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Interrogation of genomes by molecular copy-number counting (MCC)

Nature Methods volume 3, pages 447–453 (2006)Cite this article

A Corrigendum to this article was published on 01 July 2006

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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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Figure 1: Overview of the MCC method.
Figure 2: In situ hybridization of BAC clones with SK-RC-9 chromosomes to localize the t(3;5) translocation breakpoint.
Figure 3: The MCC method was used to localize the t(3;5) break to within 300 bp on chromosome 3.
Figure 4: Filter hybridization of SK-RC-9 DNA shows a rearranged segment and reveals an insertion accompanying a microdeletion.
Figure 5: The sequence and chromosomal location of the t(3;5) nonreciprocal translocation junction.
Figure 6: MCC mapping of a chromosome 3 deletion in the SK-RC-12.

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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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Author notes

  1. Angelika Daser

    Present address: Institute of Human Genetics, Johannes Gutenberg University, Langenbeckstr. 1, D-55131, Mainz, Germany

  2. Madan Thangavelu

    Present address: MRC Cancer Cell Unit, Hills Road, Cambridge, CB2 2XZ, UK

  3. Grace Chung

    Present address: Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong

  4. Louise Sparrow

    Present address: Prime Health, L1, St Georges Tce, Perth, 6000, Australia

  5. Angelika Daser and Madan Thangavelu: These authors contributed equally to this work.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

    Angelika Daser, Madan Thangavelu, Richard Pannell, Alan Forster, Grace Chung, Paul H Dear & Terence H Rabbitts

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Contributions

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.

Corresponding author

Correspondence to Terence H Rabbitts.

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The authors declare no competing financial interests.

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)

Supplementary Methods (PDF 80 kb)

Supplementary Data (PDF 56 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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