References
Aird, D., Ross, M.G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D.B., Nusbaum, C., Gnirke, A., 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18. https://doi.org/10.1186/gb-2011-12-2-r18
Al-Zaidy, S.A., Mendell, J.R., 2019. From Clinical Trials to Clinical Practice: Practical Considerations for Gene Replacement Therapy in SMA Type 1. Pediatr. Neurol. 100, 3–11. https://doi.org/10.1016/j.pediatrneurol.2019.06.007
Ayuso, E., Blouin, V., Lock, M., McGorray, S., Leon, X., Alvira, M.R., Auricchio, A., Bucher, S., Chtarto, A., Clark, K.R., Darmon, C., Doria, M., Fountain, W., Gao, G., Gao, K., Giacca, M., Kleinschmidt, J., Leuchs, B., Melas, C., Mizukami, H., Müller, M., Noordman, Y., Bockstael, O., Ozawa, K., Pythoud, C., Sumaroka, M., Surosky, R., Tenenbaum, L., van der Linden, I., Weins, B., Wright, J.F., Zhang, X., Zentilin, L., Bosch, F., Snyder, R.O., Moullier, P., 2014. Manufacturing and characterization of a recombinant adeno-associated virus type 8 reference standard material. Hum. Gene Ther. 25, 977–987. https://doi.org/10.1089/hum.2014.057
Ayuso, E., Mingozzi, F., Montane, J., Leon, X., Anguela, X.M., Haurigot, V., Edmonson, S.A., Africa, L., Zhou, S., High, K.A., Bosch, F., Wright, J.F., 2010. High AAV vector purity results in serotype- and tissue-independent enhancement of transduction efficiency. Gene Ther. 17, 503–510. https://doi.org/10.1038/gt.2009.157
Beier, S., Thiel, T., Münch, T., Scholz, U., Mascher, M., 2017. MISA-web: a web server for microsatellite prediction. Bioinforma. Oxf. Engl. 33, 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Benjamini, Y., Speed, T.P., 2012. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 40, e72. https://doi.org/10.1093/nar/gks001
Breton, C., Clark, P.M., Wang, L., Greig, J.A., Wilson, J.M., 2020. ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing. BMC Genomics 21, 239. https://doi.org/10.1186/s12864-020-6655-4
Crudele, J.M., Chamberlain, J.S., 2019. AAV-based gene therapies for the muscular dystrophies. Hum. Mol. Genet. 28, R102–R107. https://doi.org/10.1093/hmg/ddz128
D’Costa, S., Blouin, V., Broucque, F., Penaud-Budloo, M., François, A., Perez, I.C., Le Bec, C., Moullier, P., Snyder, R.O., Ayuso, E., 2016. Practical utilization of recombinant AAV vector reference standards: focus on vector genomes titration by free ITR qPCR. Mol. Ther. Methods Clin. Dev. 5, 16019. https://doi.org/10.1038/mtm.2016.19
Dohm, J.C., Lottaz, C., Borodina, T., Himmelbauer, H., 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105. https://doi.org/10.1093/nar/gkn425
Dorange, F, Le Bec, C, 2018. Analytical approaches to characterize AAV vector production & purification: Advances and challenges. Cell Gene Ther. Insights 4, 119–129. https://doi.org/10.18609/cgti.2018.015
Fazekas, A., Steeves, R., Newmaster, S., 2010. Improving sequencing quality from PCR products containing long mononucleotide repeats. BioTechniques 48, 277–285. https://doi.org/10.2144/000113369
Food and Drug Administration, 2012. Cell lines derived from human tumors for vaccine manufacture. Vaccines and related biological product advisory committee meeting. Available online: http://www.nvic.org/cmstemplates/nvic/pdf/fda/fda-briefing-09192012.pdf.
