Send to

Choose Destination
Sci Rep. 2016 Feb 18;6:21134. doi: 10.1038/srep21134.

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

Author information

KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden.
Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Center for Molecular Medicine, and Department of Cardiology, Karolinska University Hospital, Stockholm, Sweden.
KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Proteomics, SE-171 65, Solna, Sweden.
Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
Department of Medicine, Centre for Hematology, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden.


Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center