AbelU., DeichmannA., BartholomaeC., et al. (2007). Real-time definition of non-randomness in the distribution of genomic events. PLoS One, 2, e570.
2.
AbelU., DeichmannA., NowrouziA., et al. (2011). Analyzing the number of common integration sites of viral vectors—new methods and computer programs. PLoS One, 6, e24247.
3.
AiutiA., CassaniB., AndolfiG., et al. (2007). Multilineage hematopoietic reconstitution without clonal selection in ADA-SCID patients treated with stem cell gene therapy. J. Clin. Invest., 117, 2233–2240.
4.
AiutiA., BiascoL., ScaramuzzaS., et al. (2013). Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome. Science, 341, 1233151.
5.
AppeltJ.U., GiordanoF.A., EckerM., et al. (2009). QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis. Gene Ther., 16, 885–893.
Avedillo DíezI., ZychlinskiD., CociE.G., et al. (2011). Development of novel efficient SIN vectors with improved safety features for Wiskott–Aldrich syndrome stem cell based gene therapy. Mol. Pharm., 8, 1525–1537.
8.
BerryC.C., GilletN.A., MelamedA., et al. (2012). Estimating abundances of retroviral insertion sites from DNA fragment length data. Bioinformatics, 28, 755–762.
9.
BesterA.C., SchwartzM., SchmidtM., et al. (2006). Fragile sites are preferential targets for integrations of MLV vectors in gene therapy. Gene Ther., 13, 1057–1059.
BoztugK., SchmidtM., SchwarzerA., et al. (2010). Stem-cell gene therapy for the Wiskott–Aldrich syndrome. N. Engl. J. Med., 363, 1918–1927.
12.
BraunC.J., BoztugK., ParuzynskiA., et al. (2014). Gene therapy for Wiskott-Aldrich syndrome—long-term efficacy and genotoxicity. Sci. Transl. Med., 6, 227ra33.
13.
BushmanF.D. (2003). Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell, 115, 135–138.
14.
CalmelsB., FergusonC., LaukkanenM.O., et al. (2005). Recurrent retroviral vector integration at the Mds1/Evi1 locus in nonhuman primate hematopoietic cells. Blood, 106, 2530–2533.
15.
CartierN., Hacein-Bey-AbinaS., BartholomaeC.C., et al. (2009). Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy. Science, 326, 818–823.
16.
CattoglioC., FacchiniG., SartoriD., et al. (2007). Hot spots of retroviral integration in human CD34+ hematopoietic cells. Blood, 110, 1770–1778.
17.
Cavazzana-CalvoM., Hacein-BeyS., De Saint BasileG., et al. (2000). Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease. Science, 288, 669–672.
18.
CiuffiA., LlanoM., PoeschlaE., et al. (2005). A role for LEDGF/p75 in targeting HIV DNA integration. Nat. Med., 11, 1287–1289.
19.
CollasP., HusebyeH., and AlestromP. (1996). The nuclear localization sequence of the SV40 T antigen promotes transgene uptake and expression in zebrafish embryo nuclei. Transgenic Res., 5, 451–458.
20.
DeichmannA., Hacein-Bey-AbinaS., SchmidtM., et al. (2007). Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. J. Clin. Invest., 117, 2225–2232.
21.
De RidderJ., UrenA., KoolJ., et al. (2006). Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. PLoS Comput. Biol., 2, e166.
22.
De RijckJ., De KogelC., DemeulemeesterJ., et al. (2013). The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. Cell Rep., 5, 886–894.
23.
DillooD., RillD.R., GrossmannM.E., et al. (1996). Gene marking and gene therapy for transplantation medicine. J. Hematother., 5, 553–555.
24.
GabrielR., EckenbergR., ParuzynskiA., et al. (2009). Comprehensive genomic access to vector integration in clinical gene therapy. Nat. Med., 15, 1431–1436.
25.