Grimm, D., Kern, A., Rittner, K., Kleinschmidt, J.A., 1998. Novel tools for production and purification of recombinant adenoassociated virus vectors. Hum. Gene Ther. 9, 2745–2760. https://doi.org/10.1089/hum.1998.9.18-2745
Guerin, K., Rego, M., Bourges, D., Ersing, I., Haery, L., Harten DeMaio, K., Sanders, E., Tasissa, M., Kostman, M., Tillgren, M., Makana Hanley, L., Mueller, I., Mitsopoulos, A., Fan, M., 2020. A Novel Next-Generation Sequencing and Analysis Platform to Assess the Identity of Recombinant Adeno-Associated Viral Preparations from Viral DNA Extracts. Hum. Gene Ther. https://doi.org/10.1089/hum.2019.277
Kondratov, O., Marsic, D., Crosson, S.M., Mendez-Gomez, H.R., Moskalenko, O., Mietzsch, M., Heilbronn, R., Allison, J.R., Green, K.B., Agbandje-McKenna, M., Zolotukhin, S., 2017. Direct Head-to-Head Evaluation of Recombinant Adeno-associated Viral Vectors Manufactured in Human versus Insect Cells. Mol. Ther. J. Am. Soc. Gene Ther. https://doi.org/10.1016/j.ymthe.2017.08.003
Kozarewa, I., Ning, Z., Quail, M.A., Sanders, M.J., Berriman, M., Turner, D.J., 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6, 291–295. https://doi.org/10.1038/nmeth.1311
Lecomte, E., Leger, A., Penaud-Budloo, M., Ayuso, E., 2019. Single-Stranded DNA Virus Sequencing (SSV-Seq) for Characterization of Residual DNA and AAV Vector Genomes. Methods Mol. Biol. Clifton NJ 1950, 85–106. https://doi.org/10.1007/978-1-4939-9139-6_5
Lecomte, E., Tournaire, B., Cogné, B., Dupont, J.-B., Lindenbaum, P., Martin-Fontaine, M., Broucque, F., Robin, C., Hebben, M., Merten, O.-W., Blouin, V., François, A., Redon, R., Moullier, P., Léger, A., 2015. Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing. Mol. Ther. Nucleic Acids 4, e260. https://doi.org/10.1038/mtna.2015.32
Maynard, L.H., Smith, O., Tilmans, N.P., Tham, E., Hosseinzadeh, S., Tan, W., Leenay, R., May, A.P., Paulk, N.K., 2019. Fast-Seq, a simple method for rapid and inexpensive validation of packaged ssAAV genomes in academic settings. Hum. Gene Ther. Methods. https://doi.org/10.1089/hum.2019.110
Oyola, S.O., Otto, T.D., Gu, Y., Maslen, G., Manske, M., Campino, S., Turner, D.J., Macinnis, B., Kwiatkowski, D.P., Swerdlow, H.P., Quail, M.A., 2012. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13, 1. https://doi.org/10.1186/1471-2164-13-1
Penaud-Budloo, M., François, A., Clément, N., Ayuso, E., 2018a. Pharmacology of Recombinant Adeno-associated Virus Production. Mol. Ther. - Methods Clin. Dev. 8, 166–180. https://doi.org/10.1016/j.omtm.2018.01.002
Penaud-Budloo, M., François, A., Clément, N., Ayuso, E., 2018b. Pharmacology of Recombinant Adeno-associated Virus Production. Mol. Ther. - Methods Clin. Dev. 8, 166–180. https://doi.org/10.1016/j.omtm.2018.01.002
Penaud-Budloo, M., Lecomte, E., Guy-Duché, A., Saleun, S., Roulet, A., Lopez-Roques, C., Tournaire, B., Cogné, B., Léger, A., Blouin, V., Lindenbaum, P., Moullier, P., Ayuso, E., 2017. Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells. Hum. Gene Ther. Methods 28, 148–162. https://doi.org/10.1089/hgtb.2016.185
Quail, M.A., Otto, T.D., Gu, Y., Harris, S.R., Skelly, T.F., McQuillan, J.A., Swerdlow, H.P., Oyola, S.O., 2011. Optimal enzymes for amplifying sequencing libraries. Nat. Methods 9, 10–11. https://doi.org/10.1038/nmeth.1814
Radukic, M.T., Brandt, D., Haak, M., Müller, K.M., Kalinowski, J., 2019. Nanopore sequencing of native adeno-associated virus single-stranded DNA using a transposase-based rapid protocol. bioRxiv 2019.12.27.885319. https://doi.org/10.1101/2019.12.27.885319
Ross, M.G., Russ, C., Costello, M., Hollinger, A., Lennon, N.J., Hegarty, R., Nusbaum, C., Jaffe, D.B., 2013. Characterizing and measuring bias in sequence data. Genome Biol. 14, R51. https://doi.org/10.1186/gb-2013-14-5-r51
Samulski, R.J., Chang, L.S., Shenk, T., 1987. A recombinant plasmid from which an infectious adeno-associated virus genome can be excised in vitro and its use to study viral replication. J. Virol. 61, 3096–3101.
Shin, S., Park, J., 2016. Characterization of sequence-specific errors in various next-generation sequencing systems. Mol. Biosyst. 12, 914–922. https://doi.org/10.1039/c5mb00750j
Tai, P.W.L., Xie, J., Fong, K., Seetin, M., Heiner, C., Su, Q., Weiand, M., Wilmot, D., Zapp, M.L., Gao, G., 2018. Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras. Mol. Ther. Methods Clin. Dev. 9, 130–141. https://doi.org/10.1016/j.omtm.2018.02.002
Van den Hoecke, S., Verhelst, J., Saelens, X., 2016. Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene. Sci. Rep. 6, 26314. https://doi.org/10.1038/srep26314
van Dijk, E.L., Jaszczyszyn, Y., Thermes, C., 2014. Library preparation methods for next-generation sequencing: tone down the bias. Exp. Cell Res. 322, 12–20. https://doi.org/10.1016/j.yexcr.2014.01.008
Wright, J.F., 2014. Product-Related Impurities in Clinical-Grade Recombinant AAV Vectors: Characterization and Risk Assessment. Biomedicines 2, 80–97. https://doi.org/10.3390/biomedicines2010080
Xie, J., Mao, Q., Tai, P.W.L., He, R., Ai, J., Su, Q., Zhu, Y., Ma, H., Li, J., Gong, S., Wang, D., Gao, Z., Li, M., Zhong, L., Zhou, H., Gao, G., 2017. Short DNA Hairpins Compromise Recombinant Adeno-Associated Virus Genome Homogeneity. Mol. Ther. J. Am. Soc. Gene Ther. 25, 1363–1374. https://doi.org/10.1016/j.ymthe.2017.03.028