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Open Access Highly Accessed Research article

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

Dorothee Nickles1, Lohith Madireddy1, Shan Yang2, Pouya Khankhanian1, Steve Lincoln2, Stephen L Hauser1, Jorge R Oksenberg1 and Sergio E Baranzini1*

Author affiliations

1 Department of Neurology, University of California San Francisco, 513 Parnassus Ave, Room S-256, San Francisco, CA, 94143-0435, USA

2 Complete Genomics, Inc, Mountain View, CA, USA

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Citation and License

BMC Genomics 2012, 13:477  doi:10.1186/1471-2164-13-477

Published: 14 September 2012

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.

Keywords:
Next generation sequencing; EBV transformation; Lymphoblastoid cell line; Genetics