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Review
. 2015 Mar 9;4(6):1-6.
doi: 10.4161/2159256X.2014.992694. eCollection 2014 Nov-Dec.

Applications of DNA integrating elements: Facing the bias bully

Johann de Jong  1 , Lodewyk F A Wessels  2 , Maarten van Lohuizen  3 , Jeroen de Ridder  4 , Waseem Akhtar  3
Affiliations
Review

Applications of DNA integrating elements: Facing the bias bully

Johann de Jong et al. Mob Genet Elements. .

Abstract

Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed.

Keywords: chromatin position effect; epigenomics; gene therapy; insertional mutagenesis; integration bias.

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Figures

Figure 1.
Figure 1.
Schematic overview of integration bias with respect to genes for 4 different DNA integrating elements. Adapted from.
Figure 2.
Figure 2.
Integration bias can give rise to spurious Common Integration Sites (CISs). Hypothetical integration profile of a tumor screen ("Selected" in blue) and corresponding unselected background integrations ("Unselected" in red). In a typical effort for retrieving cancer genes from an IM screen, a genomic region is called as a CIS if the local integration density exceeds a certain threshold ("CIS threshold;" black dotted line). However, some of these regions may also reflect an a priori integration bias.
Figure 3.
Figure 3.
Integration bias reduces statistical power in TRIP applications. 104 integrations were generated in silico, and distributed across 2 classes (Class 1 and Class 2) in an increasingly uneven fashion. Depending on the assigned class, reporter gene expression was simulated by drawing from a class-specific distribution. Then, (A) the significance of the difference between the 2 classes was determined by Welch's t-test as a function of the size of Class 2 (dashed gray line: 2-sided 5% significance threshold; red solid line: theoretical expected value of the z-normalized t-statistic), and (B) the effect size was determined as the difference in means between the 2 classes as a function of the size of Class 2 (red solid lines: theoretical expected value and standard deviation of the sample distribution of the difference). The x-axis represents the size of Class 2, which indicates how uneven the distribution across the 2 classes is.
Figure 4.
Figure 4.
Bias for genic regions of 3 DNA integrating elements. (A) For 3 DNA integration elements , integrations were counted within and outside 5kb from genes, and p-values were determined by 2-sided binomial tests. (B) For comparison, the same analysis was done for 3 sets of matched random controls. Refer to for a detailed description of how these controls were generated.
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References

    1. Kaufmann KB, Buening H, Galy A, Schambach A, Grez M. Gene therapy on the move. EMBO Mol Med 2013; 5(11):1642-61; PMID:24106209 - PMC - PubMed
    1. Bouwman P, Aly A, Escandell JM, Pieterse M, Bartkova J, van der Gulden H, Hiddingh S, Thanasoula M, Kulkarni A, Yang Q, et al. . 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct & Mol Biol 2010; 17:688-95; PMID:20453858; http://dx.doi.org/10.1038/nsmb.1831 - DOI - PMC - PubMed
    1. Miller EH, Obernosterer G, Raaben M, Herbert AS, Deffieu MS, Krishnan A, Ndungo E, Sandesara RG, Carette JE, Kuehne AI, et al. . Ebola virus entry requires the host-programmed recognition of an intracellular receptor. EMBO J 2012; 31(8):1947-60; PMID:22395071; doi:10.1038/emboj.2012.53 - DOI - PMC - PubMed
    1. Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, et al. . Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res 2010; 70:520-31; PMID:20068150; http://dx.doi.org/10.1158/0008-5472.CAN-09-2736 - DOI - PMC - PubMed
    1. Mattison J, Kool J, Uren AG, de Ridder J, Wessels L, Jonkers J, Bignell GR, Butler A, Rust AG, Brosch M, et al. . Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach. Cancer Res 2010; 70:883-95; PMID:20103622; http://dx.doi.org/10.1158/0008-5472.CAN-09-1737 - DOI - PMC - PubMed

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