ArticleGenome medicine2019
Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores.
Article in Genome medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis 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
64 citing papers in PubMed, 1 synthesis or guideline pooled it, 128 citations in OpenAlex.
- CMDB: the comprehensive population genome variation database of China.Nucleic acids research · 2023Pooled it
- A Practical Workflow for Correcting Kit-Specific Effects in Whole-Exome Sequencing Data.Methods and protocols · 2026Article
- Genomic Selection for Milk Yield and Milk Composition Traits in Dairy Goats Using Machine Learning and Prior-Information Models.Animals : an open access journal from MDPI · 2026Article
- A Pseudohaploid-Based Imputation Strategy for Interspecific FMolecular ecology · 2026Article
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- Empirical evaluation of analytic validity of polygenic scores.Genome medicine · 2026Article
- Population genetic variation characterised through serial independent pool-seq: the Cyprus Genome Project.Scientific reports · 2026Article
- Inherited Genetic Risk of Liver Fibrosis in Lean Versus Nonlean Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD).Alimentary pharmacology & therapeutics · 2026Article
- A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.BMC bioinformatics · 2026Article
- Polygenic risk scores: Navigating the future of precision medicine through economic, ethical, and scientific advancements.iScience · 2026Review
- Genetic variants and polygenic risk scores associated with paroxysmal atrial fibrillation in the Japanese population.PloS one · 2026Article
- 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
- Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness.Scientific reports · 2025Article
- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- Fine mapping genetic variants affecting birth weight in sheep: a GWAS of 3007 individuals using low-coverage whole genome sequencing.Journal of animal science and biotechnology · 2025Article
- Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS).BMC research notes · 2025Article
- Museomics of an extinct European flat oyster population.Scientific reports · 2025Article
- DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Polygenic scores and their applications in kidney disease.Nature reviews. Nephrology · 2025Review
- Case-control association study between polygenic risk score and COVID-19 severity in a Russian population using low-pass genome sequencing.Epidemiology and infection · 2024Article
4 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
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInherited susceptibility to common, complex diseases may be caused by rare, pathogenic variants ("monogenic") or by the cumulative effect of numerous common variants ("polygenic"). Comprehensive genome interpretation should enable assessment for both monogenic and polygenic components of inherited risk. The traditional approach requires two distinct genetic testing technologies-high coverage sequencing of known genes to detect monogenic variants and a genome-wide genotyping array followed by imputation to calculate genome-wide polygenic scores (GPSs). We assessed the feasibility and accuracy of using low coverage whole genome sequencing (lcWGS) as an alternative to genotyping arrays to calculate GPSs.
methodsFirst, we performed downsampling and imputation of WGS data from ten individuals to assess concordance with known genotypes. Second, we assessed the correlation between GPSs for 3 common diseases-coronary artery disease (CAD), breast cancer (BC), and atrial fibrillation (AF)-calculated using lcWGS and genotyping array in 184 samples. Third, we assessed concordance of lcWGS-based genotype calls and GPS calculation in 120 individuals with known genotypes, selected to reflect diverse ancestral backgrounds. Fourth, we assessed the relationship between GPSs calculated using lcWGS and disease phenotypes in a cohort of 11,502 individuals of European ancestry.
resultsWe found imputation accuracy r
conclusionslcWGS is an alternative technology to genotyping arrays for common genetic variant assessment and GPS calculation. lcWGS provides comparable imputation accuracy while also overcoming the ascertainment bias inherent to variant selection in genotyping array design.
Indexed as
Identifiers
What OpenQuestion holds
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.