Comparative Analysis of HEK293 Genomic Variability

Human embryonic kidney cells HEK293 are widely used in biopharmaceutical manufacturing, with a recent surge particularly in recombinant adeno‐associated virus production. Despite their industrial relevance, comprehensive data on their genomic background and stability remains limited. Here, we systematically analyze the genetic landscape of various HEK293 cell lines in response to cultivation conditions, clonal selection, genetic manipulation and over time in culture. Adherent HEK293 were adapted to suspension growth using different serum‐free media. Whole genome sequences from these cell lines were analyzed together with previously published data from additional variants in common use. All data sets were aligned against the human reference genome, enabling the assessment of genome stability by evaluation of variants and revealing a conserved genetic core across all lines, regardless of cultivation history or phenotypic divergence. Evaluation of the functional implications of conserved core mutations identified an enrichment in genes related to cellular structure, morphology and cellular connectivity. The distribution of structural variants and single nucleotide polymorphisms indicated a gradual accumulation of mutations over time in culture rather than abrupt shifts in response to environmental changes. Notably, the integrated adenoviral genes remained highly conserved with respect to copy number, integration site and sequence integrity. These findings provide insight into the genomic evolution of HEK293 cells and offer a foundation for further multi‐omics studies aimed at optimizing HEK293 cells for applications in biopharmaceutical production.

• Publication year

  2025

• Venue

  Biotechnology and Bioengineering

• Publication date

  2025-11-10

• Fields of study

  Biology, Medicine, Materials Science

• Identifiers
  DOI 10.1002/bit.70105PMID 41211952PMCID 12779178
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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• The UCSC Genome Browser database: 2025 update

  2024cited by this paper
• The Gene Ontology knowledgebase in 2023

  2023cited by this paper
• AAV production in stable packaging cells requires expression of adenovirus 22/33K protein to allow episomal amplification of integrated rep/cap genes

  2023cited by this paper
• The impact of serum-free culture on HEK293 cells: From the establishment of suspension and adherent serum-free adaptation cultures to the investigation of growth and metabolic profiles

  2022cited by this paper
• Sustainable data analysis with Snakemake

  2021cited by this paper
• HEK293 Cell Line as a Platform to Produce Recombinant Proteins and Viral Vectors

  2021cited by this paper
• Rapid serum‐free/suspension adaptation: Medium development using a definitive screening design for Chinese hamster ovary cells

  2021cited by this paper
• Evolution from adherent to suspension: systems biology of HEK293 cell line development

  2020influential reference
• Comprehensive Analysis of Genomic Safe Harbors as Target Sites for Stable Expression of the Heterologous Gene in HEK293 Cells.

  2020cited by this paper
• The Interplay between Adeno-Associated Virus and Its Helper Viruses

  2020cited by this paper
• Genome‐wide analysis of single nucleotide variants allows for robust and accurate assessment of clonal derivation in cell lines used to produce biologics

  2020cited by this paper
• Welcome to the Tidyverse

  2019cited by this paper
• Identification of novel breakpoints for locus- and region-specific translocations in 293 cells by molecular cytogenetics before and after irradiation

  2019cited by this paper
• CHO‐Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction

  2018cited by this paper
• Karyotype variation of CHO host cell lines over time in culture characterized by chromosome counting and chromosome painting

  2018cited by this paper
• vcfr: a package to manipulate and visualize variant call format data in R

  2017cited by this paper
• Therapeutic glycoprotein production in mammalian cells.

  2017cited by this paper
• The Ensembl Variant Effect Predictor

  2016cited by this paper
• Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

  2016cited by this paper
• Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

  2016cited by this paper
• CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

  2016cited by this paper
• Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

  2016cited by this paper
• MultiQC: summarize analysis results for multiple tools and samples in a single report

  2016cited by this paper
• HEK293 in cell biology and cancer research: phenotype, karyotype, tumorigenicity, and stress-induced genome-phenotype evolution.

  2015influential reference
• Human cell lines for biopharmaceutical manufacturing: history, status, and future perspectives

  2015cited by this paper
• Step-wise and punctuated genome evolution drive phenotype changes of tumor cells.

  2015cited by this paper
• A More Scalable Alternative to Venn and Euler Diagrams forVisualizing Intersecting Sets

  2015cited by this paper
• Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

  2015cited by this paper
• VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

  2014cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• R: A language and environment for statistical computing.

  2014cited by this paper
• Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

  2014cited by this paper
• The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology.

  2013cited by this paper
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

  2013cited by this paper
• A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

  2012cited by this paper
• clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

  2012cited by this paper
• Optimization of HEK 293 cell growth by addition of non-animal derived components using design of experiments

  2011cited by this paper
• Metabolite profiling of recombinant CHO cells: designing tailored feeding regimes that enhance recombinant antibody production.

  2011cited by this paper
• ggplot2

  2011cited by this paper
• The extracellular matrix at a glance

  2010cited by this paper
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010cited by this paper
• Fast and accurate long-read alignment with Burrows–Wheeler transform

  2010cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• QuickGO: a web-based tool for Gene Ontology searching

  2009cited by this paper
• Genetic characterization of CHO production host DG44 and derivative recombinant cell lines.

  2006cited by this paper
• Mitotic infidelity and centrosome duplication errors in cells overexpressing tripeptidyl-peptidase II.

  2005cited by this paper
• Analysis of the cytogenetic stability of the human embryonal kidney cell line 293 by cytogenetic and STR profiling approaches

  2004cited by this paper
• Strategic Attack on Host Cell Gene Expression during Adenovirus Infection

  2003cited by this paper
• Genetic content and evolution of adenoviruses.

  2003cited by this paper
• Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells

  2002cited by this paper
• Viral homologs of BCL-2: role of apoptosis in the regulation of virus infection.

  2002cited by this paper
• Cloning and sequencing of the cellular-viral junctions from the human adenovirus type 5 transformed 293 cell line.

  1997influential reference
• Viral transactivating proteins.

  1997cited by this paper
• Cooperation of Stat2 and p300/CBP in signalling induced by interferon-α

  1996cited by this paper
• Improvements in the Epstein-Barr-based shuttle vector system for direct cloning in human tissue culture cells

  1992cited by this paper
• The sequence of the genome of adenovirus type 5 and its comparison with the genome of adenovirus type 2.

  1992cited by this paper
• Transcription of interferon-stimulated genes is induced by adenovirus particles but is suppressed by E1A gene products

  1988cited by this paper
• Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system

  1987cited by this paper
• Multiple functional domains in the adenovirus E1A gene.

  1987cited by this paper
• Characteristics of a human cell line transformed by DNA from human adenovirus type 5.

  1977cited by this paper
• A new technique for the assay of infectivity of human adenovirus 5 DNA.

  1973cited by this paper
• Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features

  year unknowncited by this paper

• Comparative Analysis of HEK293 Genomic Variability

  2025cites this paper