In situ genetic analysis of cellular chimerism

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Copy number variants are a recently discovered source of large-scale genomic diversity present in all individuals. We capitalize on these inherent genomic differences, focusing on deletion polymorphisms, to develop informative fluorescence in situ hybridization probes with the ability to unequivocally distinguish between donor and recipient cells in situ. These probes are accurate, specific, highly polymorphic and, notably, can be used to assign genetic identity in situ in a completely gender-independent fashion. We anticipate that these polymorphic deletion probes will be useful in further understanding the dynamics of cellular chimerism after transplantation, including the details of chronic organ rejection, post-transplant lymphoproliferative disorder and graft-versus-host disease, and in optimizing future tissue engineering and pluripotent stem cell therapies.

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Figure 1: Assessment of variable copy number states with polymorphic deletion probes.
Figure 2: FISH with PDPs in clinical bone marrow chimerism specimens.
Figure 3: In situ FISH using PDPs for assessment of chimerism in organ transplantation.
Figure 4: Informative potential of polymorphic deletion probes under Hardy-Weinberg equilibrium.
Figure 5: Experimental assessment of the informative potential of identified PDPs in 50 random individuals.


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We thank M. Han, J. Miller-Batten and J. Reid for excellent technical assistance. We thank C. Lee (Brigham and Women's Hospital) and S. Kantarci (Beth Israel Deaconess Medical Center) for helpful discussions and reagents. We thank S. Ogino for helpful discussions. This work was supported in part by intramural funding from the Department of Pathology, Massachusetts General Hospital to A.J.I.

Author information

D.W. and A.J.I. conceived of the project idea, designed and performed experiments, and wrote the manuscript. L.M.S. designed and performed experiments. Q.V., A.N., H.S. and G.K. performed FISH assays. J.R.S. contributed the autopsy cardiac transplant case and provided helpful discussions. All contributed to the editing of the manuscript.

Correspondence to A John Iafrate.

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Competing interests

A provisional application by D.W. and A.J.I. for a patent with the US Patent Office for the use of polymorphic deletion probes is pending and has not yet been licensed.

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Supplementary Methods, Supplementary Figs. 1–4 and Supplementary Table 1 (PDF 403 kb)

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Wu, D., Vu, Q., Nguyen, A. et al. In situ genetic analysis of cellular chimerism. Nat Med 15, 215–219 (2009) doi:10.1038/nm.1862

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