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Series GSE49711 Query DataSets for GSE49711
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
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)
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.
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
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
Platforms (1)
GPL17553 Illumina Hiseq 2000 (Homo sapiens)
Samples (498)
GSM1205736 SEQC_NB001
GSM1205737 SEQC_NB002
GSM1205738 SEQC_NB003
This SubSeries is part of SuperSeries:
GSE47792 SEQC Project
Reanalyzed by GSE62564
BioProject PRJNA214797

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 57.9 Mb (ftp)(http) TXT
GSE49711_SEQC_NB_TAV_J_log2.20121201.txt.gz 163.2 Mb (ftp)(http) TXT 3.1 Kb (ftp)(http) TXT 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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