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GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden .
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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 21134Article in journal (Refereed) PublishedText
Abstract [en]

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.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016. Vol. 6, 21134
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Engineering and Technology
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URN: urn:nbn:se:kth:diva-183310DOI: 10.1038/srep21134ISI: 000370363200001ScopusID: 2-s2.0-84958999591OAI: oai:DiVA.org:kth-183310DiVA: diva2:910592
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Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20160309

Available from: 2016-03-09 Created: 2016-03-07 Last updated: 2016-03-19Bibliographically approved

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Edsgärd, DanielIglesias, Maria JesusOdeberg, JacobEmanuelsson, Olof
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