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Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. | LitMetric

AI Article Synopsis

  • Lymphoblastoid cell lines (LCLs) are important in genetics research, helping scientists study human genetic diversity and develop new tools for understanding diseases.
  • This study analyzes DNA from LCLs taken from the 1000 Genomes Project to investigate how V(D)J recombination affects sequencing data, especially in areas tied to immune function.
  • The results show that V(D)J recombination can lead to inaccuracies in genotyping, potentially skewing estimates of gene frequencies and affecting disease association studies related to antibody genes.

Article 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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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668129PMC
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0261374PLOS

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