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Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Author information

1
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
2
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
3
Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
4
Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
5
Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA.
6
Undergraduate Program in Genome Sciences, National Autonomous University of Mexico, Mexico City, Mexico.
7
Department of Mathematics and Computer Science, Centre College, Danville, KY, USA.
8
Department of Biological Sciences, Salisbury University, Salisbury, MD, USA.
9
Department of Biological Sciences, University of Texas at Austin, Austin, TX, USA.
10
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
11
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu.
12
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. langmea@cs.jhu.edu.
13
Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu.
14
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. jtleek@gmail.com.
15
Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. jtleek@gmail.com.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Intron; RNA-seq; Splicing

Comment in

PMID:
28038678
PMCID:
PMC5203714
DOI:
10.1186/s13059-016-1118-6
[Indexed for MEDLINE]
Free PMC Article

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