Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

Abstract

Importance Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer. Objective To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response. Design, Setting, and Patients Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response. Main Outcomes and Measures Feasibility, use of WES for decision making, and identification of novel biomarkers. Results A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95× and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response. Conclusions and Relevance The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

“…For example, a number of studies using whole-exome sequencing to provide diagnoses for undiagnosed, suspected genetic conditions, resulted in a roughly 25% success rate, with a significant proportion of these successes resulting in the identification of mutations that had not been previously characterized 40 . In "N of 1" cancer cases for both retrospective 41 and prospective studies 42 , finding actionable mutations that can affect treatment choices happens in well over 50% of the cases, with a high percentage of the actionable mutations identified as being de novo. We anticipate that future searches for individuals resilient to various genetic defects will be most effective when combining the traditional searches for positive outliers in known extended families with very broad searches for positive outliers in the general population.…”

Institutional implementation of clinical tumor profiling on an unselected cancer population

“…Massively parallel sequencing (MPS) offers several advantages over the single-gene approach (10)(11)(12)(13)(14)(15); most importantly, it offers a more sensitive and more comprehensive genomic profile that does not apply an a priori knowledge of alterations that may be more common in a specific tumor type. Several academic centers have demonstrated that large MPS panels can be employed in practice (11,16,17), with a number of groups reporting a high rate of "actionable" (informative or clinically relevant) gene alterations in clinical cancer cohorts (4,18,19).…”

“…Several recent reports have shown that only a small proportion of patients (~5%-10%) have their cancer genomic data used as a criterion for selection of a targeted therapy or a clinical trial (16,19,20). A variety of logistic, operational, and medical reasons (20) have been cited, such as identification of the appropriate genomic target at the right time in a patient's clinical course, time to result, the value of biopsy at the time of progressive disease (21), choice of conventional treatment protocols, access to clinical trials (16,20) or off-label use of drug (19), and patient preferences (20). Similarly, evaluation of the confidence of physicians at our institutions in using genomic data to make decisions on patient treatment options (22) indicates that not all "actionable" genomic data will be acted upon.…”

Integrating genomics into clinical pediatric oncology using the molecular tumor board at the Memorial Sloan Kettering Cancer Center

“…[8,11,12] For mutations without reported annotation and for variants of unknown significance, interpretation included individual review of the published literature and cancer genome databases, including canSAR, [14] cBioPortal for Cancer Genomics, [15,16] and Tumor Portal. [17] Novel missense gene mutations were modeled using structure-homology modeling with SWISS-MODEL.…”