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

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 ([email protected]) instead of T. H. Rabbitts. _The error has been corrected in the PDF version of the

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CHANGE HISTORY * _ 08 JUNE 2006 Correspondence should be addressed to M. Thangavelu ([email protected]) instead of T. H. Rabbitts. The error has been corrected in the PDF version

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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. AUTHOR

INFORMATION Author notes * Angelika Daser Present address: Institute of Human Genetics, Johannes Gutenberg University, Langenbeckstr. 1, D-55131, Mainz, Germany * Madan Thangavelu Present

address: MRC Cancer Cell Unit, Hills Road, Cambridge, CB2 2XZ, UK * Grace Chung Present address: Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese

University of Hong Kong, Hong Kong * Louise Sparrow Present address: Prime Health, L1, St Georges Tce, Perth, 6000, Australia * Angelika Daser and Madan Thangavelu: These authors contributed

equally to this work. AUTHORS AND AFFILIATIONS * 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 Authors * Angelika Daser View author publications You can also search for this author inPubMed Google Scholar * Madan Thangavelu View author

publications You can also search for this author inPubMed Google Scholar * Richard Pannell View author publications You can also search for this author inPubMed Google Scholar * Alan

Forster View author publications You can also search for this author inPubMed Google Scholar * Louise Sparrow View author publications You can also search for this author inPubMed Google

Scholar * Grace Chung View author publications You can also search for this author inPubMed Google Scholar * Paul H Dear View author publications You can also search for this author inPubMed

 Google Scholar * Terence H Rabbitts View author publications You can also search for this author inPubMed Google Scholar 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. ETHICS

DECLARATIONS COMPETING INTERESTS 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) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Received: 07 March 2006 * Accepted: 17 April 2006 * Published: 23 May 2006 *

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