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DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

Chun-Mei Lu, Johnson Kwan, Adolf Baumgartner, Jingly F. Weier, Mei Wang, Tomas Escudero, Santiago Munné, Horst F. Zitzelsberger and Heinz-Ulrich G. Weier

Department of Chemical and Materials Engineering, National Chin-Yi University of Technology, Taiping City, Taichung, Taiwan, Republic of China (CML); Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory, Berkeley, California (JK,H-UGW); Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California (AB,JFW); Reprogenetics, LLC, Livingston, New Jersey (TE,SM); California Institute of Technology, Pasadena, California (MW); and Helmholtz Zentrum Muenchen, Neuherberg, Germany (HFZ)

Correspondence to: H.-Ulli Weier, University of California, E.O. Lawrence Berkeley National Laboratory, MS 977-250, 1 Cyclotron Road, Berkeley, CA 94720. E-mail: ugweier{at}lbl.gov

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. (J Histochem Cytochem 57:587–597, 2009)

Key Words: translocation • chromosome aberration • cytogenetics • thyroid cancer • IVF • PGD • fluorescence in situ hybridization • bacterial artificial chromosome • DNA probes

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