Concordance rate in cattle and sheep between genotypes differing in Illumina GenCall quality score

Abstract

Summary Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12 428 767 genotypes in total post‐editing) and 80 sheep (1 557 360 SNPs genotypes in total post‐editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of <0.300, 0.300–0.549, and ≥0.550 in the cattle (sheep in parenthesis) was 0.9467 (0.9864), 0.9707 (0.9953), and 0.9994 (0.99997) respectively; the respective allele concordance rate was 0.9730 (0.9930), 0.9849 (0.9976), and 0.9997 (0.99998). Hence, concordance eroded as the GC score of the called genotype reduced, albeit the impact was not dramatic and was not very noticeable until a GC score of <0.55. Moreover, the impact was greater and more consistent in the cattle population than in the sheep population. Furthermore, an impact of GC score on genotype concordance rate existed even for the same SNP GenTrain value; the GenTrain value is a statistical score that depicts the shape of the genotype clusters and the relative distance between the called genotype clusters.

Application potential of chicken DNA chip in domestic pigeon species – Preliminary results

“…In 2021, Berry et al quantified the rate of genotype and allele matching between single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score on 771 cattle and 80 sheep samples. They found that the effect was larger and more consistent in the cattle population with more individuals than in the sheep population.…”

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

“…The confidence of the called genotype is calculated as 1 - genotype cluster probability [ 53 ] with 0 meaning highest confidence and 1 worst confidence. We removed genotype calls above a confidence of 0.05 (default = 0.15) since higher quality genotypes improve the concordance rate with sequencing data [ 54 ]. Furthermore, the call rate of a variant had to exceed the threshold of 0.95 and had to pass QC parameters defined in the best practices [ 53 ].…”

Study on the concordance between different SNP‐genotyping platforms in sheep

“…In this context, we should consider that different studies have reported variable amounts of genotyping errors in SNP‐chip datasets (Berry et␣al . 2016, 2021; Wu et␣al . 2019) that may impact the results of the subsequent analyses.…”

“…In this context, we should consider that different studies have reported variable amounts of genotyping errors in SNP-chip datasets (Berry et al 2016(Berry et al , 2021Wu et al 2019) that may impact the results of the subsequent analyses. For example, genotyping errors have been found to decrease the power to detect genuine associations between phenotype and genotype data (Gordon et al 2002;Sun et al 2004).…”