ArticlePloS one2021
Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 13 citations in OpenAlex.
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.Bioinformatics (Oxford, England) · 2026Article
- Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus.Genome research · 2025Article
- Genotyping of selected germline adaptive immune system loci using short-read sequencing data.Genome research · 2025Article
- IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads.Cell reports methods · 2025Article
- Complete sequencing of ape genomes.Nature · 2025Article
- Complete sequencing of ape genomes.bioRxiv : the preprint server for biology · 2024Article
- Lymphoblastoid cell lines do not recapitulate physiological circulating B cell subtypes.Current research in immunology · 2024Article
- Polygenic genetic variation affecting antibody formation underlies hypertensive renal injury in the stroke-prone spontaneously hypertensive rat.American journal of physiology. Renal physiology · 2023Article
- Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.Nature communications · 2023Article
- ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data.Cell systems · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Lymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and methodologies for augmenting disease genetics research. While the validity of variant callsets from LCLs has been demonstrated for most of the genome, previous work has shown that DNA extracted from LCLs is modified by V(D)J recombination within the immunoglobulin (IG) loci, regions that harbor antibody genes critical to immune system function. However, the impacts of V(D)J on short read sequencing data generated from LCLs has not been extensively investigated. In this study, we used LCL-derived short read sequencing data from the 1000 Genomes Project (n = 2,504) to identify signatures of V(D)J recombination. Our analyses revealed sample-level impacts of V(D)J recombination that varied depending on the degree of inferred monoclonality. We showed that V(D)J associated somatic deletions impacted genotyping accuracy, leading to adulterated population-level estimates of allele frequency and linkage disequilibrium. These findings illuminate limitations of using LCLs and short read data for building genetic resources in the IG loci, with implications for interpreting previous disease association studies in these regions.
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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.