ArticleScientific reports2015
Analysis of genome-wide RNA-sequencing data suggests age of the CEPH/Utah (CEU) lymphoblastoid cell lines systematically biases gene expression profiles.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Chromatin activity identifies differential gene regulation across human ancestries.Genome biology · 2024Article
- A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies.Scientific reports · 2022Article
- On the cross-population generalizability of gene expression prediction models.PLoS genetics · 2020Article
- Population-Specific Genetic and Expression Differentiation in Europeans.Genome biology and evolution · 2020Article
- Individual Differences in the Response of Human β-Lymphoblastoid Cells to the Cytotoxic, Mutagenic, and DNA-Damaging Effects of a DNA Methylating Agent,Chemical research in toxicology · 2019Article
- Accuracy of Gene Expression Prediction From Genotype Data With PrediXcan Varies Across and Within Continental Populations.Frontiers in genetics · 2019Article
- Expression reflects population structure.PLoS genetics · 2018Article
- Transcriptional signature of lymphoblastoid cell lines ofOncotarget · 2017Article
- Pervasive coexpression of spatially proximal genes is buffered at the protein level.Molecular systems biology · 2017Article
- Human Epistatic Interaction Controls IL7R Splicing and Increases Multiple Sclerosis Risk.Cell · 2017Article
- Global variation in gene expression and the value of diverse sampling.Current opinion in systems biology · 2017Article
- Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples.PloS one · 2017Article
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Authors and funding
4 authors.
Funding
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Abstract
In human, Lymphoblastoid cell lines (LCLs) from the CEPH/CEU (Centre d'Etude du Polymorphisme Humain - Utah) family resource have been extensively used for examining the genetics of gene expression levels. However, we noted that CEU/CEPH cell lines were collected and transformed approximately thirty years ago, much earlier than the other cell lines from the pertaining individuals, which we suspected could potentially affect gene expression, data analysis and results interpretation. In this study, by analyzing RNA sequencing data of CEU and the other three European populations as well as an African population, we systematically examined and evaluated the potential confounding effect of LCL age on gene expression levels and patterns. Our results indicated that gene expression profiles of CEU samples have been biased by the older age of CEU cell lines. Interestingly, most of CEU-specific expressions are associated with functions related to cell proliferation, which are more likely due to older age of cell lines than intrinsic characters of the population. We suggested the results be carefully explained when CEU LCLs are used for transcriptomic data analysis in future studies.
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