ArticleBioinformatics (Oxford, England)2013
Improved ancestry inference using weights from external reference panels.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 papers, 8 of them syntheses that pooled it.
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Who cites it
145 citing papers in PubMed, 8 syntheses or guidelines pooled it.
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- Genetically adjusted PSA levels for prostate cancer screening.Nature medicine · 2023Pooled it
- GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.Nature communications · 2022Pooled it
- Common X-Chromosome Variants Are Associated with Parkinson Disease Risk.Annals of neurology · 2021Pooled it
- International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.Nature communications · 2019Pooled it
- Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability.Molecular psychiatry · 2018Pooled it
- Putative linkage signals identified for breast cancer in African American families.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Trial
- Germline Variation and Somatic Alterations in Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Genetic Modifiers of ABCA1 Activity Interact with APOE Isoforms to Mediate Alzheimer's Disease Risk.Annals of neurology · 2026Article
- Maternal and offspring genome-wide association study of C-reactive protein reveals limited polygenic association with gestational diabetes mellitus.BMC genomics · 2026Article
- Multi-threshold polygenic risk improves hippocampal-based cognitive decline prediction.Genome medicine · 2026Article
- Contributions of genetic liability and the COVID-19 pandemic to rising psychopathology among youth in the United States.Translational psychiatry · 2026Article
- Blood DNA Methylation Predicts Long-Term Risk of Dementia in Prospective Cohorts.medRxiv : the preprint server for health sciences · 2026Article
- Endothelial Susceptibility-Related Genetic Variants and Hypertensive Disorders of Pregnancy-Brief Report.Arteriosclerosis, thrombosis, and vascular biology · 2026Article
- Identification of DNA methylation signatures of smoking in women and associations with cardiovascular disease mortality.Communications biology · 2026Article
- Polygenic Contribution to Sensorineural Hearing Loss Implicates Novel Risk Loci and Convergence with Congenital Hearing Loss Genes.Journal of the Association for Research in Otolaryngology : JARO · 2026Article
- Genetic associations with longevity in a Calabrian cohort: an exploratory genome-wide study.GeroScience · 2026Article
- Co-occurring clonal hematopoiesis exhibits strong selection and high leukemia risk.Nature communications · 2026Article
85 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
motivationInference of ancestry using genetic data is motivated by applications in genetic association studies, population genetics and personal genomics. Here, we provide methods and software for improved ancestry inference using genome-wide single nucleotide polymorphism (SNP) weights from external reference panels. This approach makes it possible to leverage the rich ancestry information that is available from large external reference panels, without the administrative and computational complexities of re-analyzing the raw genotype data from the reference panel in subsequent studies.
resultsWe extensively validate our approach in multiple African American, Latino American and European American datasets, making use of genome-wide SNP weights derived from large reference panels, including HapMap 3 populations and 6546 European Americans from the Framingham Heart Study. We show empirically that our approach provides much greater accuracy than either the prevailing ancestry-informative marker (AIM) approach or the analysis of genome-wide target genotypes without a reference panel. For example, in an independent set of 1636 European American genome-wide association study samples, we attained prediction accuracy (R(2)) of 1.000 and 0.994 for the first two principal components using our method, compared with 0.418 and 0.407 using 150 published AIMs or 0.955 and 0.003 by applying principal component analysis directly to the target samples. We finally show that the higher accuracy in inferring ancestry using our method leads to more effective correction for population stratification in association studies. AVAILABILITY: The SNPweights software is available online at http://www.hsph.harvard.edu/faculty/alkes-price/software/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.