Justification for setting the individual animal genotype call rate threshold at eighty-five percent

Area of Science:

• Animal Genetics
• Genomic Data Quality

Background:

• SNP array data quality is crucial for accurate genetic analyses.
• Individual animal call rate is a common quality control metric, but its impact on genotype data integrity is not well understood.

Purpose of the Study:

• To investigate the effect of varying call rate thresholds on genotype data integrity.
• To quantify factors contributing to variability in animal call rates.

Main Methods:

• Analysis of 142,342 cattle samples genotyped on an Illumina SNP panel (14,371 SNPs).
• Comparison of genotype and allele concordance rates across different call rate thresholds.
• Evaluation of imputation accuracy and parentage validation reliability based on call rates.

Main Results:

• Factors like sex, herd, and genotyping date influenced individual animal call rates.
• Genotype and allele concordance improved with increasing call rates, reaching 0.998 and 0.999 respectively at 95-99% call rate.
• Imputation accuracy for missing genotypes reached 0.95 at 95-99% call rate, and parentage validation became reliable above 85% call rate.

Conclusions:

• A minimum animal call rate of 85% is suggested to ensure high-quality genotype data.
• This threshold balances data accuracy with the costs of resampling and regenotyping.
• The findings provide evidence-based recommendations for SNP genotyping quality control in cattle.