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Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

Authors Joesch-Cohen LM, Glusman G

Received 27 November 2016

Accepted for publication 13 January 2017

Published 23 February 2017 Volume 2017:7 Pages 1—9

DOI https://doi.org/10.2147/AGG.S128824

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Amy Norman

Peer reviewer comments 2

Editor who approved publication: Dr John Martignetti

Lena M Joesch-Cohen, Gustavo Glusman

Institute for Systems Biology, Seattle, WA, USA

Abstract: Lymphoblastoid cell lines (LCLs) represent a convenient research tool for expanding the amount of biologic material available from an individual. LCLs are commonly used as reference materials, most notably from the Genome in a Bottle Consortium. However, the question remains how faithfully LCL-derived genome assemblies represent the germline genome of the donor individual as compared to the genome assemblies derived from peripheral blood mononuclear cells. We present an in-depth comparison of a large collection of LCL- and peripheral blood mononuclear cell-derived genomes in terms of distributions of coverage and copy number alterations. We found significant differences in the depth of coverage and copy number calls, which may be driven by differential replication timing. Importantly, these copy number changes preferentially affect regions closer to genes and with higher GC content. This suggests that genomic studies based on LCLs may display locus-specific biases, and that conclusions based on analysis of depth of coverage and copy number variation may require further scrutiny.

Keywords: genomics, whole-genome sequencing, viral transformation, copy number changes, bioinformatics

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