ArticleBMC genomics2021
Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- QTL mapping and genomic prediction of resistance to apple blotch (Molecular breeding : new strategies in plant improvement · 2026Article
- A bittersweet symphony: genetic insights into cider apple fruit quality.G3 (Bethesda, Md.) · 2026Article
- An advanced genotyping tool to inspect grapevine variability: the AxiomFrontiers in plant science · 2026Article
- AxioSAFE: an accessible, semi-automatic filtering tool for the curation of genotyping datasets.Bioinformatics advances · 2026Article
- Article
- Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.Heredity · 2024Article
- Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Horticulture research · 2024Article
- Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.Horticulture research · 2024Article
- Fade into you: genetic control of pigmentation patterns in red-flesh apple (Frontiers in plant science · 2024Article
- Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN).Genes · 2023Article
- DNA profiling with the 20K apple SNP array revealsFrontiers in plant science · 2022Article
- Multi-omics analyses revealHorticulture research · 2022Article
- Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).BMC genomics · 2021Article
- The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry.Horticulture research · 2021Article
- Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundSingle nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls.
resultsConcordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3' end of the probe.
conclusionsThe Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.
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