Evaluating the efficiency and accuracy of a commercial test for estimating genetic risk of bovine congestive heart failure

Background: Bovine congestive heart failure (BCHF) is a significant cause of death in feedlot cattle in the Western Great Plains of North America. Single nucleotide polymorphisms (SNPs) in the ARRDC3 and NFIA genes have been previously associated with BCHF and genetic tests can classify animals by their risk for disease. Here, our aims were to evaluate the efficiency (genotypes obtained / samples tested) of a rapid DNA extraction kit and the accuracy of a 2-SNP assay for BCHF risk. Methods: Skin biopsies from 100 cattle were randomized and extracted with a proprietary rapid DNA extraction kit. A custom duplex, combined sequence amplification and nucleotide detection (C-SAND) assay was developed and run once on a commercial thermocycling machine to determine the genotypes. Both the rapidly extracted DNA and highly purified reference DNA from the same individuals were genotyped with the 2-SNP assay by operators blinded to the sample identity. The C-SAND genotypes were compared to known genotypes derived from a bead array assay. A priori standards for missing and incorrect genotypes were set at less than 3% and 1%, respectively. Results: When using reference DNA samples, there were no missing and no incorrect C-SAND-derived genotypes, meeting the a priori standards. When DNA samples from the rapid extraction kit were used, genotypes were not determined for 5% of the samples. Of the 95 samples successfully extracted, there were 0% and 3% incorrect genotypes for the respective ARRDC3 and NFIA SNPs. Conclusions: This duplex C-SAND assay and thermocycling machine combination were efficient and accurate when reference DNA was used, meeting a priori standards. Although the reduced efficiency of the rapid extraction kit can be overcome by repeated testing, increased genotype errors present an important issue. Despite these challenges, this rapid extraction kit and assay can be a reasonable tool for producers to select animals with reduced BCHF risk. ### Competing Interest Statement The authors declare the following competing interests: co-authors A.H., D.P., and H.P. are full-time employees at MatMaCorp, a molecular diagnostics company that builds instruments and develops test kits for human and animal health applications. There are no patents, products in development, or marketed products to declare. These interests do not alter the authors adherence to all the journals policies on sharing data and materials. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The USDA is an equal opportunity provider and employer.