Abstract B45: Development of a next-generation sequencing (NGS) assay for pediatric, childhood, and young adult cancer research with comprehensive DNA and RNA variant detection
Authors: Nickolay A. Khazanov, Chaitali Parikh, Habib Hamidi, Scott P. Myrand, Efren Ballesteros-Villagrana, Jingwei Ni, Paul D. Williams, Karen L. Clyde, Dinesh Cyanam, Armand Bankhead, Manimozhi Manivannan, Mark Tomilo, Susan Ewald, Jon K. Sherlock, Janice K. Au-Young, Jaclyn Biegel, Jonathan Buckley, Matthew Hiemenz, Dejerianne Ostrow, Alex Judkins, Xiaowu Gai, Tracy Busse, Alan Wayne, Deepa Bhojwani, Raca Gordana, Matthew Oberley, David Parham, Seth Sadis, Timothy Triche
Journal: Cancer Research (2018)

Abstract Introduction: Recurrent somatic alterations associated with pediatric, childhood, and young adult cancers have not been as intensively studied as those associated with adult cancers. Consequently, whole-exome and transcriptome approaches are still being used to support discovery efforts. However, due to several initiatives aimed at profiling genomic alterations associated with childhood cancers, a set of recurrent somatic alterations has been defined. To accelerate research in this area, we have developed a novel targeted next-generation sequencing (NGS) assay to detect relevant somatic alterations previously reported in these cancer types. Methods: The assay was developed using Ion AmpliSeq targeted sequencing technology to cover the major gene variants associated with childhood cancers, including both solid tumor and hematologic cancer types. Over 200 gene targets were included on the basis of consultation with expert pediatric oncologists, literature review of the recent pediatric cancer genomic publications, as well as inclusion of relevant markers from adult cancers that are also observed in childhood cancers. Variant classes include mutations, copy number variations, gene fusions, and gene expression. Mutations in 130 genes, copy number variants in 28 genes, and over 1,400 distinct fusion isoforms in 88 fusion driver genes are analyzed. Variant calling algorithms for both DNA and RNA were optimized and combined into a single Ion Reporter workflow. Results: The assay generated an average read depth of &amp;gt;3,000 reads per DNA amplicon with high uniformity (&amp;gt;95%), when up to 7 sample DNA-RNA pairs were analyzed with the 540 chip of the Ion S5 sequencing instrument. Minimal allele frequency detected for key hotspots was 5%. Sensitive and reproducible detection of CNV and fusion variants associated with pediatric solid tumors (EWSR1-FL1 and KIAA1549-BRAF fusions, MYC and EGFR amplification) and hematologic cancers (ETV6-RUNX1 and PML-RARA fusions) was demonstrated in orthogonally profiled FFPE, blood, and bone marrow samples. Performance was robust across sample types. Similar results were observed with manual and automated library preparation. Conclusions: A novel NGS assay, designed specifically for pediatric, childhood, and young adult cancers, and capable of detecting relevant DNA and RNA alterations from the same sample, was developed and validated. The assay is useful for characterizing relevant alterations in a wide range of cancers, including childhood leukemias and lymphomas as well as solid tumors including neuroblastoma, rhabdomyosarcoma, retinoblastoma, osteosarcoma, Ewing sarcoma, Wilms tumor, and brain and spinal cord tumors. A review of the analytical studies will be presented. Citation Format: Nickolay A. Khazanov, Chaitali Parikh, Habib Hamidi, Scott P. Myrand, Efren Ballesteros-Villagrana, Jingwei Ni, Paul D. Williams, Karen L. Clyde, Dinesh Cyanam, Armand Bankhead, III, Manimozhi Manivannan, Mark Tomilo, Susan Ewald, Jon K. Sherlock, Janice K. Au-Young, Jaclyn Biegel, Jonathan Buckley, Matthew Hiemenz, Dejerianne Ostrow, Alex Judkins, Xiaowu Gai, Tracy Busse, Alan Wayne, Deepa Bhojwani, Raca Gordana, Matthew Oberley, David Parham, Seth Sadis, Timothy Triche. Development of a next-generation sequencing (NGS) assay for pediatric, childhood, and young adult cancer research with comprehensive DNA and RNA variant detection [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B45.