ArticlePloS one2021
How array design creates SNP ascertainment bias.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed.
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- Methods to detect selection history in a population under ongoing directional selection.Genetics · 2026Article
- Development and application of a 5K targeted liquid SNP panel for Hetian chickens based on genotyping by targeted sequencing.Poultry science · 2026Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.Journal, genetic engineering & biotechnology · 2026Article
- Genetic Diversity and Population Structure of Two Mexican Creole Cattle Populations.Animals : an open access journal from MDPI · 2026Article
- Mining of important genetic loci and evaluation of genetic effects for growth traits in Baicheng You Chicken.Poultry science · 2026Article
- Estimating the Abundance of a Cryptic, Endangered Marsupial, Mala (Ecology and evolution · 2026Article
- Comprehensive Analysis of 122 Guinea Fowl Genomes Across Three Continents Delineates Their Domestication and Evolutionary Patterns with Special Reference to India.International journal of molecular sciences · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Genome-based medicine in Korea: the Korea National Institute of Health infrastructure for precision medicine.Childhood kidney diseases · 2026Review
- Removing array-specific batch effects in GWAS mega-analyses by applying a two-step imputation workflow.Bioinformatics advances · 2026Article
- Genomic prediction using a cost-effective mid-density SNP platform in spring wheat.Frontiers in plant science · 2026Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Article
- Genetic diversity and selection signatures in sheep breeds.Journal of applied genetics · 2025Article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach.Plant methods · 2025Article
- Review
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
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