title: Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations.
abstract: Molecular 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.
  
  
  
  The 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.
  
  
  
  NGS 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.
  
  
  
  Our 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.
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Jennifer A
authors.identifier: 0000-0002-9135-3391
authors.initials: JA
authors.lastname: Oberg
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Julia L
authors.initials: JL
authors.lastname: Glade Bender
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Sulis
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Pendrick
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Anthony N
authors.initials: AN
authors.lastname: Sireci
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Hsiao
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Turk
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.|Present address: Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Filemon S
authors.initials: FS
authors.lastname: Dela Cruz
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Hanina
authors.initials: H
authors.lastname: Hibshoosh
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Helen
authors.initials: H
authors.lastname: Remotti
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Zylber
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Jiuhong
authors.initials: J
authors.lastname: Pang
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Present address: Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Diolaiti
authors.affiliation: Department of Clinical Genetics, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Carrie
authors.initials: C
authors.lastname: Koval
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Andrews
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Garvin
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Darrell J
authors.initials: DJ
authors.lastname: Yamashiro
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.|Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Wendy K
authors.initials: WK
authors.lastname: Chung
authors.affiliation: Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA.|Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Emerson
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.|Present address: MNG Laboratories, 5424 Glenridge Drive, Atlanta, GA, 30342, USA.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Nagy
authors.affiliation: Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Mahesh M
authors.initials: MM
authors.lastname: Mansukhani
authors.affiliation: Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA. kunga@mskcc.org.|Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA. kunga@mskcc.org.|Present address: Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. kunga@mskcc.org.
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Kung
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D005260:Female; D006402:Hematologic Diseases / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D015514:Oncogene Proteins, Fusion / Q000235:genetics* / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics* / Q000378:metabolism
chemical_list: D015514:Oncogene Proteins, Fusion; D012334:RNA, Neoplasm
keywords: Pediatric oncology; Precision medicine; RNA sequencing; Whole exome sequencing