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DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

Lu, Chun-Mei and Kwan, Johnson and Baumgartner, Adolf and Weier, Jingly F. and Wang, Mei and Escudero, Tomas and Munné, Santiago and Zitzelsberger, Horst F. and Weier, Heinz-Ulrich G. (2009) DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints. Journal of Histochemistry and Cytochemistry, 57 (6). pp. 587-597. ISSN 0022-1554.

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Structural chromosome aberrations are hallmarks of many human genetic diseases. The precise mapping of translocation breakpoints in tumors is important for identification of genes with altered levels of expression, prediction of tumor progression, therapy response, or length of disease-free survival, as well as the preparation of probes for detection of tumor cells in peripheral blood. Similarly, in vitro fertilization (IVF) and preimplantation genetic diagnosis (PGD) for carriers of balanced, reciprocal translocations benefit from accurate breakpoint maps in the preparation of patient-specific DNA probes followed by a selection of normal or balanced oocytes or embryos. We expedited the process of breakpoint mapping and preparation of case-specific probes by utilizing physically mapped bacterial artificial chromosome clones. Historically, breakpoint mapping is based on the definition of the smallest interval between proximal and distal probes. Thus, many of the DNA probes prepared for multiclone and multicolor mapping experiments do not generate additional information. Our pooling protocol, described here with examples from thyroid cancer research and PGD, accelerates the delineation of translocation breakpoints without sacrificing resolution. The turnaround time from clone selection to mapping results using tumor or IVF patient samples can be as short as 3 to 4 days.

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Additional Information:© 2009 The Histochemical Society, Inc. Presented in part at HCS2005, Nordwijkerhout, The Netherlands, April 27–30, 2005. Received for publication January 30, 2009; accepted February 2, 2009. Originally published as JHC exPRESS on February 16, 2009. This work was supported in part by National Institutes of Health Grants CA-80792, CA-88258, CA-123370, and HD- 44313, and a grant from the Director, Office of Energy Research, Office of Health and Environmental Research, U.S. Department of Energy, under contract DE-AC02-05CH11231. J.F.W. was supported in part by Grant HD-45736 from the National Institutes of Health and a grant from the University of California Discovery Program, which also supported A.B. We acknowledge editorial help provided by E. Lowe, and support from staff at Reprogenetics, who provided metaphase spreads and initial mapping data. Ideograms were kindly provided by D. Adler, PhD, Department of Pathology, University of Washington. We would like to express our thanks to the scientists at the Human Genome Center, California Institute of Technology, Pasadena, whose generosity has made these studies possible.
Funding AgencyGrant Number
Department of EnergyDE-AC02-05CH11231
University of CaliforniaUNSPECIFIED
Subject Keywords:translocation; chromosome aberration; cytogenetics; thyroid cancer; IVF; PGD; fluorescence in situ hybridization; bacterial artificial chromosome; DNA probes
Issue or Number:6
Record Number:CaltechAUTHORS:20090909-082137768
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:15683
Deposited By: Tony Diaz
Deposited On:10 Sep 2009 23:51
Last Modified:03 Oct 2019 01:01

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