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Two Studies Explore Clinical Utility of Tumor Sequencing in Pediatric Oncology

NEW YORK (GenomeWeb) – Two independent clinical pilot studies have found that on the order of 40 percent of pediatric cancer patients harbor mutations in their tumor or germline that have potential clinical significance, either for diagnosis or treatment.

The studies — one led by researchers at Texas Children's Cancer Center and Baylor College of Medicine and focusing on newly diagnosed patients, the other by a team at the Dana-Farber Cancer Institute, Boston Children's Hospital, Brigham and Women's Hospital and elsewhere and focusing on finding treatments for patients with advanced or high-risk cancer — were published in JAMA Oncology today.

The first study, resulting from the Baylor College of Medicine Advancing Sequencing in Childhood Cancer Care (BASIC3) project, which is funded as part of the National Institutes of Health's Clinical Sequencing Exploratory Research (CSER) consortium, set out to determine the diagnostic yield of tumor and germline whole-exome sequencing in children with cancer.

The study looked at 150 children who were newly diagnosed with solid tumors and had not received treatment yet. The patients, about a third of whom had a tumor of the central nervous system, were enrolled between August 2012 and June 2014, the first 150 of a planned total of 280 patients the BASIC3 project plans to enroll.

For 121 patients, the researchers were able to obtain sufficient tumor samples for sequence analysis. These patients received whole-exome sequencing on both their tumor and a blood sample, performed by Baylor's CAP-accredited and CLIA-certified Whole Genome Laboratory, and all patients received exome sequencing on their blood sample. Each tumor/normal pair was sequenced on a single lane of an Illumina HiSeq with a mean coverage of 272-fold.

Following the data analysis, families and doctors received a tumor report and a germline report. The tumor report included somatic mutations with established clinical utility, potential clinical utility, mutations in consensus cancer genes, and other mutations. The germline report contained pathogenic mutations, likely pathogenic mutations, and variants of unknown significance in genes related to cancer susceptibility or other patient phenotypes; incidental findings in medically actionable genes; pharmacogenetic variants; and, if parents requested, carrier status information for recessive disorders.

Tumor sequencing revealed somatic mutations of established clinical utility in 3 percent of patients, and of potential clinical utility in 24 percent. In another 20 percent of patients, the researchers found mutations in consensus cancer genes. Fewer than half of the somatic mutations were in genes known to be recurrently mutated in that patient's tumor type.

The researchers also found that 10 percent of patients harbored germline mutations relating to their phenotype. These included 13 pathogenic or likely pathogenic variants in cancer susceptibility genes, such as TP53, BRCA1, and VHL.

Overall, 5 percent of patients had incidental findings, which included the genes recommended for testing by the American College of Medical Genetics and Genomics and mutations in mitochondrial DNA. Almost all patients had uncertain germline variants in cancer genes, almost 90 percent had pharmacogenetic variants, and 85 percent of patients were carriers for a recessive disorder.

Taken together, tumor and germline whole-exome sequencing revealed potentially clinically relevant mutations or medically actionable incidental findings in 39 percent of the 121 patients who had tumor analyses done.

"In a significant number of cases, results revealed mutations in genes that we would not even have thought of testing for, because they were not known to be associated with childhood cancer," said Sharon Plon, co-senior author of the study and a professor of molecular and human genetics at Baylor, in a statement. "These results suggest that using focused genetic testing could miss important findings."

The other study, called iCat for "individualized cancer therapy" and led by senior author Katherine Janeway of the Dana-Farber Cancer Institute, set out to determine whether clinical genomic technologies can find actionable alterations and result in personalized therapy recommendations in pediatric patients with advanced solid tumors.

In total, this study analyzed 100 patients with recurrent, refractory, or high-risk solid tumors in areas other than the central nervous system. Patients had to be 30 years or younger at enrollment but three quarters were under 18. They were enrolled between September 2012 and November 2013 and submitted tumor samples from their diagnosis, recurrence, or both, or from a control surgical procedure.

Patients' tumor samples were initially tested with the Sequenom OncoMap assay, which detects 471 mutations in 41 cancer genes, but later the researchers switched to the next-generation sequencing-based OncoPanel, which runs on an Illumina HiSeq and looks at the exons of 275 cancer genes and 91 introns from 30 genes to detect rearrangements. Both tests were performed by the CLIA-certified Center for Advanced Molecular Diagnostics at Brigham and Women's Hospital. 

In addition, when sufficient tumor tissue was available, the researchers used array comparative genomic hybridization (aCGH), conducted in the CLIA-certified labs of Boston Children's Hospital and Claritas Genomics, to look for copy number variations. Some patients with sufficient tumor sample also received RNA sequencing to detect gene fusions. In total, 89 patients had at least one successful tumor profiling test.

Based on the results, 31 percent of patients received at least one iCat recommendation, which was made if an actionable alteration was present in the tumor and a matched targeted therapy that the patient had not previously received was available, either through a clinical trial or as a US Food and Drug Administration-approved drug.

Most commonly, the actionable alteration was a copy number alteration, followed by a deleterious mutation. Six iCat recommendations were based on variants of unknown significance that were likely pathogenic.

But the fact that patients received treatment recommendations did not necessarily mean they actually obtained the treatment: Only three patients were in fact put on a targeted therapy that matched their iCat recommendation, and none of them "had an objective response," the authors wrote.

A survey of the patients' oncologists revealed several reasons they did not deliver the iCat-recommended therapy: the disease was too advanced or the patient had died; the disease was not active, well-controlled with another therapy, or doctors were attempting third-line therapy first; the patients' status was not appropriate for iCat therapy for other reasons; or the recommended therapy was not available through a clinical trial.

In addition to the iCat recommendations, 12 percent of patients had other molecular profiling results with potential clinical significance, such as alterations indicating the presence of a cancer predisposition syndrome, for a total of 43 percent of patients who received actionable results.

The fact that a large proportion of patients obtained clinically significant results "may justify incorporating return of results into future genomics research projects in pediatric solid tumors," the authors wrote.

"Continuing to perform tumor profiling in the context of clinical genomics research protocols permits further investigation of barriers to receipt of matched targeted therapy and assessment of the clinical impact of a precision cancer medicine approach," they concluded.

In an editorial published along with the two articles, Javed Khan and Lee Helman of the National Cancer Institute commented that "the use of genome-based therapy in pediatric tumors remains in its infancy but is rapidly advancing" and that the two studies "show some current limitations of this approach."

The BASIC3 study, they wrote, "demonstrates the breadth of data that can be generated from whole-exome sequencing, but most of the data, as yet, cannot be translated into a therapeutic regimen recommendation." The iCat study, on the other hand, "highlights the problem of implementation of genome-based precision therapy in children with cancer, given that only three of 31 patients actually received the recommended therapy."

"Nevertheless, there is a reason for optimism," they wrote. With the cost of sequencing dropping, sequencing assays will become routine diagnostic tests, they predicted, that will help researchers better understand tumor heterogeneity and tumor mutations. "This sequencing will usher in a new era of unprecedented comprehensive analysis of the genome for all children with high-risk, refractory, or relapsed cancers — a necessary first step to the demonstration of the clinical utility and validity of genome-based precision therapy," they concluded.