title: Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
abstract: Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0.
  
  
  
  We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data.
  
  
  
  Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.
authors.affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.|Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Nellore
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.|Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.|Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Jaffe
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Fortin
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Undergraduate Program in Genome Sciences, National Autonomous University of Mexico, Mexico City, Mexico.
authors.forename: José
authors.initials: J
authors.lastname: Alquicira-Hernández
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.|Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Collado-Torres
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Department of Mathematics and Computer Science, Centre College, Danville, KY, USA.
authors.forename: Siruo
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Department of Biological Sciences, Salisbury University, Salisbury, MD, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Phillips
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Department of Biological Sciences, University of Texas at Austin, Austin, TX, USA.
authors.forename: Nishika
authors.initials: N
authors.lastname: Karbhari
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.|McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Kasper D
authors.initials: KD
authors.lastname: Hansen
authors.affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu.|Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. langmea@cs.jhu.edu.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu.
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. jtleek@gmail.com.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. jtleek@gmail.com.
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Leek
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods; D005091:Exons; D005786:Gene Expression Regulation; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D022821:RNA Splice Sites; D012326:RNA Splicing / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA
chemical_list: D022821:RNA Splice Sites
keywords: Intron; RNA-seq; Splicing