ReviewBioEssays : news and reviews in molecular, cellular and developmental biology2013
SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it.
Review in BioEssays : news and reviews in molecular, cellular and developmental biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 195 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
195 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Genome-wide association study provides novel insight into the genetic architecture of severe obesity.PLoS genetics · 2025Pooled it
- GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data.International journal of molecular sciences · 2022Pooled it
- A multi-trait meta-analysis with imputed sequence variants reveals twelve QTL for mammary gland morphology in Fleckvieh cattle.Genetics, selection, evolution : GSE · 2016Pooled it
- Development and deployment of a public mid-density genotyping panel for crimson clover (Trifolium incarnatum L.) based on whole-genome re-sequencing of diverse germplasm.The plant genome · 2026Article
- Genetic Bottleneck and Panmixia Following the Collapse of a Great Lakes Lake Whitefish Fishery.Evolutionary applications · 2026Article
- Development and validation of a high density SNP array for indigenous Indian pigs.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Targeted population genomics uncovers demographic history and genetic divergence in north American wild cranberry.Horticulture research · 2026Article
- Leveraging Next-Generation Tools for Genetic Assessment and Demographic Monitoring in Threatened and Elusive Humboldt Martens.Evolutionary applications · 2026Article
- An Assessment of Allelic and SNP Bias in a Genome-Wide SNP Enrichment Kit for Killer Whales.Ecology and evolution · 2026Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- Integrative multi-omics analysis identifies GNAZ and SLC5A4 as critical regulators of gestation length in Large White pigs.Genetics, selection, evolution : GSE · 2026Article
- Runs of homozygosity reveal population dynamics and selection across global cattle.Journal of animal science and biotechnology · 2026Article
- Decoding causal m6A: a bioinformatics roadmap for psychiatric disorders.Briefings in bioinformatics · 2026Review
- Unscrambling the history of African indicine cattle genomes.iScience · 2026Article
- Design and Application of a Genome-Wide SNP Array to Improve Conservation Outcomes in the Critically Endangered Southern Corroboree Frog.Molecular ecology resources · 2026Article
- Harnessing Deep Learning in Searching Wild Relatives of Domestic Animals.Molecular ecology resources · 2026Article
- Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns.Ecology and evolution · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- AmpliRAD: A New Method Combining Amplicon and RAD Sequencing.Ecology and evolution · 2026Article
- An advanced genotyping tool to inspect grapevine variability: the AxiomFrontiers in plant science · 2026Article
135 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Whole genome sequencing and SNP genotyping arrays can paint strikingly different pictures of demographic history and natural selection. This is because genotyping arrays contain biased sets of pre-ascertained SNPs. In this short review, we use comparisons between high-coverage whole genome sequences of African hunter-gatherers and data from genotyping arrays to highlight how SNP ascertainment bias distorts population genetic inferences. Sample sizes and the populations in which SNPs are discovered affect the characteristics of observed variants. We find that SNPs on genotyping arrays tend to be older and present in multiple populations. In addition, genotyping arrays cause allele frequency distributions to be shifted towards intermediate frequency alleles, and estimates of linkage disequilibrium are modified. Since population genetic analyses depend on allele frequencies, it is imperative that researchers are aware of the effects of SNP ascertainment bias. With this in mind, we describe multiple ways to correct for SNP ascertainment bias.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.