DOI: 10.5061/dryad.6djh9w17c
title: Data for: Global frequency analyses of canine progressive rod-cone degeneration–progressive retinal atrophy and collie eye anomaly using commercial genetic testing data

description: Hundreds of genetic variants associated with canine traits and disorders
 have been identified, with commercial tests offered. However, the
 geographic distributions and changes in allele and genotype frequencies
 over prolonged, continuous periods of time are lacking. This study
 utilized a large set of genotypes from dogs tested for the progressive
 rod-cone degeneration–progressive retinal atrophy (prcd-PRA) G&gt;A
 missense PRCD variant (n = 86,667) and the collie eye anomaly
 (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial
 genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science
 & Diagnostics). These data were analyzed using the chi-square
 goodness-of-fit test, time-trend graphical analysis, and regression
 modeling in order to evaluate how test results changed over time. The
 results span fifteen years, representing 82 countries and 67 breeds/breed
 mixes. Both diseases exhibited significant differences in genotype
 frequencies (p = 2.7 × 10−152 for prcd-PRA and 0.023 for CEA) with
 opposing graphical trends. Regression modeling showed time progression to
 significantly affect the odds of a dog being homozygous or heterozygous
 for either disease, as do variables including breed and breed popularity.
 This study shows that genetic testing informed breeding decisions to
 produce fewer affected dogs. However, the presence of dogs homozygous for
 the disease variant, especially for prcd-PRA, was still observed fourteen
 years after test availability, potentially due to crosses of unknown
 carriers. This suggests that genetic testing of dog populations should
 continue.
description: Data for this study comprised genotype status for prcd-PRA
 (n=86,667 dogs) and CEA (n=33,834 dogs) tested by a commercial genetic
 testing company (OptiGen, LLC acquired by Mars Petcare in 2018) between
 the years 2004-2019. These data underwent statistical analysis (Chi-square
 goodness-of-fit, logistic regression modeling, multinomial regression
 modeling) to determine significance of changing allele and genotype
 frequencies over time as well as the impact of dog breed, geography,
 progress of time, and popularity on overall likelihood of a dog developing
 either disease or having a carrier status.
description: # Genotype and sample data from Clark et al. "Global Frequency
 Analyses of Canine Progressive Rod-Cone Degeneration–Progressive Retinal
 Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data"
 ## Description of the data
 and file structure Genotype and metainformation for domestic dog samples
 that were owner-submitted to commercial genetic testing companies OptiGen,
 LLC and Mars Petcare between the years of 2004-2019. In total, there were
 86,667 samples tested for Progressive Rod-Cone Degeneration-Progressive
 Retinal Atrophy (prcd-PRA) and 33,834 samples tested for Collie Eye
 Anomaly (CEA), both diseases prevalent across different dog breeds and
 with an effect on canine eyesight. Data file: Clark2023_Dataset.xlsx Data
 is provided as an .xlsx file with two spreadsheets of similar arrangement
 - one for CEA and one for prcd-PRA samples. Each row on the table
 represents anonymized samples while columns represent variables: *Sample:
 number assigned to distinguish samples anonymously *Year: year in which
 owner submitted canine DNA sample to company for analysis *Breed:
 owner-reported sample dog breed, mix of breeds, or generalized "mixed
 breed" *Genotype: number of disease-associated variants present in
 DNA sample -Normal = Homozygous wild-type (0 copies of disease variant
 present in sample) -Carrier = Heterozygous (1 copy of disease variant
 present in sample) -Affected = Homozygous for associated allele (2 copies
 of disease variant present in sample) *OwnerCountry: owner-reported
 country of sample origin *Continent: continent of sample origin;
 determined from OwnerCountry *AKC: breed classification of sample
 according to the American Kennel Club (AKC); determined from Breed *FCI:
 breed classification of sample according to the Federation Cynologique
 Internationale (FCI); determined from Breed *Clade: grouping of breeds
 according to genetic relationship that sample belongs to; determined from
 Breed *Rank2005: (CEA dataset only) popularity ranking of sample breed
 according to AKC registration counts in the year 2005 (first year of data
 within the CEA dataset); determined from Breed *Rank2004: (prcd-PRA
 dataset only) popularity ranking of sample breed according to AKC
 registration counts in the year 2004 (first year of data within the
 prcd-PRA dataset); determined from Breed *Rank2019: popularity ranking of
 sample breed according to AKC registration counts in the year 2019 (last
 year of data within either the CEA or prcd-PRA dataset); determined from
 Breed Any value of "0" represents missing information where
 Breed value was not associated with a known AKC, FCI, Clade, Rank2005,
 Rank2004, Rank2019 value.