Identification of Genetic Susceptibility Factors Associated with Canine Gastric Dilatation-Volvulus

Abstract

Canine gastric dilatation-volvulus (GDV) is a common life-threatening condition occurring primarily in large and giant breeds with a 3.9% to 36.7% lifetime risk. The genetic correlates of GDV have not previously been systematically explored. We undertook an inter-breed genome-wide association analysis (GWAS) of 253 dogs from ten breeds including 106 healthy dogs and 147 dogs with at least one GDV episode. SNP array genotyping followed by imputation was conducted on 241 samples to identify GDV-associated single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs). A subset of 33 dogs (15 healthy dogs and 18 GDV patients from the three most represented breeds) was characterized by whole genome sequencing (WGS). After genome-wide Bonferroni correction, we identified a significant putatively protective intergenic SNP (rs851737064) across all breeds. The signal was most significant in Collies, German Shorthaired Pointers, and Great Danes. Subsequent focused analysis across these three breeds identified 12 significant additional putatively protective or deleterious SNPs. Notable significant SNPs included those occurring in genes involved in gastric tone and motility including VHL, NALCN, and PRKCZ. These data provide important new clues to canine GDV risk factors and facilitate generation of hypotheses regarding the genetic and molecular underpinnings this syndrome.

Association between Human Genetic Variants and the Vaginal Bacteriome of Pregnant Women

“…Further regional associations were assessed for those SNPs that reached the genome-wide significance level ( P < 5 × 10 −8 ) and had the lowest P values within a ±250-kb window by locuszoom and imputed 1000 Genomes Project (Phase 3) reference panel data from BEAGLE 5.1 ( http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/ ). Only the results with genomic inflation factor (GIF) λ of <1.1 were considered a subtle population structure and shown in the study ( 66 , 67 ). The estimates for λ were either extracted from the PLINK log files or calculated by the estlambda() function from the R GenABEL package with the method = ‘median’ option.…”