The Genomic and Transcriptomic Landscape of a HeLa Cell Line

HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology. Copyright Landry et al., "The Genomic and Transcriptomic Landscape of a HeLa Cell Line," G3: Genes | Genomes | Genetics (2013).

• Study Design:
  • Case Set
• Study Type:
  • Whole Genome Sequencing
• Total number of consented subjects: 1
• Subject Sample Telemetry Report (SSTR)

• Primary Phenotype: Uterine Cervical Neoplasms

• Principal Investigators
  • Lars M. Steinmetz. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Wolfgang Huber. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Jan O. Korbel. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
• Corresponding Investigators
  • Lars M. Steinmetz. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Wolfgang Huber. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
• Lead Investigators
  • Jonathan J. M. Landry. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Paul Theodor Pyl. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
• Other Investigators
  • Tobias Rausch. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Thomas Zichner. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Manu M. Tekkedil. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Adrian M. Stütz. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Anna Jauch. University Hospital Heidelberg, Institute of Human Genetics, 69120 Heidelberg, Germany.
  • Raeka S. Aiyar. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Gregoire Pau. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Nicolas Delhomme. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
  • Julien Gagneur. EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
• Funding Source
  • Lars M. Steinmetz (PI). University of Luxembourg - Institute for Systems Biology Program, Luxembourg, Luxembourg.