OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies

Matthew C Hiemenz; Dejerianne G Ostrow; Tracy M Busse; Jonathan Buckley; Dennis T Maglinte; Moiz Bootwalla; James Done; Jianling Ji; Gordana Raca; Alex Ryutov; Xinjie Xu; Chao Jie Zhen; Jeffrey M Conroy; Florette K Hazard; Joshua L Deignan; Beverly B Rogers; Amanda L Treece; David M Parham; Xiaowu Gai; Alexander R Judkins; Timothy J Triche; Jaclyn A Biegel

doi:10.1016/j.jmoldx.2018.06.009

OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies

J Mol Diagn. 2018 Nov;20(6):765-776. doi: 10.1016/j.jmoldx.2018.06.009. Epub 2018 Aug 20.

Authors

Matthew C Hiemenz¹, Dejerianne G Ostrow², Tracy M Busse², Jonathan Buckley³, Dennis T Maglinte², Moiz Bootwalla², James Done², Jianling Ji³, Gordana Raca³, Alex Ryutov², Xinjie Xu⁴, Chao Jie Zhen⁵, Jeffrey M Conroy⁶, Florette K Hazard⁷, Joshua L Deignan⁸, Beverly B Rogers⁹, Amanda L Treece¹⁰, David M Parham³, Xiaowu Gai³, Alexander R Judkins³, Timothy J Triche³, Jaclyn A Biegel³

Affiliations

¹ Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California. Electronic address: [email protected].
² Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
³ Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California.
⁴ Cytogenetics and Genomic Microarray, ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.
⁵ Department of Pathology, University of Chicago, Chicago, Illinois.
⁶ OmniSeq Inc., Buffalo, New York; Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York.
⁷ Department of Pathology, Stanford University School of Medicine, Stanford, California.
⁸ Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.
⁹ Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia.
¹⁰ Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Denver, Colorado.

PMID: 30138724
DOI: 10.1016/j.jmoldx.2018.06.009

Abstract

The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Child
Gene Amplification
High-Throughput Nucleotide Sequencing / methods*
Humans
INDEL Mutation / genetics
Limit of Detection
Neoplasms / genetics*
Oncogene Fusion
Polymorphism, Single Nucleotide / genetics
Reproducibility of Results
Sensitivity and Specificity