ArticleRNA (New York, N.Y.)2019
Ancestry patterns inferred from massive RNA-seq data.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus.International journal of molecular sciences · 2020Pooled it
- RNAScope-Ancestry: A Cross-Modality Framework for Inferring Genetic Ancestry from RNA-Seq with Application to MECA.Research square · 2026Article
- Breast cancer clustering integrating complete gene expression profiles and genetic ancestry.PloS one · 2026Article
- Identifying behavior regulatory leverage over mental disorders transcriptomic network hubs toward lifestyle-dependent psychiatric drugs repurposing.Human genomics · 2025Article
- Equitable machine learning counteracts ancestral bias in precision medicine.Nature communications · 2025Article
- A diagnostic host-specific transcriptome response for Mycoplasma pneumoniae pneumonia to guide pediatric patient treatment.Nature communications · 2025Article
- Optimization of computational ancestry inference for use in cancer cell lines.Biology methods & protocols · 2025Article
- Whole exome sequencing identifies new susceptibility candidates underlying community-acquired pneumonia.Genes & diseases · 2024Article
- Cross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework.Briefings in bioinformatics · 2024Article
- Genotype prediction of 336,463 samples from public expression data.bioRxiv : the preprint server for biology · 2024Article
- High placental expression of FLT1, LEP, PHYHIP and IL3RA - In persons of African ancestry with severe preeclampsia.Placenta · 2023Article
- Direct inference and control of genetic population structure from RNA sequencing data.Communications biology · 2023Article
- A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity.Environmental research · 2022Article
- Clinical implementation of RNA sequencing for Mendelian disease diagnostics.Genome medicine · 2022Article
- African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures.Scientific reports · 2021Article
- RNA-Seq Data-Mining Allows the Discovery of Two Long Non-Coding RNA Biomarkers of Viral Infection in Humans.International journal of molecular sciences · 2020Article
- Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants' Mimics Wild Type Infection.Frontiers in immunology · 2020Article
- Human Alveolar and Splenic Macrophage Populations Display a Distinct Transcriptomic Response to Infection WithFrontiers in immunology · 2020Article
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5 authors.
Funding
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Abstract
There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNA-seq data in 25 data sets where information on ethnicity was reported. Genome data of reference continental populations retrieved from The 1000 Genomes Project were used for comparisons. Remarkably, only eight out of 25 data sets passed FastQC default filters. We demonstrate that, for these eight population sets, the ancestral background of donors could be inferred very efficiently, even in data sets including samples with complex patterns of admixture (e.g., American-admixed populations). For most of the gene expression data sets of suboptimal quality, ancestral inference yielded odd patterns. The present study thus brings a cautionary note for gene expression studies highlighting the importance to control for the potential confounding effect of ancestral genetic background.
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