Abstract 2628: Molecular diagnosis for pediatric cancer through integrative analysis of whole-genome, whole-exome and transcriptome sequencing
Authors: Zhang Jinghui , Rusch Michael , Nakitandwe Joy , Zhang Zhaojie , Edmonson Michael N. , Parker Matthew , Ma Xiaotu , Becksfort Jared , Thrasher Andrew , Gu Jiali , Li Yongjin , Hedlund Erin , Patel Aman , Easton John , Yergeau Donald , Vadodaria Bhavin , Chen Xiang , Gruber Tanja A. , McGee Rose , Ellison David , Shurtleff Sheila , Downing James R. 
Published: July 2016

Abstract
Next-generation sequencing (NGS) of the whole genome, whole exome, and transcriptome has enabled characterization of genetic landscapes of multiple cancers. By analyzing over 2,000 pediatric cancer patients, we have developed a comprehensive database for recurrent somatic alterations and pathogenic germline mutations as part of the St. Jude/Washington University Pediatric Cancer Genome Project. However, there is no systematic evaluation on whether NGS is able to identify germline and somatic lesions reported by existing molecular diagnostic assays and what combination of NGS platforms is best suited for clinical sequencing. Here we report the first comprehensive study that employs whole-genome sequencing at 30-45X coverage, whole-exome sequencing at 100X coverage and transcriptome sequencing using matched tumor/normal samples from cancer patients. A pilot study was carried out to perform NGS analysis on 78 children of leukemia, solid tumor or brain tumor with a total of 112 diagnostic or prognostic biomarkers previously characterized by multiple molecular diagnostic assays. We implemented an analysis pipeline that integrates the genetic lesions detected by all three NGS platforms to characterize somatic and germline single nucleotide variations (SNVs), short insertions and deletions (indels), structural variations including fusions, karyotypes, copy number alterations, loss of heterozygosity, tumor purity and tumor-in-normal contamination. The turn-around time for data analysis is 2 weeks with an overall sensitivity of 99% on detecting known biomarkers. Extensive validation of &gt;3,000 somatic sequence mutations or structural variations from 38 cases shows that the specificity for somatic SNV, indel and structural variation is at 98%, 95% and 84% across the genome. We demonstrate that in addition to providing cross-validation, multi-platform NGS is required for detecting all genetic lesions of pathological significance including complex re-arrangements such as chromothripsis. In addition to known pathogenic or likely pathogenic mutations, our analysis has also unveiled novel pathogenic mutations (e.g. a germline deletion in TP53 in one patient with medulloblastoma) and identified multiple variants of unknown significance that may be worth further exploration (e.g. an in-frame deletion of exons 3-9 of DNMT3A in one neuroblastoma). Our study demonstrates that NGS is able to detect a wide range of genetic lesions currently characterized by multiple molecular diagnostic assays, providing critical insight into the design of clinical sequencing for ongoing studies.
Citation Format: Jinghui Zhang, Michael Rusch, Joy Nakitandwe, Zhaojie Zhang, Michael N. Edmonson, Matthew Parker, Xiaotu Ma, Jared Becksfort, Andrew Thrasher, Jiali Gu, Yongjin Li, Erin Hedlund, Aman Patel, John Easton, Donald Yergeau, Bhavin Vadodaria, Xiang Chen, Tanja A. Gruber, Rose McGee, David Ellison, Sheila Shurtleff, James R. Downing. Molecular diagnosis for pediatric cancer through integrative analysis of whole-genome, whole-exome and transcriptome sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2628.