DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

Chun-Mei Lu ¹, Johnson Kwan ¹, Adolf Baumgartner ¹, Jingly F. Weier ¹, Mei Wang ¹, Tomas Escudero ¹, Santiago Munné ¹, Horst F. Zitzelsberger ¹ and Heinz-Ulrich G. Weier ^1*

¹ Department of Chemical and Materials Engineering, National Chin-Yi University of Technology, Taiping City, Taichung, Taiwan (C-ML); 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, California (AB,JFW); Reprogenetics, LLC, Livingston, New Jersey (TE,SM); California Institute of Technology, Pasadena, California (MW); and Helmholtz Zentrum Muenchen, Neuherberg, Germany (HFZ)

^* To whom correspondence should be addressed. E-mail: ugweier{at}lbl.gov.

Submitted on January 30, 2009
Accepted on 2 February 2009

	Abstract

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 pre-implantation 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 (BAC) 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 multi-clone and multi-color 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 three to four days.

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

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    Twitter    What's this?

Guidelines | Subscriptions | About | exPRESS - Current - Archive | Business Information | Contact

The Journal of Histochemistry & Cytochemistry is owned, published, and licensed by The Histochemical Society © 2009