Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

Abstract

BackgroundAccurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms.MethodsGenotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates.ResultsA mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes.Conclusions and implicationsOur results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1

“…The lowest mean genotype concordance (61.6%) was observed for monomorphic SNP while the highest (98.89%) was observed for SNP with MAF > 0.05 to ≤ 0.10 (Table 3). The study of Berry et al (2016) observed similar results.…”

“…Similar mean genotype concordance rates were reported by other studies in livestock and humans. An evaluation of 49,859 SNPs in sheep samples (n = 84) genotyped by Illumina and Affymetrix platforms reported a 98.1% mean genotype concordance rate per SNP (Berry et al, 2016). This study reported that only a small proportion (~0.3%) of homozygous genotypes in one platform was called as alternate homozygous in the other platform.…”

“…Diverse genotyping platforms with varying SNP densities are often used across various subsets of animals for genomic evaluation. Previous reports showed that quality metrics and distribution of quality data differ across genotyping platforms in human (Hong et al, 2012) and livestock (Berry et al, 2016). This study evaluated data obtained from two genotyping platforms, SowPro90 and Porcine SNP60 BeadArray, and established the optimal quality control parameters across platforms to identify high-confidence genotypes for downstream analysis.…”

Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

“…evaluated the reproducibility of genotypes from the same SNP locus generated on technical duplicate samples for the same Illumina platform or different Illumina platforms. A total of 1,400 of the remaining SNPs in the present study, reported by Berry et al (2016) to not have 100% concordance on the same Illumina genotype platform, were not considered further. Neither were an additional 1,278 SNPs that had <100% concordance on different Illumina genotype platforms were considered (Berry et al, 2016).…”

“…A total of 1,400 of the remaining SNPs in the present study, reported by Berry et al (2016) to not have 100% concordance on the same Illumina genotype platform, were not considered further. Neither were an additional 1,278 SNPs that had <100% concordance on different Illumina genotype platforms were considered (Berry et al, 2016). Only flock book-recorded animals from the main breeds of Belclare (n = 1,074), Charollais (n = 2,778), Suffolk (n = 1,799), Texel (n = 3,056), and Vendeen (n = 683) were retained.…”