ArticleBMC genomics2011
Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 52 citations in OpenAlex.
- Dendrosomal nanocurcumin prevents EBV-associated cell transformation by targeting the lytic cycle genes of the Epstein-Barr virus in the generation of lymphoblastoid cell line.Iranian journal of basic medical sciences · 2023Article
- Comparison of mitochondrial DNA sequences from whole blood and lymphoblastoid cell lines.Scientific reports · 2022Article
- Estimating sequencing error rates using families.BioData mining · 2021Article
- Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci.PloS one · 2021Article
- Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing.Genetics in medicine : official journal of the American College of Medical Genetics · 2020Article
- Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research.Scientific reports · 2019Article
- Measuring coverage and accuracy of whole-exome sequencing in clinical context.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing.Oncotarget · 2018Article
- A collection of XY female cell lines.Human cell · 2018Article
- Deep sequencing of the mitochondrial genome reveals common heteroplasmic sites in NADH dehydrogenase genes.Human genetics · 2018Article
- Mosaicism in health and disease - clones picking up speed.Nature reviews. Genetics · 2017Review
- Differences between the genomes of lymphoblastoid cell lines and blood-derived samples.Advances in genomics and genetics · 2017Article
- Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines.Genomics data · 2016Article
- Article
- Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants.Human molecular genetics · 2015Article
- Characteristics of de novo structural changes in the human genome.Genome research · 2015Article
- In vitro human cell line models to predict clinical response to anticancer drugs.Pharmacogenomics · 2015Review
- Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments.PloS one · 2015Article
- Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data.BMC genomics · 2014Article
- Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.Cancer informatics · 2014Review
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. While LCLs have been used extensively in cellular and genetic studies, the process of cell transformation and expansion during culturing may introduce genomic changes that may impact their use and the interpretation of subsequent genetic findings.
resultsWe performed whole exome sequencing on a tetrad family using DNA derived from peripheral blood mononuclear cells (PBMCs) and LCLs from each individual. We generated over 4.7 GB of mappable sequence to a 125X read coverage per sample. An average of 19,354 genetic variants were identified. Comparison of the two DNA sources from each individual showed an average concordance rate of 95.69%. By lowering the variant calling parameters, the concordance rate between the paired samples increased to 99.82%. Sanger sequencing of a subset of the remaining discordant variants did confirm the presence of de novo mutations arising in LCLs.
conclusionsBy varying software stringency parameters, we identified 99% concordance between DNA sequences derived from the two different sources from the same donors. These results suggest that LCLs are an appropriate representation of the genetic material of the donor and suggest that EBV transformation can result in low-level generation of de novo mutations. Therefore, use of PBMC or early passage EBV-transformed cells is recommended. These findings have broad-reaching implications, as there are thousands of LCLs in public biorepositories and individual laboratories.
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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.