Comprehensive RNA-seq Transcriptomic Profiling in the Malignant Progression of Gliomas

Overview

Journal Sci Data

Specialty Science

Date 2017 Mar 15

PMID 28291232

Citations 173

Authors

Zheng Zhao

Fanlin Meng

Wen Wang

Zheng Wang

Chuanbao Zhang

Tao Jiang

Affiliations

Soon will be listed here.

Abstract

Gliomas are the most common and lethal intracranial tumours. RNA sequencing technologies and advanced data analyses recently enabled the characterization of transcriptomic information, including protein-coding gene expression, non-coding gene expression, alternative splicing, and fusion gene detection, to facilitate detection of diseases and altered phenotypes. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to delineate comprehensive transcriptome profiling in the malignant progression of human gliomas. Three hundred twenty five gliomas with different grades were collected over the past twelve years. Using the Illumina HiSeq 2,000 system, over 92 million high quality 101-bp paired-end reads were generated per sample, yielding a total of 30 billion reads. This comprehensive dataset will be useful to deepen the comprehensive understanding of gliomas, providing an opportunity to generate new therapies, diagnoses, and preventive strategies.

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References

Stupp R, Hegi M, Mason W, van den Bent M, Taphoorn M, Janzer R . Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 2009; 10(5):459-66. DOI: 10.1016/S1470-2045(09)70025-7. View

Chen H, Yu K, Tang X, Bao Z, Jiang T, Fan X . Enhanced expression and phosphorylation of the MET oncoprotein by glioma-specific PTPRZ1-MET fusions. FEBS Lett. 2015; 589(13):1437-43. DOI: 10.1016/j.febslet.2015.04.032. View

Jiang T, Mao Y, Ma W, Mao Q, You Y, Yang X . CGCG clinical practice guidelines for the management of adult diffuse gliomas. Cancer Lett. 2016; 375(2):263-273. DOI: 10.1016/j.canlet.2016.01.024. View

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

Li B, Dewey C . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. PMC: 3163565. DOI: 10.1186/1471-2105-12-323. View

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):R36. PMC: 4053844. DOI: 10.1186/gb-2013-14-4-r36. View

Ostrom Q, Gittleman H, Fulop J, Liu M, Blanda R, Kromer C . CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2008-2012. Neuro Oncol. 2015; 17 Suppl 4:iv1-iv62. PMC: 4623240. DOI: 10.1093/neuonc/nov189. View

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

10.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

. Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nat Med. 2016; 22(11):1314-1320. DOI: 10.1038/nm.4204. View

13.

Louis D, Ohgaki H, Wiestler O, Cavenee W, Burger P, Jouvet A . The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007; 114(2):97-109. PMC: 1929165. DOI: 10.1007/s00401-007-0243-4. View

14.

Robinson M, Oshlack A . A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010; 11(3):R25. PMC: 2864565. DOI: 10.1186/gb-2010-11-3-r25. View

15.

Harrow J, Frankish A, Gonzalez J, Tapanari E, Diekhans M, Kokocinski F . GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22(9):1760-74. PMC: 3431492. DOI: 10.1101/gr.135350.111. View

16.

Wang K, Singh D, Zeng Z, Coleman S, Huang Y, Savich G . MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010; 38(18):e178. PMC: 2952873. DOI: 10.1093/nar/gkq622. View

17.

Kim D, Langmead B, Salzberg S . HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4):357-60. PMC: 4655817. DOI: 10.1038/nmeth.3317. View

18.

Bao Z, Chen H, Yang M, Zhang C, Yu K, Ye W . RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas. Genome Res. 2014; 24(11):1765-73. PMC: 4216918. DOI: 10.1101/gr.165126.113. View

19.

Cheng W, Ren X, Zhang C, Cai J, Liu Y, Han S . Bioinformatic profiling identifies an immune-related risk signature for glioblastoma. Neurology. 2016; 86(24):2226-34. DOI: 10.1212/WNL.0000000000002770. View

20.

Van Meir E, Hadjipanayis C, Norden A, Shu H, Wen P, Olson J . Exciting new advances in neuro-oncology: the avenue to a cure for malignant glioma. CA Cancer J Clin. 2010; 60(3):166-93. PMC: 2888474. DOI: 10.3322/caac.20069. View