High-Throughput Long Noncoding RNA Profiling for Diagnostic and Prognostic Markers in Cancer: Opportunities and Challenges

References

• Jia H , OsakM , BoguGK , StantonLW , JohnsonR , LipovichL . Genome-wide computational identification and manual annotation of human long noncoding RNA genes . RNA16 ( 8 ), 1478 – 1487 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Derrien T , JohnsonR , BussottiGet al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression . Genome Res.22 ( 9 ), 1775 – 1789 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Djebali S , DavisCA , MerkelAet al. Landscape of transcription in human cells . Nature489 ( 7414 ), 101 – 108 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Iyer MK , NiknafsYS , MalikRet al. The landscape of long noncoding RNAs in the human transcriptome . Nat. Genet.47 ( 3 ), 199 – 208 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Sultan M , AmstislavskiyV , RischTet al. Influence of RNA extraction methods and library selection schemes on RNA-seq data . BMC Genomics15 , 675 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Wright MW . A short guide to long non-coding RNA gene nomenclature . Hum. Genomics8 , 7 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Mattick JS , RinnJL . Discovery and annotation of long noncoding RNAs . Nat. Struct. Mol. Biol.22 ( 1 ), 5 – 7 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Xue Y , MaG , GuDet al. Genome-wide analysis of long noncoding RNA signature in human colorectal cancer . Gene556 ( 2 ), 227 – 234 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Hu Y , ChenHY , YuCYet al. A long non-coding RNA signature to improve prognosis prediction of colorectal cancer . Oncotarget5 ( 8 ), 2230 – 2242 ( 2014 ).
   PubMedGoogle Scholar
• Zhang XQ , SunS , LamKFet al. A long non-coding RNA signature in glioblastoma multiforme predicts survival . Neurobiol. Dis.58 , 123 – 131 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Prensner JR , ZhaoS , ErhoNet al. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1 . Lancet Oncol.15 ( 13 ), 1469 – 1480 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• White NM , CabanskiCR , Silva-FisherJM , DangHX , GovindanR , MaherCA . Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer . Genome Biol.15 ( 8 ), 429 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Garzon R , VoliniaS , PapaioannouDet al. Expression and prognostic impact of lncRNAs in acute myeloid leukemia . Proc. Natl Acad. Sci. USA111 ( 52 ), 18679 – 18684 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Chen H , XuJ , HongJ , TangR , ZhangX , FangJY . Long noncoding RNA profiles identify five distinct molecular subtypes of colorectal cancer with clinical relevance . Mol. Oncol.8 ( 8 ), 1393 – 1403 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Pertea M , PerteaGM , AntonescuCM , ChangTC , MendellJT , SalzbergSL . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads . Nat. Biotechnol.33 ( 3 ), 290 – 295 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Wang L , ParkHJ , DasariS , WangS , KocherJP , LiW . CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model . Nucleic Acids Res.41 ( 6 ), e74 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Sun K , ChenX , JiangP , SongX , WangH , SunH . iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data . BMC Genomics14 ( Suppl. 2 ), S7 ( 2013 ).
   PubMedGoogle Scholar
• Kong L , ZhangY , YeZQet al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine . Nucleic Acids Res.35 , W345 – W349 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Sun K , ZhaoY , WangH , SunH . Sebnif: an integrated bioinformatics pipeline for the identification of novel large intergenic noncoding RNAs (lincRNAs) – application in human skeletal muscle cells . PLoS ONE9 ( 1 ), e84500 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Gong C , MaquatLE . lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements . Nature470 ( 7333 ), 284 – 288 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Lu Q , RenS , LuMet al. Computational prediction of associations between long non-coding RNAs and proteins . BMC Genomics14 , 651 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Bellucci M , AgostiniF , MasinM , TartagliaGG . Predicting protein associations with long noncoding RNAs . Nat. Methods8 ( 6 ), 444 – 445 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Li JH , LiuS , ZhengLLet al. Discovery of protein-lncRNA interactions by integrating large-scale CLIP-Seq and RNA-Seq datasets . Front. Bioeng. Biotechnol.2 , 88 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Simon R . Analysis of DNA microarray expression data . Best Pract. Res. Clin. Haematol.22 ( 2 ), 271 – 282 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Cheng J , GreshockJ , ShiL , ZhengS , MeniusA , LeeK . Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis . BMC Syst. Biol.7 ( Suppl. 4 ), S2 ( 2013 ).
   PubMedGoogle Scholar
• Sun Z , YangP . Gene expression profiling on lung cancer outcome prediction: present clinical value and future premise . Cancer Epidemiol. Biomarkers Prev.15 ( 11 ), 2063 – 2068 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Yang P , SunZ . Gene-expression profiling in lung cancer: still early days . Pharmacogenomics8 ( 2 ), 129 – 132 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Goncalves R , BoseR . Using multigene tests to select treatment for early-stage breast cancer . J. Natl Compr. Canc. Netw.11 ( 2 ), 174 – 182 ( 2013 ).
   PubMed Web of Science ®Google Scholar