During the Beef Improvement Federation’s recent post-conference tour in the Lincoln, Neb. area, the group visited the brand-new laboratory facilities of GeneSeek, one of the leading companies in genomic testing and profiling for cattle and other livestock.
GeneSeek is a division of Neogen, which also includes the Igenity genomic profiles for beef and dairy cattle. The new facility, located in a commercial area on the outskirts of Lincoln, has the capacity to analyze well over one million samples per year, and company officials expect this year’s total to approach one million.
The laboratory facility is designed for automation and efficient flow of samples and information, with several distinct areas serving specific roles.
The sample-reception area constantly receives shipments of hair, blood, saliva, semen and tissue samples for genetic testing, disease diagnostics or in some cases, pregnancy diagnosis. Staff members log each sample into the company’s Laboratory Information Management System and assign each a barcode for accurate tracking and information transfer. Sample quality varies widely, and poor-quality samples can slow the process, especially if they are not usable and need to be re-submitted. The company recommends submitting a clean, dry sample, stored according to instructions for the sample type and clearly labeled.
Next the samples for genetic analysis go to the DNA extraction area for isolation and purification of DNA. In most cases with blood, hair or semen samples, just a small portion of the sample is extracted with the rest stored for future use. Technicians arrange the samples into 96-well plates before fragmenting the cells to expose the DNA and then isolating the DNA from other material in the sample.
During the third stage, samples undergo a polymerase chain reaction (PCR) process to target and amplify genes of interest. The Transffer 1 lab serves as a staging area where components of the chemical reaction are prepared and the DNA is placed in its final plating. Several automated liquid-handling robots help speed the process and ensure an accurate and traceable transfer of the samples. Samples from the Transfer 1 lab pass through a window to the Transfer 2 area, where various preparations target the specific information sought from the DNA sample.
The lab accommodates several types of DNA analysis, ranging from fairly simple tests for parentage or genetic defects to tests using high-density chips for genomic profiling such as the Illumina GGP-HD chip with capacity for nearly 78,000 single nucleotide polymorphismsor or SNPs. During the post-PCR stage, a number of analytical instruments are used to complete the DNA analysis, with the machine depending on the type of analysis being conducted. These include LICor units, Sequenom Mass Array machines, Illumina iScan and HiScan and the Affymetrix Gene Titan.
Finally, the genotype data goes to a group of analysts who prepare the information for customers, with the data customized to customer needs, such as specific “results” for cattle producers. For breed associations, the company works with Iowa State University to create a Molecular Breeding Value for specific traits.
Sample storage is the final stage, with samples moving either to warm or cold storage depending on the sample type. Stored samples act as a backup in case new testing is needed, and also as an archive that could be accessed as new tests become available. The frozen storage facility is housed in a concrete bunker backed by a 1,000 horsepower diesel generator in conjunction with a high-capacity battery backup to protect data servers in case the power goes out.
The facility also includes a veterinary diagnostic laboratory, where specialists use a simple blood card, tissue sample or hair sample for the detection of persistent infection with Bovine Viral Diarrhea Virus (BVDV) in cattle with next-day turnaround for sample. All sample types can be used for simultaneous genomic testing, so the combination of a genomic profile with BVDV testing provides assurance of freedom from BVDV infection in valuable breeding animals, and an estimate of genetic merit early in life.
GeneSeek also is a certified BioTracking laboratory offering the BioPRYN early stage bovine detection pregnancy diagnostic assay service for beef and dairy cattle producers. BioPRYN is a safe and accurate pregnancy detection tool, based on blood samples, that complements veterinary services on the farm and provides an alternative to palpation and ultrasound in cattle. BioPRYN measures the presence of pregnancy-specific protein B (PSPB) in the blood circulation of the animal, a protein only produced by the placenta of a growing fetus.
For more information visit the Neogen website.