By Aaron Krol
July 19, 2013 | At Genentech’s Mouse Genetics Department in South San Francisco, Dr. Rhonda Wiler and her team are proving that the simplest investments in IT can yield the biggest returns.
Dr. Wiler’s department oversees a breeding facility for genetically engineered mice, which produces over 40,000 pups a month representing almost a thousand distinct genetic lines. Keeping track of so many animals, while running regular genotypic assays and maintaining a humane living environment, is a labor-intensive job, with plenty of opportunities for waste and redundancy. But a recent innovation in Genentech’s cage changing procedure showcased the savings that can be achieved when waste is tackled aggressively, and won Genentech the Judges’ Prize at the 2013 Bio-IT World Best Practices Awards.
|L to R: Doug Garrett, Erik Bierwagen, Rhonda Wiler
Changing cages for washing is an important feature of mouse husbandry, providing clean bedding and food, and clearing animal excreta. It’s also a stressful time for the mice, and a time-consuming task for the veterinary staff. When staff observed that the current system—an entire rack of 160 cages was changed together every two weeks—occasionally led to the changing of clean cages with plenty of food, Dr. Wiler decided to experiment with a more data-driven strategy.
Genentech already collected detailed information on the history of all the mice and cages, through their colony management system (CMS), developed in-house and implemented in 2008. CMS is a flexible bioinformatics system that incorporates portable devices, such as tablets, so that staff can both access and enter data remotely as they perform tasks.
“CMS has allowed us to capture information at a level that people never had considered doing before,” said Erik Bierwagen, Principal Programmer Analyst at Genentech, “maintaining detailed information about every single animal in the facility, addressing and barcoding every single location within our facility, and capturing all the key details of the genetics of the animals.” Tasked with streamlining the cage change procedure, Bierwagen and his in-house programmers at the Bioinformatics & Computational Biology Department set to work creating a new software tool, Directed Cage Change (DCC), to record and prompt cage changes.
The trouble with the old system was that cages are sometimes moved from one rack to another, or have to be changed prematurely for weaning or mating. As a result, not all cages in a given rack have waited the same amount of time to be changed. In addition, some cages contain more mice than others; lower occupancy cages can afford to be changed less frequently. A preliminary analysis in CMS suggested that, with all these variables accounted for, over six thousand cages a week were being changed unnecessarily. DCC would eliminate this redundancy.
Instead of assigning an entire rack of cages to be changed, DCC tracks the status of each cage individually, based on its occupancy and most recent changing. A cage with a single mouse can be changed once every four weeks, and a breeding cage with 10-day-old pups once a week, without throwing off any other cages’ schedules. DCC also records unexpected changing events, and updates each cage’s history accordingly.
The key to making DCC functional is an intuitive user interface on the mobile devices already in use at the facility. A veterinarian can select a specific rack on her tablet, and see a map in which the cages that need to be changed are highlighted in blue. Like other software built out of CMS, this procedure is smoothly integrated into the staff’s daily routine and requires little training to use.
The DCC program outperformed expectations, reducing the number of cages changed each week by 40%. This saves not only in labor, but also food, bedding, water, and electricity. The DCC program also produced less quantifiable, but equally important benefits: in the veterinary staff’s increased sense of job satisfaction, and in better living conditions for the mice. A preliminary analysis has revealed fewer evidence of stress behavior such as pup cannibalization or male fighting after DCC’s implementation, and even increased breeding in certain colonies.
Altogether, the DCC system saved Genentech a staggering $411,000 a year, for an initial investment of just $40,000 in software development. While updating the procedures for cage changes in a mouse breeding facility may not be the most glamorous of projects, this huge return on investment highlights the results that can be achieved on every level of the industry with attention to bioinformatics systems.
“I was not surprised that there was a positive return on investment, but was very happily surprised at the magnitude,” said Bierwagen, adding that CMS has been helping the team discover new efficiencies ever since its implementation. CMS has already paved the way for high-throughput genotyping that saves Genentech $750,000 annually, and large-scale cryopreservation of genetic lines that has allowed the facility to breed 100,000 fewer mice each year.
DCC’s “staggering ROI” and creative use of bioinformatics were recognized this April, when Genentech took home the Judges’ Prize at the 2013 Bio-IT World Best Practices Awards, part of the Bio-IT World Conference & Expo held in Boston. The annual Best Practices competition recognizes excellence in data management in the life sciences, and draws a distinguished panel of judges from the field.