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. 2022 Oct;53(5):706-708.
doi: 10.1111/age.13241. Epub 2022 Jul 3.

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

Nathan A Kinsey  1 , Janelle M Belanger  1 ; Dog Biomedical Variant Database Consortium; Anita M Oberbauer  1
Affiliations

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

Nathan A Kinsey et al. Anim Genet. 2022 Oct.

Abstract

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.

Keywords: bioinformatics; canis lupus familiaris; genomics; lethal recessive; sequence mapping; whole genome sequencing.

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Conflict of interest statement

CONFLICT OF INTEREST The authors declare no conflicts of interest.

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