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Biomedicines 2014, 2(2), 195-210; doi:10.3390/biomedicines2020195
Article

Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing

1,†
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 and 1,5,6,*
Received: 25 September 2013; in revised form: 26 March 2014 / Accepted: 28 April 2014 / Published: 6 May 2014
(This article belongs to the Special Issue Feature Papers)
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Abstract: Integration of viral vectors into a host genome is associated with insertional mutagenesis and subjects in clinical gene therapy trials must be monitored for this adverse event. Several PCR based methods such as ligase-mediated (LM) PCR, linear-amplification-mediated (LAM) PCR and non-restrictive (nr) LAM PCR were developed to identify sites of vector integration. Coupling the power of next-generation sequencing technologies with various PCR approaches will provide a comprehensive and genome-wide profiling of insertion sites and increase throughput. In this bioinformatics study, we aimed to develop and apply quality metrics to viral insertion data obtained using next-generation sequencing. We developed five simple metrics for assessing next-generation sequencing data from different PCR products and showed how the metrics can be used to objectively compare runs performed with the same methodology as well as data generated using different PCR techniques. The results will help researchers troubleshoot complex methodologies, understand the quality of sequencing data, and provide a starting point for developing standardization of vector insertion site data analysis.
Keywords: viral insertion site; quality metrics; next-generating sequencing; integration site PCR viral insertion site; quality metrics; next-generating sequencing; integration site PCR
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Gao, H.; Hawkins, T.; Jasti, A.; Chen, Y.-H.; Mockaitis, K.; Dinauer, M.; Cornetta, K. Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing. Biomedicines 2014, 2, 195-210.

AMA Style

Gao H, Hawkins T, Jasti A, Chen Y-H, Mockaitis K, Dinauer M, Cornetta K. Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing. Biomedicines. 2014; 2(2):195-210.

Chicago/Turabian Style

Gao, Hongyu; Hawkins, Troy; Jasti, Aparna; Chen, Yu-Hsiang; Mockaitis, Keithanne; Dinauer, Mary; Cornetta, Kenneth. 2014. "Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing." Biomedicines 2, no. 2: 195-210.


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