. Pierce and J. Bennett, The status of RPE65 gene therapy trials: safety and efficacy, Cold Spring Harb Perspect Med, vol.5, p.9, 2015.
DOI : 10.1101/cshperspect.a017285
URL : http://perspectivesinmedicine.cshlp.org/content/5/9/a017285.full.pdf

A. Nathwani, . Tuddenham, . Eg, S. Rangarajan, C. Rosales et al., Adenovirus-Associated Virus Vector???Mediated Gene Transfer in Hemophilia B, New England Journal of Medicine, vol.365, issue.25, pp.2357-2365, 2011.
DOI : 10.1056/NEJMoa1108046
URL : http://europepmc.org/articles/pmc3265081?pdf=render

K. Gao, M. Li, L. Zhong, Q. Su, J. Li et al., Empty virions in AAV8 vector preparations reduce transduction efficiency and may cause total viral particle dose-limiting side effects, Molecular Therapy - Methods & Clinical Development, vol.1, p.20139, 2014.
DOI : 10.1038/mtm.2013.9
URL : https://doi.org/10.1038/mtm.2013.9

J. Allen, . Debelak, R. Dj, . Miller, and . Ad, Identification and elimination of replication-competent adeno-associated virus (AAV) that can arise by nonhomologous recombination during AAV vector production, J Virol, vol.71, pp.6816-6822, 1997.

B. Dong, X. Duan, H. Chow, L. Chen, H. Lu et al., Proteomics Analysis of Co-Purifying Cellular Proteins Associated with rAAV Vectors, PLoS ONE, vol.10, issue.2, p.86453, 2014.
DOI : 10.1371/journal.pone.0086453.s002
URL : https://doi.org/10.1371/journal.pone.0086453

J. Allay, S. Sleep, S. Long, . Tillman, . Dm et al., Good Manufacturing Practice Production of Self-Complementary Serotype 8 Adeno-Associated Viral Vector for a Hemophilia B Clinical Trial, Human Gene Therapy, vol.22, issue.5, pp.595-604, 2011.
DOI : 10.1089/hum.2010.202
URL : http://europepmc.org/articles/pmc3081439?pdf=render

G. Ye, . Scotti, . Mm, J. Liu, L. Wang et al., Clearance and characterization of residual HSV DNA in recombinant adeno-associated virus produced by an HSV complementation system, Gene Therapy, vol.33, issue.2, pp.135-144, 2011.
DOI : 10.1073/pnas.55.6.1467
URL : http://www.nature.com/gt/journal/v18/n2/pdf/gt2010102a.pdf

A. Martino, M. Suzuki, . Markusic, . Dm, I. Zolotukhin et al., The genome of self-complementary adeno-associated viral vectors increases Toll-like receptor 9-dependent innate immune responses in the liver, Blood, vol.117, issue.24, pp.6459-6468, 2011.
DOI : 10.1182/blood-2010-10-314518

S. Faust, P. Bell, . Cutler, . Bj, . Ashley et al., CpG-depleted adeno-associated virus vectors evade immune detection, Journal of Clinical Investigation, vol.123, issue.7, pp.2994-3001, 2013.
DOI : 10.1172/JCI68205
URL : http://www.jci.org/articles/view/68205/files/pdf

. Fda-briefing and . Document, Cell Lines Derived from Human Tumors for Vaccine Manufacture

G. Chadeuf, C. Ciron, . Moullier, and A. Salvetti, Evidence for Encapsidation of Prokaryotic Sequences during Recombinant Adeno-Associated Virus Production and Their in Vivo Persistence after Vector Delivery, Molecular Therapy, vol.12, issue.4, pp.744-753, 2005.
DOI : 10.1016/j.ymthe.2005.06.003

J. Wright and O. Zelenaia, Vector Characterization Methods for Quality Control Testing of Recombinant Adeno-Associated Viruses, Methods Mol Biol, vol.737, pp.247-278, 2011.
DOI : 10.1007/978-1-61779-095-9_11

Y. Noordman, . Lubelski, . Bakker, and . Ac, Mutated rep encoding sequences for use in AAV production, 2013.

P. Nony, G. Chadeuf, J. Tessier, . Moullier, and A. Salvetti, Evidence for Packaging of rep-cap Sequences into Adeno-Associated Virus (AAV) Type 2 Capsids in the Absence of Inverted Terminal Repeats: a Model for Generation of rep-Positive AAV Particles, Journal of Virology, vol.77, issue.1, pp.776-781, 2003.
DOI : 10.1128/JVI.77.1.776-781.2003

B. Hauck, . Murphy, . Sl, . Smith, G. Qu et al., Undetectable Transcription of cap in a Clinical AAV Vector: Implications for Preformed Capsid in Immune Responses, Molecular Therapy, vol.17, issue.1, pp.144-152, 2009.
DOI : 10.1038/mt.2008.227

H. Lu, G. Qu, X. Yang, . Xu, and W. Xiao, Capsid Protein Synthesis from Replication-Competent AAV Contamination in the Liver, Human Gene Therapy, vol.22, issue.5, pp.625-632, 2011.
DOI : 10.1089/hum.2011.005
URL : http://europepmc.org/articles/pmc3081442?pdf=render

