Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA

Nora S. Sánchez, PhD; Michael P. Kahle, PhD; Ann Marie Bailey, PhD; Chetna Wathoo, MD; Kavitha Balaji, PhD; Mehmet Esat Demirhan, MD, Dong Yang, PhD; Milind Javle, MD; Ahmed Kaseb, MD; Cathy Eng, MD; Vivek Subbiah, MD; Filip Janku, MD, PhD; Victoria M. Raymond, MS; Richard B. Lanman, MD; Kenna R. Mills Shaw, PhD; Funda Meric-Bernstam, MD


JCO Precis Oncol. 2019;2019(3) 

In This Article

Patients and Methods


From November 2014 through February 2018, 575 patients with advanced cancers were prospectively consented for enrollment ( identifier: NCT01772771) and underwent cfDNA testing using a Clinical Laboratory Improvement Act–certified, College of American Pathologists–accredited laboratory, New York State Department of Health–approved panel that includes 70 to 73 genes commonly altered in cancer (Guardant360; Guardant Health, Redwood City, CA). Criteria for enrollment were active metastatic/local inoperable advanced cancer, consideration of clinical trial enrollment within the next two lines of therapy, and exhausted tissue block or archival tissue older than 1 year or available tissue block but progression on compelling intervening therapy. Human investigations were performed after approval by the MD Anderson institutional review board and in accordance with an assurance filed with and approved by the US Department of Health and Human Services.

Comprehensive Genomic Testing in Plasma

cfDNA was extracted from whole blood collected in 10-mL Streck tubes. Samples were shipped to a Clinical Laboratory Improvement Act–certified, College of American Pathologists–accredited laboratory (Guardant Health). After double ultracentrifugation, 5 to 30 ng of cfDNA were isolated and analyzed by digital sequencing as previously described.[9–14] Samples were tested on either a 70- or 73-gene panel (DDR2, MAPK1 [ERK2], and MAPK3 [ERK1]) were added) for the detection of point mutations, select insertion-deletion alterations (indels), copy number amplifications, and fusions.[3]

Actionable Genes Defined

Variants identified by the Guardant360 panel were annotated for their functional significance by the Institute for Personalized Cancer Therapy–Precision Oncology Decision Support team at MD Anderson Cancer Center. Variants were ascribed a clinical potential for actionability using criteria described previously[15,16] and herein. Sixty-seven genes were considered actionable. Only variants that occurred within an actionable gene were annotated.[17,18]

A gene is considered actionable if it has an established biologic role in cancer and there is a clinically available drug to which the gene confers sensitivity or resistance, where actionability can be applicable to all or select alteration or tumor types. The 67 panel genes and Precision Oncology Decision Support–designated actionability are listed in the Data Supplement. Of note, other genes are included in the Guardant360 panel, such as tumor suppressor genes, which may not be targetable, but clonal driver mutations in these genes are usually variants at the highest allele fractions, which makes them ideal candidates to index the degree of tumor DNA shedding into the bloodstream and to determine the relative subclonality of other variants in the same sample.

Defining a Variant's Potential for Clinical Action

Variants reported in an actionable gene were annotated as follows:

  • Functional significance (FS): activating, activating inferred, inactivating, inactivating inferred, inactivating and neomorphic, unknown, or likely benign

  • Actionable variant call (AVC; from highest level of evidence [LOE] to lowest): yes: literature-based (peer-reviewed scientific literature); yes: functional genomics (Institute for Personalized Cancer Therapy internal functional genomics platform); yes: inferred (intermediate LOE includes inferences dictated by the type of alteration and is mostly applicable to frameshift/truncation alterations where loss of region is inferred to be activating/inactivating); potentially (lower LOE where there are indirect and/or limited data to support the function of a specific alteration); unknown; or no (FS call is likely benign or inactivating alteration in an oncogene)

  • Actionable for call: the combination of an FS call and AVC: therapeutic intervention, resistance to drugs, or enrollment in select clinical trials.

Finally, gene actionability can be applicable to all, or specific, tumor types. For example, KRAS is actionable for therapeutic intervention for all tumor types; however, for colorectal tumors, KRAS is also actionable for resistance to cetuximab and panitumumab (Data Supplement).

A fifth parameter to sum these parameters into one final call specifically that describes each variant's potential for treatment with targeted therapy is the variant's potential for clinical action: high potential for clinical action (HPCA), low potential for clinical action, or not recommended for clinical action. Although specific Food and Drug Administration–approved indications and/or National Comprehensive Cancer Network guidelines are not included within this parameter, the upstream annotation process depends on gene-level actionability. The workflow for categorizing a variant's potential for clinical action is illustrated in the Data Supplement.

Clinical Trials Identified on the Basis of Patient Genomic Profile

Trial retrieval was restricted to variants that were deemed actionable and to trials available at the MD Anderson Cancer Center at the time of patient annotation.

Patient Follow-up

Patients were followed for at least 6 months after the initial annotation to collect treatment decisions, performance status (PS), and trial screening/enrollment (and reasons for eligibility/ineligibility).