ArticleGenome research2021
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis that pooled it.
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Who cites it
75 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs.BMC genomics · 2023Pooled it
- Evaluating concordance of preimplantation genetic testing-whole-genome sequencing with genetic findings in live-born children.F&S reports · 2026Article
- Novel type 1 diabetes polygenic scores improve identification of type 1 diabetes in diverse populations.medRxiv : the preprint server for health sciences · 2026Article
- Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.G3 (Bethesda, Md.) · 2026Article
- Long-read low-pass sequencing enhances variant detection in a peanut MAGIC population.G3 (Bethesda, Md.) · 2026Article
- A blended genome and exome sequencing method captures genetic variation in an unbiased and cost-effective manner.Nature genetics · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Empirical evaluation of analytic validity of polygenic scores.Genome medicine · 2026Article
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Eye can see clearly now: Identifying the locus associated with a white-eye mutation in honey bees (Apis mellifera).Insect molecular biology · 2026Article
- Sequencing and health data resource of children of African ancestry.Genetics in medicine : official journal of the American College of Medical Genetics · 2026Article
- A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.BMC bioinformatics · 2026Article
- Genome-Wide Association Study of Gross Hair Weight and Hair Length Traits in Different Body Regions of Tianzhu White Yak.Biomolecules · 2026Article
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Opportunities and computational challenges in large-scale whole-genome sequencing data analysis.Journal of animal science · 2026Review
- An Advanced Entropy Approach for Minimizing False Discoveries in Imputation-Based Association Analyses.Research square · 2025Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
15 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array [GSA]) on 120 DNA samples derived from African- and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave-one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome-wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼0.5× and higher compared to the Illumina GSA.
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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.