ArticlePloS one2014
Fast principal component analysis of large-scale genome-wide data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers, 8 of them syntheses that pooled it.
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Who cites it
174 citing papers in PubMed, 8 syntheses or guidelines pooled it.
- The influence of fetal sex on maternal blood pressure in pregnancy.BMC medicine · 2025Pooled it
- Loci on chromosome 20 interact with rs16969968 to influence cigarettes per day in European ancestry individuals.Drug and alcohol dependence · 2024Pooled it
- A genome-wide association study of social trust in 33,882 Danish blood donors.Scientific reports · 2024Pooled it
- Multi-ancestry meta-analysis and fine-mapping in Alzheimer's disease.Molecular psychiatry · 2023Pooled it
- Genome-wide meta-analysis of brain volume identifies genomic loci and genes shared with intelligence.Nature communications · 2020Pooled it
- Genetic variants of calcium and vitamin D metabolism in kidney stone disease.Nature communications · 2019Pooled it
- Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry.Human molecular genetics · 2018 · on this mapPooled it
- Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways.Nature genetics · 2018Pooled it
- Strategies for collection, management, and release of data for multi-site longitudinal studies: Lessons from the ABCD Data Analysis, Informatics, & Resource Center.Developmental cognitive neuroscience · 2026Article
- Explicitly modeling genetic ancestry to improve polygenic prediction accuracy for height in a large, admixed cohort of US Latinos: Findings from HCHS/SOL.HGG advances · 2026Article
- Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs.bioRxiv : the preprint server for biology · 2026Article
- Review
- A simple approach for multiple observations improves power to detect genetic effects and genomic prediction accuracy.HGG advances · 2026Article
- Examining the association between fetal HLA-C, maternal KIR haplotypes and birth weight.PLoS genetics · 2026Article
- Inflammation and Oxidative-Stress Pathways Are Associated with Idiopathic Sudden Hearing Loss: A Genome-Wide Association Study in 15,494 Japanese Individuals.International journal of molecular sciences · 2026Article
- A multi-ancestry genetic reference for the Quebec population.Nature communications · 2026Article
- Computationally efficient whole-genome quantile regression at biobank scale.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Natural selection exerted by historical coronavirus epidemic(s): comparative genetic analysis in China Kadoorie Biobank and UK Biobank.BMC genomics · 2025Article
- The burden of endometriosis on quality of life in Danish women: an analysis of the Danish Blood Donor Study.BMC medicine · 2025Article
- A simple approach for multiple observations improves power to detect genetic effects and genomic prediction accuracy.medRxiv : the preprint server for health sciences · 2025Article
114 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
No grant is acknowledged in the PubMed record.
Abstract
Principal component analysis (PCA) is routinely used to analyze genome-wide single-nucleotide polymorphism (SNP) data, for detecting population structure and potential outliers. However, the size of SNP datasets has increased immensely in recent years and PCA of large datasets has become a time consuming task. We have developed flashpca, a highly efficient PCA implementation based on randomized algorithms, which delivers identical accuracy in extracting the top principal components compared with existing tools, in substantially less time. We demonstrate the utility of flashpca on both HapMap3 and on a large Immunochip dataset. For the latter, flashpca performed PCA of 15,000 individuals up to 125 times faster than existing tools, with identical results, and PCA of 150,000 individuals using flashpca completed in 4 hours. The increasing size of SNP datasets will make tools such as flashpca essential as traditional approaches will not adequately scale. This approach will also help to scale other applications that leverage PCA or eigen-decomposition to substantially larger datasets.
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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.