Abstract
Human cancers and some congenital traits are characterized by cytogenetic aberrations including translocations, amplifications, duplications or deletions that can involve gain or loss of genetic material. We have developed a simple method to precisely delineate such regions with known or cryptic genomic alterations. Molecular copy-number counting (MCC) uses PCR to interrogate miniscule amounts of genomic DNA and allows progressive delineation of DNA content to within a few hundred base pairs of a genomic alteration. As an example, we have located the junctions of a recurrent nonreciprocal translocation between chromosomes 3 and 5 in human renal cell carcinoma, facilitating cloning of the breakpoint without recourse to genomic libraries. The analysis also revealed additional cryptic chromosomal changes close to the translocation junction. MCC is a fast and flexible method for characterizing a wide range of chromosomal aberrations.
*Note: Correspondence should be addressed to M. Thangavelu (mt370@hutchison-mrc.cam.ac.uk) instead of T. H. Rabbitts. The error has been corrected in the PDF version of the article.
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Change history
08 June 2006
Correspondence should be addressed to M. Thangavelu (mt370@hutchison-mrc.cam.ac.uk) instead of T. H. Rabbitts. The error has been corrected in the PDF version of the article.
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Acknowledgements
This work was supported by the Medical Research Council. G.C. was partly supported by the Kay Kendall Leukemia Fund. We thank L. Old for generously supplying the renal cell line SK-RC-9 and N. Copeland for providing an inverse PCR protocol.
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A.D., M.T., R.P., A.F. and G.C. conducted the experimental procedures; A.D., M.T., P.H.D. and T.H.R. devised the project; A.D., P.H.D. and T.H.R. wrote the manuscript.
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Supplementary information
Supplementary Fig. 1
Painting of SK-RC-9 metaphase chromosomes. (PDF 81 kb)
Supplementary Fig. 2
Identification of micro-deletion in SK-RC-9 chromosome t(3;5). (PDF 33 kb)
Supplementary Fig. 3
Agarose gel fractionation of PCR products for round one MCC of SK-RC-12 DNA. (PDF 99 kb)
Supplementary Fig. 4
Filter hybridization of SK-RC-12 DNA to confirm genomic alteration detected by MCC. (PDF 66 kb)
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Daser, A., Thangavelu, M., Pannell, R. et al. Interrogation of genomes by molecular copy-number counting (MCC). Nat Methods 3, 447–453 (2006). https://doi.org/10.1038/nmeth880
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DOI: https://doi.org/10.1038/nmeth880
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