GabrielR., LombardoA., ArensA., et al. (2011). An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol., 29, 816–823.
26.
GasparH.B., ParsleyK.L., HoweS., et al. (2004). Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. Lancet, 364, 2181–2187.
27.
GlimmH., SchmidtM., FischerM., et al. (2005). Efficient marking of human cells with rapid but transient repopulating activity in autografted recipients. Blood, 106, 893–898.
28.
GuenecheaG., GanO.I., DorrellC., and DickJ.E. (2001). Distinct classes of human stem cells that differ in proliferative and self-renewal potential. Nat. Immunol., 2, 75–82.
29.
Hacein-Bey-AbinaS., Von KalleC., SchmidtM., et al. (2003a). A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N. Engl. J. Med., 348, 255–256.
30.
Hacein-Bey-AbinaS., Von KalleC., SchmidtM., et al. (2003b). LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science, 302, 415–419.
31.
Hacein-Bey-AbinaS., GarrigueA., WangG.P., et al. (2008). Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J. Clin. Invest., 118, 3132–3142.
32.
HemattiP., HongB.K., FergusonC., et al. (2004). Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells. PLoS Biol., 2, e423.
33.
HoweS.J., MansourM.R., SchwarzwaelderK., et al. (2008a). Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients. J. Clin. Invest., 118, 3143–3150.
34.
InagakiK., LewisS.M., WuX., et al. (2007). DNA palindromes with a modest arm length of greater, similar 20 base pairs are a significant target for recombinant adeno-associated virus vector integration in the liver, muscles, and heart in mice. J. Virol., 81, 11290–11303.
35.
KaeppelC., BeattieS.G., FronzaR., et al. (2013). A largely random AAV integration profile after LPLD gene therapy. Nat. Med., 19, 889–891.
36.
KohnD.B. (1997). Gene therapy for haematopoietic and lymphoid disorders. Clin. Exp. Immunol., 107Suppl 1, 54–57.
37.
KohnD.B., HershfieldM.S., CarbonaroD., et al. (1998). T lymphocytes with a normal ADA gene accumulate after transplantation of transduced autologous umbilical cord blood CD34+ cells in ADA-deficient SCID neonates. Nat. Med., 4, 775–780.
38.
LaufsS., GentnerB., NagyK.Z., et al. (2003). Retroviral vector integration occurs in preferred genomic targets of human bone marrow-repopulating cells. Blood, 101, 2191–2198.
39.
LemischkaI.R., and JordanC.T. (2001). The return of clonal marking sheds new light on human hematopoietic stem cells. Nat. Immunol., 2, 11–12.
40.
LiZ., DuellmannF., SchiedlmeierB., et al. (2002). Murine leukemia induced by retroviral gene marking. Science, 296, 497.
41.
LiH., MalaniN., HamiltonS.R., et al. (2011). Assessing the potential for AAV vector genotoxicity in a murine model. Blood, 117, 3311–3319.
42.
MitchellR.S., BeitzelB.F., SchroderA.R., et al. (2004). Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol., 2, E234.
43.
MuellerP.R., and WoldB. (1989). In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science, 246, 780–786.
44.
MullisK., FaloonaF., ScharfS., et al. (1986). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol., 51Pt 1, 263–273.
45.
NakaiH., MontiniE., FuessS., et al. (2003). AAV serotype 2 vectors preferentially integrate into active genes in mice. Nat. Genet., 34, 297–302.
46.
NoltaJ.A., DaoM.A., WellsS., et al. (1996). Transduction of pluripotent human hematopoietic stem cells demonstrated by clonal analysis after engraftment in immune-deficient mice. Proc. Natl. Acad. Sci. USA, 93, 2414–2419.
47.
NowrouziA., Penaud-BudlooM., KaeppelC., et al. (2012). Integration frequency and intermolecular recombination of rAAV vectors in non-human primate skeletal muscle and liver. Mol. Ther., 20, 1177–1186.
48.
