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BMC Genomics. 2012 Sep 14;13:477. doi: 10.1186/1471-2164-13-477.

In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing.

Author information

  • 1Department of Neurology, University of California San Francisco, San Francisco, CA 94143-0435, USA.

Abstract

BACKGROUND:

A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject's DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach.

RESULTS:

We used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels).

CONCLUSIONS:

Our results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias.

PMID:
22974163
[PubMed - indexed for MEDLINE]
PMCID:
PMC3473256
Free PMC Article

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