title: Opportunities and methods for studying alternative splicing in cancer with RNA-Seq.
abstract: The biogenesis, development and metastases of cancer are associated with many variations in the transcriptome. Alternative splicing of genes is a major post-transcriptional regulation mechanism that is involved in many types of cancer. The next-generation sequencing applied on RNAs (RNA-Seq) provides a new technology for studying transcriptomes. It provides an unprecedented opportunity for quantitatively studying alternative splicing in a systematic way. This mini-review summarizes the current RNA-Seq studies on cancer transcriptomes especially studies on cancer-related alternative splicing, and discusses the strategy for quantitative study of alternative splicing in cancers with RNA-Seq, the bioinformatics methods available and existing questions.
authors.affiliation: Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and MOE Key Laboratory for Bioinformatics, Department of Automation, Tsinghua University, Beijing 100084, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Feng
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Qin
authors.forename: Xuegong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000628:therapy; D010641:Phenotype; D057285:Precision Medicine; D011237:Predictive Value of Tests; D011379:Prognosis; D012334:RNA, Neoplasm / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D014408:Biomarkers, Tumor; D012334:RNA, Neoplasm