OkouD.T., SteinbergK.M., MiddleC., et al. (2007). Microarray-based genomic selection for high-throughput resequencing. Nat. Methods, 4, 907–909.
49.
OttM.G., SchmidtM., SchwarzwaelderK., et al. (2006). Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1. Nat. Med., 12, 401–409.
50.
ParuzynskiA., ArensA., GabrielR., et al. (2010). Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat. Protoc., 5, 1379–1395.
51.
PetersB., DirscherlS., DantzerJ., et al. (2008). Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. Gene Ther., 15, 1294–1298.
52.
PfeiferG.P., SteigerwaldS.D., MuellerP.R., et al. (1989). Genomic sequencing and methylation analysis by ligation mediated PCR. Science, 246, 810–813.
53.
PopescuN.C. (2003). Genetic alterations in cancer as a result of breakage at fragile sites. Cancer Lett., 192, 1–17.
54.
PorrecaG.J., ZhangK., LiJ.B., et al. (2007). Multiplex amplification of large sets of human exons. Nat. Methods, 4, 931–936.
55.
RecchiaA., BoniniC., MagnaniZ., et al. (2006). Retroviral vector integration deregulates gene expression but has no consequence on the biology and function of transplanted T cells. Proc. Natl. Acad. Sci. USA, 103, 1457–1462.
56.
RosenbergS.A., BlaeseR.M., BrennerM.K., et al. (1997). Human gene marker/therapy clinical protocols. Hum. Gene Ther., 8, 2301–2338.
57.
SaikiR.K., GelfandD.H., StoffelS., et al. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487–491.
58.
ScherdinU., RhodesK., and BreindlM. (1990). Transcriptionally active genome regions are preferred targets for retrovirus integration. J. Virol., 64, 907–912.
59.
SchmidtM., ZicklerP., HoffmannG., et al. (2002). Polyclonal long-term repopulating stem cell clones in a primate model. Blood, 100, 2737–2743.
60.
SchmidtM., CarbonaroD.A., SpeckmannC., et al. (2003). Clonality analysis after retroviral-mediated gene transfer to CD34+ cells from the cord blood of ADA-deficient SCID neonates. Nat. Med., 9, 463–468.
61.
SchmidtM., Hacein-Bey-AbinaS., WisslerM., et al. (2005). Clonal evidence for the transduction of CD34+ cells with lymphomyeloid differentiation potential and self-renewal capacity in the SCID-X1 gene therapy trial. Blood, 105, 2699–2706.
62.
SchmidtM., SchwarzwaelderK., BartholomaeC., et al. (2007). High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR). Nat. Methods, 4, 1051–1057.
63.
SchroderA.R., ShinnP., ChenH., et al. (2002). HIV-1 integration in the human genome favors active genes and local hotspots. Cell, 110, 521–529.
64.
SchwarzwaelderK., HoweS.J., SchmidtM., et al. (2007). Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo. J. Clin. Invest., 117, 2241–2249.
65.
SilverJ., and KeerikatteV. (1989). Novel use of polymerase chain reaction to amplify cellular DNA adjacent to an integrated provirus. J. Virol., 63, 1924–1928.
66.
SteinS., OttM.G., Schultze-StrasserS., et al. (2010). Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat. Med., 16, 198–204.
67.
WangG.P., BerryC.C., MalaniN., et al. (2010). Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood, 115, 4356–4366.
68.
WaterstonR.H., LanderE.S., and SulstonJ.E. (2002). On the sequencing of the human genome. Proc. Natl. Acad. Sci. USA, 99, 3712–3716.
69.
WuX., LiY., CriseB., and BurgessS.M. (2003). Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1749–1751.
70.
YuH., KoilkondaR.D., ChouT.H., et al. (2012). Gene delivery to mitochondria by targeting modified adenoassociated virus suppresses Leber's hereditary optic neuropathy in a mouse model. Proc. Natl. Acad. Sci. USA, 109, E1238–E1247.