Genetic testing limits the spread of inherited kidney disease while avoiding inbreeding in domestic cats
Data files
Abstract
More than 56,000 genetic variants were evaluated in 81 domestic cats to clarify the genetic structure, genetic diversity, and effective population size at two time points: before genetic testing started (2019) and after genetic testing became popular (2022).
https://doi.org/10.5061/dryad.6hdr7sr82
The data format is a Plink bed, so you can use PLINK software (https://www.cog-genomics.org/plink/) to handle the data easily.
Quality control was performed using PLINK version 1.90 (Chang et al., 2015). Missing rates for each locus (geno option) and individual cats (mind option) were both <5%. We did not examine the Hardy-Weinberg equilibrium, as we did not assume random mating for pedigreed cats. Population genetic analyses should not include close relatives (Manichaikul et al., 2010); therefore, we conducted robust relationship-based pruning using the king-cutoff option in PLINK version 2.00a2LM (threshold of 0.176) to exclude pairings between monozygotic twins and first-degree relatives. For allele frequency-based quality control, we excluded SNPs with a minor allele frequency <0.01.
Several software tools, such as PLINK, can be used to analyze the following datasets further. A text editor like EmEditor can be used to open .bim and .fam files. After converting the data to PED/MAP format using PLINK (with the command below), the contents of the .bed file can also be viewed with a text editor.
Example:
plink --bfile PER --allow-extra-chr --recode --chr-set 95 --out PER_ped
ScottishFold
PER.bed: : PLINK bed file
PER.bim : PLINK bim file
PER.fam : PLINK fam file
Persian
PER.bed: : PLINK bed file
PER.bim : PLINK bim file
PER.fam : PLINK fam file
Scottish Folds and Persian cats were genotyped by using Infinium iSelect 63K Cat DNA Array (Illumina Inc.).
- Ukawa, Hisashi; Kida, Akane; Ataka, Kai et al. (2024). Widespread genetic testing control inherited polycystic kidney disease in cats [Preprint]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.12.15.628535