Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants

Kinsey, Nathan A.; Belanger, Janelle M.; Dog Biomedical Variant Database, Consortium; Oberbauer, Anita M. (2022). Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Animal genetics, 53(5), pp. 706-708. Wiley 10.1111/age.13241

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Deficient homozygosity of a variant maintained in a population suggests that
the variant may be embryonic lethal. We examined whole genome sequence data
from 675 canids to investigate for variants with missing homozygosity and high
predicted impact. Our analysis identified 45 variants, in 32 genes. However,
further scrutiny of the sequence reads revealed that all but one of these variants
were artifacts of the variant calling process when using CanFam3.1, a widely
utilized canine reference genome. We demonstrate that the use of multiple,
newer reference genomes could reduce artifacts and lead to more accurate
variant identification.

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