Allele Auditing

Allele Auditing

  • Availability of long read DNA sequencing has revealed that many models made through modern CRISPR methods or traditional transgenic methods unexpectedly result in alleles that differ greatly from what users believe. These unappreciated differences can greatly impact results.
  • Typical molecular characterization methods for genome-edited models almost always rely on PCR amplification. PCR obscures complex duplications and other large-scale, unexpected DNA repair events. See FAQ for more information.
  • Heightened expectations of Rigor & Reproducibility require a solution to resolve these issues.
  • Confirmation of your allele can be provided using long read, whole-genome DNA sequencing followed by careful inspection of your locus .

Service pipeline

  • Models generated in any manner can be confirmed using this service, though CRISPR-generated models are most commonly examined.
  • Models should be homozygous for maximal likelihood of project success.
  • Rodent models are most easily processed by using whole blood. We can facilitate this by sending your model to the UWBC Animal Models Core ( to obtain the sample.
  • Cell line models can be processed by providing a cell pellet. For cell lines AGEL has created, this can easily be done in the course of generating your cell line.
  • You will be provided the aligned PacBio reads (BAM) and a summary of the analysis.

Submit your project details when you are ready to commit resources to the project. If you’d like to discuss your project beforehand, please reach out to

For more information, please check the UWCCC website


Allele Auditing is currently priced at $2500 per sample. This includes obtaining the sample, high molecular weight DNA extraction, barcoding, library prep, whole genome sequencing, quality filtering, alignment, and manual inspection of your locus.

Discounts are available for UW Carbone Cancer Center members