Technical note: Droplet digital PCR precisely and accurately quantifies sex skew in bovine semen

Quantifying the relative population of sperm cells bearing the X or Y chromosome in a sexed-semen sample has historically been limited to methods that are either low throughput and sensitive to user subjectivity (e.g., fluorescence in situ hybridization), conterminous (using the same technology to generate and confirm the sex skew), or relatively insensitive (including quantitative PCR with a change detection threshold of 2×). Customers pay a premium for sexed semen and should have access to reliable sex skew data, generated by an accurate, precise test that is orthogonal to the method used to generate sexed semen. Droplet digital PCR (ddPCR) has the capacity to provide an accurate and precise sex skew quantitation by subdividing a pool of template DNA into nanoliter-scale droplets containing either 1 or 0 copies of template DNA. Then PCR amplification is conducted in the droplets, and the number of copies of the amplicon of interest can be counted as the number of fluorescence-positive droplets based on classic quantitative PCR fluorescent reporters. We have optimized and validated a multiplexed ddPCR assay that uses this copy counting method to quantify the sex skew (ratio of X or Y chromosomes) in frozen-thawed bovine sexed semen. The assay interrogates at least 1,000 cells per sample well, quantifying X and Y chromosome copy numbers along with an autosomal gene, GAPDH, used as an internal assay control to confirm total cells counted. The ddPCR sex skew assay achieved a 0.5-percentage-point variance for %X or %Y with a broad linear detection range, from 10 to 95% X, and provided reproducible skew values across a range of 9 to 27 ng of genomic DNA input. This approach overcomes some limitations of other sex skew assays by quantifying absolute X and Y chromosome copy numbers, thus providing a rigorous, independent assessment of sex-skewed semen.