Genetic Visions-ST

The accepted standard high coverage genome sequence of an animal is at 30x coverage. This means that every base in the genome has been read an average of 30 times and so the sequence is highly accurate. High coverage sequence directly reveals the genotype of the animal for several million SNPs which can be used in predicting the genetic merit of the animal as well as discovering what beneficial or deleterious mutations they carry.

This even includes deleterious mutations that are unknown today. As soon as new mutations are defined, customers can explore the genomes of their animals to discover if they are carriers of any newly understood mutation, or free from the mutation. Lower depth coverage at 5x, 10x, or 20x provides information on the genome with lower accuracy, but at lower cost.

Low pass sequencing, in combination with imputation, can provide full genome information on animals with good accuracy and low cost, covering several million SNPs. Accuracy depends on the size of the reference population used for the imputation step.

AI companies need to be certain that the semen straws that they sell contain only the sperm cells of the expected bull. Low-pass sequencing with imputation has the power to identify sperm from other bulls in a dose of semen with a detection limit of 5%.

The process involves sequencing the DNA from one straw of semen from each batch at 0.5x and then running the data through a bioinformatics pipeline that includes imputation and QC analysis. Customers receive a report stating if the sample is free from contamination, or is contaminated.

In addition customers receive the sequence data files (fastq) for the 0.5x coverage. Each time a semen dose from a bull is run through the process, the customer will receive fastq files, which can be accumulated so that after, for example, 20 straws have been sequenced, the customer will have 10x coverage on the bull.