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| Status |
Public on May 22, 2015 |
| Title |
RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We generated gene expression profiles from 498 primary neuroblastomas using RNA-Seq and microarrays. We sought to systematically evaluate the capability of RNA deep-sequencing (RNA-Seq)-based classification for clinical endpoint prediction in comparison to microarray-based ones. The neuroblastoma cohort was randomly divided into training and validation sets, and 360 predictive models on six clinical endpoints were generated and evaluated. While prediction performances did not differ considerably between the two technical platforms, the RNA-Seq data processing pipelines, or feature levels (i.e., gene, transcript, and exon junction levels), RNA-Seq models based on the AceView database performed best on most endpoints. Collectively, our study reveals an unprecedented complexity of the neuroblastoma transcriptome, and provides guidelines for the development of gene expression-based predictive classifiers using high-throughput technologies.
Sample clinical characteristics definitions:
dataset: Expression data set used for classification training (1) or validation (2)
Sex: M = male; F= female
age at diagnosis: the age in days at diagnosis
mycn status: Amplification status of the MYCN proto-oncogene (amplified = 1, no amplification = 0; no information = N/A)
high risk: Clinically considered as high-risk neuroblastoma (yes=1, no= 0)
INSS stage: disease stage according to International Neuroblastoma Staging System (INSS) (1, 2, 3, 4 and 4S)
class label: Maximally divergent disease courses - unfavorable (= 1): patient died despite intensive chemotherapy, favorable (=0): patient survived without chemotharapy for at least 1000 days post diagnosis; not applicable (N/A)
progression: Occurrence of a tumor progression event (yes=1; no=0)
death from disease: Occurrence of death from the disease (yes=1; no=0)
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| Overall design |
Gene expression of 498 neuroblastoma samples was quantified by RNA sequencing as well as by microarray analyses in order to understand the neuroblastoma transcriptome and predict clinical endpoints.
Due to patient privacy issues the raw data was not submitted. The clinical study was done in Germany, and since there are no NIH PI and no US accreditation, the raw data could not be submitted to dbGaP.
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| Contributor(s) |
Zhang W, Shi L, Thierry-Mieg D, Thierry-Mieg J, Albanese D, Furlanello C, Peng Z, Fischer M |
| Citation(s) |
25150839, 25150838, 25254650 |
| Submission date |
Aug 09, 2013 |
| Last update date |
Feb 08, 2017 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
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| Phone |
+86-18616827008
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| Organization name |
Fudan University
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| Department |
School of Life Sciences
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| Lab |
Center for Pharmacogenomics
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| Street address |
2005 Songhu Road
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| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platforms (1) |
| GPL17553 |
Illumina Hiseq 2000 (Homo sapiens) |
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| Samples (498)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| Reanalyzed by |
GSE62564 |
| BioProject |
PRJNA214797 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49711_SEQC_NB_MAV_G_log2.20121127.txt.gz |
39.6 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_J_log2.20121127.txt.gz |
191.7 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_README_20121202.txt |
4.6 Kb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_README_20121211.txt |
7.0 Kb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_README_20130212.txt |
7.5 Kb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_T_log2.20121127.txt.gz |
175.4 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_MAV_Th_log2.20121210.txt.gz |
133.7 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TAV_G_log2.final.txt.gz |
57.9 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TAV_J_log2.20121201.txt.gz |
163.2 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TAV_ReadMe.final.txt |
3.1 Kb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TAV_T_log2.final.txt.gz |
228.5 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TUC_G_log2.txt.gz |
77.6 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TUC_J_log2.txt.gz |
284.6 Mb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TUC_README.txt |
1.4 Kb |
(ftp)(http) |
TXT |
| GSE49711_SEQC_NB_TUC_T_log2.txt.gz |
133.9 Mb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data are available on Series record |
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