Oncotarget

Research Papers:

Clinical evaluation of integrated panel testing by next-generation sequencing for somatic mutations in neuroblastomas with MYCN unamplification

Yanna Cao, Yan Jin, Jinpu Yu, Jingfu Wang, Yanli Qiu, Xiaofeng Duan, Yingnan Ye, Yanan Cheng, Li Dong, Xiaolong Feng, Daowei Wang, Zhongyuan Li, Xiangdong Tian, Huijuan Wang, Jie Yan and Qiang Zhao _

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Oncotarget. 2017; 8:49689-49701. https://doi.org/10.18632/oncotarget.17917

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Abstract

Yanna Cao1,*, Yan Jin1,*, Jinpu Yu2, Jingfu Wang1, Yanli Qiu1, Xiaofeng Duan1, Yingnan Ye2, Yanan Cheng2, Li Dong2, Xiaolong Feng3, Daowei Wang1, Zhongyuan Li1, Xiangdong Tian1, Huijuan Wang1, Jie Yan1 and Qiang Zhao1

1Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin, 300060, P.R. China

2Department of Cancer Molecular Diagnostic Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin, 300060, P.R. China

3Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, P.R. China

*These authors contributed equally to this work

Correspondence to:

Qiang Zhao, email: qiangzhao169@sina.com

Jie Yan, email: yanjie631016@126.com

Keywords: neuroblastoma, DNA copy number variations, high-throughput nucleotide sequencing, prognosis, treatment

Received: January 24, 2017     Accepted: May 01, 2017     Published: May 17, 2017

ABSTRACT

Neuroblastomas (NBs) exhibit heterogeneity and show clinically significant prognosis classified by genetic alterations. Among prognostic genes or genome factors, MYCN amplification (MNA) is the most established genomic marker of poor prognosis in patients with NB. However, the prognostic classification of more than 60% of patients without MNA has yet to be clarified. In this study, the application of target next-generation sequencing (NGS) was extended on the basis of a comprehensive panel of regions where copy number variations (CNVs) or point mutations occurred to improve the prognostic evaluation of these patients and obtain the sequence of 33 patients without MNA. A mean coverage depth of 887× was determined in the target regions in all of the samples, and the mapped read percentage was more than 99%. Somatic mutations in patients without MNA could be precisely defined on the basis of these findings, and 17 unique somatic aberrations, including 14 genes, were identified in 11 patients. Among these variations, most were CNVs with a number of 13. The 3-year event-free survival (EFS) of CNV(−) patients was 60.0% compared with the EFS (16.7%) of CNV(+) patients (P = 0.015, HR = 0.1344, 95%, CI = 0.027 to 0.678). CNVs were also associated with unfavorable histological characteristics (P = 0.003) and likely to occur in stage 4 (P = 0.041). These results might further indicate the role of CNVs in NB chemotherapy resistance (P = 0.059) and show CNVs as a therapeutic target. In multivariate analysis, the presence of CNVs was a clinically negative prognostic marker that impaired the outcome of patients without MNA and associated with poor prognosis in this tumor subset. Comprehensive genetic/genomic profiling instead of focusing on single genetic marker should be performed through in-depth NGS that could reveal prognostic information, improve NB target therapy, and provide a basis for investigations on NB pathogenesis.


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