Clinical utility of custom-designed NGS panel testing in pediatric tumors.

TitleClinical utility of custom-designed NGS panel testing in pediatric tumors.
Publication TypeJournal Article
Year of Publication2019
AuthorsSurrey LF, MacFarland SP, Chang F, Cao K, Rathi KS, Akgumus GT, Gallo D, Lin F, Gleason A, Raman P, Aplenc R, Bagatell R, Minturn J, Mosse Y, Santi M, Tasian SK, Waanders AJ, Sarmady M, Maris JM, Hunger SP, Li MM
JournalGenome Med
Volume11
Issue1
Pagination32
Date Published2019 May 28
ISSN1756-994X
Abstract

BACKGROUND: Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved towards broad-based next-generation sequencing (NGS) panels. Here, we report the laboratory validation and clinical utility of a large cohort of clinical NGS somatic sequencing results in diagnosis, prognosis, and treatment of a wide range of pediatric cancers.

METHODS: Subjects were accrued retrospectively at a single pediatric quaternary-care hospital. Sequence analyses were performed on 367 pediatric cancer samples using custom-designed NGS panels over a 15-month period. Cases were profiled for mutations, copy number variations, and fusions identified through sequencing, and their clinical impact on diagnosis, prognosis, and therapy was assessed.

RESULTS: NGS panel testing was incorporated meaningfully into clinical care in 88.7% of leukemia/lymphomas, 90.6% of central nervous system (CNS) tumors, and 62.6% of non-CNS solid tumors included in this cohort. A change in diagnosis as a result of testing occurred in 3.3% of cases. Additionally, 19.4% of all patients had variants requiring further evaluation for potential germline alteration.

CONCLUSIONS: Use of somatic NGS panel testing resulted in a significant impact on clinical care, including diagnosis, prognosis, and treatment planning in 78.7% of pediatric patients tested in our institution. Somatic NGS tumor testing should be implemented as part of the routine diagnostic workup of newly diagnosed and relapsed pediatric cancer patients.

DOI10.1186/s13073-019-0644-8
Alternate JournalGenome Med
PubMed ID31133068