Powering genomic discovery in dogs with low-pass sequencing

by Kathleen Morrill and Elinor Karlsson at U Mass Medical School and the Broad Institute, and Joe Pickrell at Gencove

Darwin’s Dogs is using using Gencove’s low-pass sequencing to discover the genetic basis of dog disease. Sign up at darwinsark.org!

Darwin’s Dogs is a citizen science project that allows pet owners to participate in genomic science and learn more about the DNA of their dog. By combining reports from owners about dog traits with a simple saliva swab, we can identify the specific genetic variants that make each dog unique.

As a proof of concept, Gencove sequenced (to 1x coverage) and imputed the genomes over 300 dogs with height measurements from their owners. This allowed us to perform a genome-wide association study of dog height using over 8M genetic markers. The results are below — we were able to identify a number of known genes important in dog size (for example the insulin-like growth factor 1, or IGF1) as well as other previously-unknown associations (for example near the gene MED13L).

To compare low-pass sequencing to the alternative technology of genotyping arrays, we genotyped over 400 dogs on an Affymetrix array and performed the same analysis. The results are below: five of the same genes also show up in this scan, but some variants detected in the low-pass sequencing do not show up when using genotyping.

Though preliminary, these results are consistent with other results from Gencove suggesting that low-pass sequencing increases the power to identify genetic variants associated with traits. We’re excited to increase sample numbers with the public launch of Darwin’s Ark — to participate sign your dog up here!