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A polyclonal allelic expression assay for detecting regulatory effects of transcript variants

Margot Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen
doi: https://doi.org/10.1101/794081
Margot Brandt
1New York Genome Center, New York, NY
2Department of Systems Biology, Columbia University, New York, NY
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Alper Gokden
1New York Genome Center, New York, NY
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Marcello Ziosi
1New York Genome Center, New York, NY
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Tuuli Lappalainen
1New York Genome Center, New York, NY
2Department of Systems Biology, Columbia University, New York, NY
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  • For correspondence: tlappalainen@nygenome.org
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Abstract

We present an assay to experimentally test regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 35 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of eQTLs and 65 control variants. We detected significant effects generally in the expected direction, demonstrating the ability of the assay to capture regulatory effects of eQTL variants and nonsense-mediated decay triggered by premature stop-gained variants. The results suggest a utility for validating transcript-level effects of genetic variants.

Footnotes

  • https://doi.org/10.6084/m9.figshare.9883232.v1

  • https://doi.org/10.17504/protocols.io.7c6hize

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 07, 2019.
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A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Margot Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen
bioRxiv 794081; doi: https://doi.org/10.1101/794081
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A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Margot Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen
bioRxiv 794081; doi: https://doi.org/10.1101/794081

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