) had at least one alteration in a potentially actionable gene that was undetected with the more limited CLIA panel testing. Sixty-four genomic alterations identified on the research panel were subsequently tested using an orthogonal CLIA assay. Of 16 mutations tested in the CLIA environment, 12 (75%) were confirmed. Twenty-five (52%) of 48 copy number alterations were confirmed. Nine (26.5%) of 34 patients with confirmed results received genotype-matched therapy. Seven of these patients were enrolled onto genotype-matched targeted therapy trials.

Conclusion: Expanded cancer gene sequencing identifies more actionable genomic alterations. The option of CLIA validating research results can provide alternative targets for personalized cancer therapy.

Keywords: CLIA; clinical trial; genomics; precision medicine; somatic mutation.

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Conflict of interest statement

CONFLICTS OF INTEREST

The authors declare no potential conflicts of interest and have no financial disclosures.

Figures

Figure 1
Figure 1. Study design for identification of clinically actionable somatic genomic alterations
Figure 2
Figure 2. Number of patients with previously unknown actionable mutations (green), Amplification (red) and Deletions (blue) for each gene detected in the T200 platform
Figure 3
Figure 3. Detection and validation of somatic alterations using hybrid capture sequencing in research setting
A. Somatic alterations detected using hybrid capture sequencing. n = number of patients. B. CLIA validation of T200 findings. n = number of patients, n* = number of alterations, a = Overall numbers remove duplication of patients that had both amplification and deletion concomitantly. MAF = Mutant allelic frequency, CN = Copy number.
See this image and copyright information in PMC

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