We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%.
Original language
English
Publication year
Feb 2018
Publication status
Published - Feb 2018
Event
The 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand Duration: 11 Feb 2018 → 16 Feb 2018 Conference number: 11
Conference
Conference
The 11th World Congress on Genetics Applied to Livestock Production
