Marker Assisted Speed Congenics

Over the last 2-3 decades, genetically engineered mutant (transgenic, knockout or knock-in) mice have become extremely popular in biomedical research. As of now there are over several thousand mutant mice that have been generated across the world. A big problem with these mutants is that not all of them are generated on one genetic background, but they are generated on different genetic backgrounds called "strains". It is now well documented that some specific strains of mice are more suitable for certain types of studies than others. When genetically engineered mice generated are in a mixed strain or in a strain with an unsuitable background than their intended purpose, the investigators transfer the mutation into a strain of choice by utilizing a breeding strategy called backcrossing.

Backcrossing in the traditional sense involves breeding the mutant mouse to the recipient mouse strain of choice for 10 or more generations, thus obtaining a so called “congenic” for the recipient strain. This painstaking process takes about 2.5 to 3 years of time; a fact that often limits its feasibility and usefulness given the pace of scientific research. In recent years, however, a technique called “Marker Assisted Speed Congenics” (MASC) has been developed that achieves making a congenic strain in 5 generations unlike the traditional backcrossing scenario which required 10 generations. The research team at the University of Nebraska Medical Center Mouse Genome Engineering Core Facility (MGECF) has designed, tested and validated a panel of over 100 molecular probes that cover all the chromosomes. These probes, due to their polymorphisms between various strains of mice, have been tested for their suitability to perform MASC assays on a genome-wide scale and offers the advantage over other technologies available due to their flexibility of use. 

Service details

The Investigator’s lab:

  • Provides the tail pieces (or DNA) from the mice of known genotype (at least 10 samples* for each generation plus 2 controls- donor and recipient strain samples)
  • Provides details about the mouse line, mutation, name of recipient and donor strains, generation number etc.

*In order to increase the chances of obtaining an offspring with highest recipient genome contribution, about 10 to 20 samples are recommended to be screened in each generation.


  • DNA extraction
  • PCR and gel electrophoresis
  • Imaging
  • Compilation and interpretation of the data
  • Recommendation of the best animal(s) to choose for the next generation breeding.


There is a 4-tiered pricing structure that takes into account the number of PCR reactions required to perform the assay.  

Number of PCR Reactions Price per Reaction
1-250 reactions $2.50
251-500 reactions $2.00
501-750 reactions $1.50
>751 reactions $1.00

Approximate (hypothetical) cost of a Marker Assisted Speed Congenic project 

Generation # # of Samples # of Markers Price ($)
N2 10 100 1,750.00
N3 10 35 825.00
N4 10 12 300.00
N5 10 4 100.00
N6 10 2 25.00
    Total 3,000.00