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Genome Res. 2013 Apr;23(4):679-86. doi: 10.1101/gr.147322.112. Epub 2013 Jan 8.

RNA-seq-based mapping and candidate identification of mutations from forward genetic screens.

Author information

1
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. amiller@fhcrc.org

Abstract

Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life; however, identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates. We have developed an RNA-seq-based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, we develop an easily accessible bioinformatics pipeline allowing for implementation of all steps of the method. Overall, we show that RNA-seq is a fast, reliable, and cost-effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.

PMID:
23299976
PMCID:
PMC3613584
DOI:
10.1101/gr.147322.112
[Indexed for MEDLINE]
Free PMC Article
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