ArticleNature communications2014
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 273 papers, 11 of them syntheses that pooled it.
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Who cites it
273 citing papers in PubMed, 11 syntheses or guidelines pooled it.
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- Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation.Cell reports. Medicine · 2024Pooled it
- GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification.Nature genetics · 2023Pooled it
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- Genetic variant inAnnals of medicine · 2021Pooled it
- Gene-environment correlations and causal effects of childhood maltreatment on physical and mental health: a genetically informed approach.The lancet. Psychiatry · 2021Pooled it
- Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population.Arthritis research & therapy · 2020Pooled it
- An analysis of genetically regulated gene expression across multiple tissues implicates novel gene candidates in Alzheimer's disease.Alzheimer's research & therapy · 2020Pooled it
- Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium.Molecular psychiatry · 2019Pooled it
- Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes.Scientific reports · 2021Trial
- Genetic Predictors of Severe Skin Toxicity in Patients with Stage III Colon Cancer Treated with Cetuximab: NCCTG N0147 (Alliance).Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2021Trial
- Integrated Genomic and Transcriptomic Study RevealsCirculation. Genomic and precision medicine · 2026Article
- Genome-wide association study of paediatric bacteraemia and sepsis.EBioMedicine · 2026Article
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- Trans-ethnic estimation and implications of genetic impact on continuous glycemic profiles.Cell discovery · 2026Article
- Genetic Differences in Purple Finch (Ecology and evolution · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Integrative mendelian randomization approaches for therapeutic target prioritisation in immune-mediated diseases.Scientific reports · 2026Article
213 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.
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