Estimating abundances of retroviral insertion sites from DNA fragment length data

Bioinformatics

Volumn 28, Issue 6, 2012, Pages 755-762

  Berry, Charles C ^a   Gillet, Nicolas A ^b   Melamed, Anat ^c   Gormley, Niall ^d   Bangham, Charles R M ^c   Bushman, Frederic D ^e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF LIÈGE   (Belgium)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d Illumina   (United Kingdom)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENETICS; HUMAN; HUMAN T CELL LEUKEMIA VIRUS 1; HUMAN T CELL LEUKEMIA VIRUS INFECTION; VIROLOGY; VIRUS DNA CELL DNA INTERACTION;

ALGORITHMS; HTLV-I INFECTIONS; HUMAN T-LYMPHOTROPIC VIRUS 1; HUMANS; VIRUS INTEGRATION;

EID: 84859054812     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts004     Document Type: Article

References (28)

1. Aird, D. et al. (2011) Analyzing and minimizing PCR amplification bias in illumina sequencing libraries. Genome Biol., 12, R18.
2. Baker, S. (1994) The multinomial-poisson transformation. Statistician, 43, 495-504.
3. Brady, T. et al. (2011) A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Res, 39, e72.
4. Cavazzana-Calvo, M. et al. (2010) Transfusion independence and hmga2 activation after gene therapy of human [bgr]-thalassaemia. Nature, 467, 318-322.
5. Chao, A. (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43, 783-791.
6. Chao, A. and Lee, S. (1992) Estimating the number of classes via sample coverage. J. Am. Stat. Assoc., 87, 210-217.
7. Chao, A. and Shen, T. (2003) Nonparametric estimation of Shannons index of diversity when there are unseen species in sample. Environ. Ecol. Stat., 10, 429-443.
8. De Boor, C. (2001) A Practical Guide to Splines, vol. 27. Springer, New York.
9. Deichmann, A. et al. (2007) Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in scid-x1 gene therapy. J. Clin. Investig., 117, 2232.
10. Dempster, A. et al. (1977) Maximum likelihood from incomplete data via the em algorithm. J. R. Stat. Soc. Ser. B, 39, 1-38.
11. Efron, B. (2004) Large-scale simultaneous hypothesis testing. J. Am. Stat. Assoc., 99, 96-104.
12. Feller, W. (1945) On the normal approximation to the binomial distribution. Ann. Math. Stat., 16, 319-329.
13. Finzi, D. et al. (1997) Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science, 278, 1300.
14. Gabriel, R. et al. (2009). Comprehensive genomic access to vector integration in clinical gene therapy. Nat. Med., 15, 1436.
15. Gillet, N. A. et al. (2011) The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood, 117, 3113-3122.
16. Hacein-Bey-Abina, S. et al. (2003)Aserious adverse event after successful gene therapy for x-linked severe combined immunodeficiency. N. Engl. J. Med., 348, 256.
17. Hacein-Bey-Abina, S. et al. (2008) Insertional oncogenesis in 4 patients after retrovirusmediated gene therapy of scid-x1. J. Clin. Investig., 118, 3142.
18. Hacein-Bey-Abina, S. et al. (2010) Efficacy of gene therapy for x-linked severe combined immunodeficiency. N. Engl. J. Med., 363, 364.
19. Han, Y. et al. (2007) Experimental approaches to the study of HIV-1 latency. Nat. Rev. Microbiol., 5, 106.
20. Meekings, K. N. et al. (2008) HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with ham/tsp. PLoS Pathogens, 4, e1000027.
21. Miller, R. (1974) The jackknife-a review. Biometrika, 61, 1.
22. Mitchell, R. S. et al. (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol., 2, e234.
23. Schmidt, M. 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, 468.
24. Schroder, A. R. W. et al. (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell, 110, 529.
25. Wang, G. P. et al. (2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res., 17, 1194.
26. Wang, G. P. et al. (2008) DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res., 36, e49.
27. Wang, G. P. 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.
28. Wu, X. et al. (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1751.