Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Yao-Cheng Lin (), Morgane Boone, Leander Meuris, Irma Lemmens, Nadine Van Roy, Arne Soete, Joke Reumers, Matthieu Moisse, Stéphane Plaisance, Radoje Drmanac, Jason Chen, Frank Speleman, Diether Lambrechts, Yves Van de Peer, Jan Tavernier () and Nico Callewaert ()
Additional contact information
Yao-Cheng Lin: VIB
Morgane Boone: Unit for Medical Biotechnology, Inflammation Research Center, VIB
Leander Meuris: Unit for Medical Biotechnology, Inflammation Research Center, VIB
Irma Lemmens: VIB
Nadine Van Roy: Center for Medical Genetics, Ghent University Hospital (MRB)
Arne Soete: Bioinformatics Core Facility, Inflammation Research Center, VIB
Joke Reumers: Laboratory for Translational Genetics
Matthieu Moisse: Laboratory for Translational Genetics
Stéphane Plaisance: VIB BioInformatics Training and Services (BITS)
Radoje Drmanac: Complete Genomics Inc.
Jason Chen: Complete Genomics Inc.
Frank Speleman: Center for Medical Genetics, Ghent University Hospital (MRB)
Diether Lambrechts: Laboratory for Translational Genetics
Yves Van de Peer: VIB
Jan Tavernier: VIB
Nico Callewaert: Unit for Medical Biotechnology, Inflammation Research Center, VIB

Nature Communications, 2014, vol. 5, issue 1, 1-12

Abstract: Abstract The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.

Date: 2014
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DOI: 10.1038/ncomms5767

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