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

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.

Pubmed ID: 23299976


  • Miller AC
  • Obholzer ND
  • Shah AN
  • Megason SG
  • Moens CB


Genome research

Publication Data

April 2, 2013

Associated Grants

  • Agency: NINDS NIH HHS, Id: F32NS074839
  • Agency: PHS HHS, Id: NIDCD R21DC012097
  • Agency: NIDCD NIH HHS, Id: R01 DC010791
  • Agency: NICHD NIH HHS, Id: R01 HD076585
  • Agency: NINDS NIH HHS, Id: R01 NS082567
  • Agency: NICHD NIH HHS, Id: R01HD037909
  • Agency: NHGRI NIH HHS, Id: R01HG002995
  • Agency: NINDS NIH HHS, Id: R21 NS076950

Mesh Terms

  • Animals
  • Chromosome Mapping
  • Computational Biology
  • Gene Expression Regulation
  • Genetic Linkage
  • Genetic Testing
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Internet
  • Mutation
  • Polymorphism, Single Nucleotide
  • RNA Splicing
  • Reproducibility of Results
  • Sequence Analysis, RNA
  • Zebrafish