P. Kapranov, L. Chen, D. Dederich, B. Dong, J. He et al., Native Molecular State of Adeno-Associated Viral Vectors Revealed by Single-Molecule Sequencing, Human Gene Therapy, vol.23, issue.1, pp.46-55, 2012.
DOI : 10.1089/hum.2011.160
URL : http://europepmc.org/articles/pmc3260442?pdf=render

Y. Wang, C. Ling, L. Song, L. Wang, . Aslanidi et al., Limitations of Encapsidation of Recombinant Self-Complementary Adeno-Associated Viral Genomes in Different Serotype Capsids and Their Quantitation, Human Gene Therapy Methods, vol.23, issue.4, pp.225-233, 2012.
DOI : 10.1089/hgtb.2012.090

L. Bryant, . Christopher, . Dm, A. Giles, C. Hinderer et al., Lessons Learned from the Clinical Development and Market Authorization of Glybera, Human Gene Therapy Clinical Development, vol.24, issue.2, pp.55-64, 2013.
DOI : 10.1089/humc.2013.087
URL : http://europepmc.org/articles/pmc3992977?pdf=render

E. Ayuso, V. Blouin, M. Lock, S. Mcgorray, X. Leon et al., Manufacturing and Characterization of a Recombinant Adeno-Associated Virus Type 8 Reference Standard Material, Human Gene Therapy, vol.25, issue.11, pp.977-987, 2014.
DOI : 10.1089/hum.2014.057
URL : http://europepmc.org/articles/pmc4236062?pdf=render

N. Louis, . Evelegh, and F. Graham, Cloning and Sequencing of the Cellular???Viral Junctions from the Human Adenovirus Type 5 Transformed 293 Cell Line, Virology, vol.233, issue.2, pp.423-429, 1997.
DOI : 10.1006/viro.1997.8597

T. Nicholls and M. Minczuk, In D-loop: 40years of mitochondrial 7S DNA, Experimental Gerontology, vol.56, pp.175-181, 2014.
DOI : 10.1016/j.exger.2014.03.027

J. Aiken, J. Williamson, . Borchardt, . Lm, and . Marsh, Presence of mitochondrial D-loop DNA in scrapie-infected brain preparations enriched for the prion protein, J Virol, vol.64, pp.3265-3268, 1990.

A. European-medicines, Glybera : EPAR -Public assessment report, 2012.

J. Wilson, A call to arms for improved vector analytics! Hum, Gene Ther Methods, vol.26, pp.1-2, 2015.
DOI : 10.1089/hgtb.2015.1502

D. Gavin, FDA Statement Regarding the Use of Adeno-Associated Virus Reference Standard Materials, Human Gene Therapy Methods, vol.26, issue.1, p.3, 2015.
DOI : 10.1089/hgtb.2015.1501

M. Strong, G. Xu, L. Morici, S. Bon-durant, S. Baddoo et al., Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples, PLoS Pathogens, vol.111, issue.11, p.1004437, 2014.
DOI : 10.1371/journal.ppat.1004437.s012
URL : https://doi.org/10.1371/journal.ppat.1004437

M. Laurence, . Hatzis, . Brash, and . De, Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes, PLoS ONE, vol.8, issue.5, p.97876, 2014.
DOI : 10.1371/journal.pone.0097876.s012
URL : https://doi.org/10.1371/journal.pone.0097876

D. Aird, . Ross, . Mg, . Chen, . Ws et al., Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries, Genome Biology, vol.12, issue.2, p.18, 2011.
DOI : 10.1093/bioinformatics/btp324
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2011-12-2-r18?site=genomebiology.biomedcentral.com

B. Cogné, R. Snyder, P. Lindenbaum, J. Dupont, R. Redon et al., NGS library preparation may generate artifactual integration sites of AAV vectors, Nature Medicine, vol.19, issue.6, pp.577-578, 2014.
DOI : 10.1016/j.jmoldx.2011.01.006

B. Thorne, . Takeya, . Rk, and R. Peluso, Manufacturing Recombinant Adeno-Associated Viral Vectors from Producer Cell Clones, Human Gene Therapy, vol.20, issue.7, pp.707-714, 2009.
DOI : 10.1089/hum.2009.070

. Smith, . Levy, and R. Kotin, A Simplified Baculovirus-AAV Expression Vector System Coupled With One-step Affinity Purification Yields High-titer rAAV Stocks From Insect Cells, Molecular Therapy, vol.17, issue.11, pp.1888-1896, 2009.
DOI : 10.1038/mt.2009.128
URL : https://doi.org/10.1038/mt.2009.128

E. Ayuso, F. Mingozzi, J. Montane, X. Leon, . Anguela et al., High AAV vector purity results in serotype- and tissue-independent enhancement of transduction efficiency, Gene Therapy, vol.17, issue.4, pp.503-510, 2010.
DOI : 10.1182/blood-2007-03-080093
URL : http://www.nature.com/gt/journal/v17/n4/pdf/gt2009157a.pdf

I. Kozarewa and D. Turner, 96-Plex Molecular Barcoding for the Illumina Genome Analyzer, Methods Mol Biol, vol.733, pp.279-298, 2011.
DOI : 10.1007/978-1-61779-089-8_20