Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

Abstract

BackgroundMolecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated.MethodsThe Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient’s electronic medical record.ResultsNGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients.ConclusionsOur results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-016-0389-6) contains supplementary material, which is available to authorized users.

Investigation of clinically relevant germline variants detected by next-generation sequencing in patients with childhood cancer: a review of the literature

“…Mody et al 15 detected pathogenic or likely pathogenic germline variants in 9/91 (9.9%) patients with childhood cancer (table 1, online supplementary table S2). Oberg et al 16 detected pathogenic or likely pathogenic germline variants in 18/90 (20.0%) patients (table 1, online supplementary table S2). However, germline variants reported in 4/18 patients occurred in non-cancer-associated genes including RYR1 , TNNT2 and UGT1A1, associated with malignant hyperthermia, dilated cardiomyopathy and drug response, respectively 16.…”

“…Oberg et al 16 detected pathogenic or likely pathogenic germline variants in 18/90 (20.0%) patients (table 1, online supplementary table S2). However, germline variants reported in 4/18 patients occurred in non-cancer-associated genes including RYR1 , TNNT2 and UGT1A1, associated with malignant hyperthermia, dilated cardiomyopathy and drug response, respectively 16. Chang et al 17 detected pathogenic or likely pathogenic germline variants in 7/59 (11.8%) patients with non-CNS solid tumours (table 1, online supplementary table S2).…”

“…Parsons et al 14 and Chang et al 17 used the Roche SeqCap exome capture system. Oberg et al 16 used the Agilent SureSelect exome capture system. All studies performed sequencing on an Illumina HiSeq instrument 13–18.…”

“…Parsons et al 14 reported pathogenic or likely pathogenic germline variants that were relevant to any medical phenotype that the patient exhibited. Oberg et al 16 described all medically relevant pathogenic or likely pathogenic germline variants, regardless of patient phenotype. To interpret variant pathogenicity, the studies used the published literature and public databases and/or molecular review panels and/or the ACMG guidelines 20.…”

Application of Next-Generation Sequencing in the Era of Precision Medicine

“…RT-qPCR and microarrays) [91]. RNA-seq can measure expression of tumour antigens or immune checkpoint receptors and ligands after a given treatment, giving some answers about patient drug response [91,99,100]. Gene expression signatures can also be used for cancer types' classiication that directly impact prognosis and treatment deinition and response [100].…”