Data Mining Empowers the Generation of a Novel Class of Chromosomespecific DNA Probes

Abstract

Probes that allow accurate delineation of chromosome-specific DNA sequences in interphase or metaphase cell nuclei have become important clinical tools that deliver life-saving information about the gender or chromosomal make-up of a product of conception or the probability of an embryo to implant, as well as the definition of tumorspecific genetic signatures. Often such highly specific DNA probes are proprietary in nature and have been the result of extensive probe selection and optimization procedures. We describe a novel approach that eliminates costly and time consuming probe selection and testing by applying data mining and common bioinformatics tools. Similar to a rational drug design process in which drug-protein interactions are modeled in the computer, the rational probe design described here uses a set of criteria and publicly available bioinformatics software to select the desired probe molecules from libraries comprised of hundreds of thousands of probe molecules. Examples describe the selection of DNA probes for the human X and Y chromosomes, both with unprecedented performance, but in a similar fashion, this approach can be applied to other chromosomes or species. Journal of

Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization

“…The Y-specific BAC clone RP11-242E13 targets a highly repeated DNA sequence [52], while the X-specific clone RP11-294C12 targets a cluster of repeated alpha satellite DNA [38]. Thus, this probe combination is expected to bind to multiple sites along the long arm of the human Y chromosome and throughout the centromeric region of the X chromosome [31,38]. …”

“…The UCSC Genome Browser GRCh37/hg19, built February 2009, was used to identify bacterial artificial chromosome (BAC) clones with high satellite DNA content in the non-centromeric and non-telomeric regions of the short and long arms of human chromosomes 16, X and Y [38]. The graphic user interface was set to display BAC end pairs and repeat DNA elements.…”

“…Our laboratories have an established track record of production of novel DNA probes and innovative cell assays, many of which have found their way into contemporary cancer research or PGD analysis [18,21,23,24,26,31–38]. To facilitate the broad distribution of molecular cytogenetic assays and make DNA probes, as well as multiplex FISH tests, available to the less experienced laboratory, we have undertaken probe production pilot studies, which take advantage of the vast resources generated in the course of the Human Genome Project, such as physical maps and recombinant DNA libraries.…”

“…The vast majority of these chromosome enumerator probes (CEPs) target highly reiterated, tandemly-repeated DNA sequences in order to bind many copies of a rather small probe sequence to the target, which may be confined to a tightly localized area or volume. Different ways of isolating and purifying such DNA probes exist [31,37,38,40–45]. To the best of our knowledge, the procedures described in the present communication allow a laboratory with common equipment to prepare specific DNA probes in just a few days and, thus, represent the most efficient, rapid and cost-conscious approach to the generation of chromosome-specific DNA probes.…”

J Microbial Biochem Technol

“…Similar to a rational drug design process in which drug-protein interactions are modeled in the computer, the rational probe design described here uses a set of criteria and publicly available bioinformatics software to select the desired probe molecules from libraries comprised of hundreds of thousands of probe molecules [44].Summary data from recent studies provide overwhelming evidence that bioinformatics tools are useful in protein interactions [45] microorganisms provide a large pool of bioactive compounds, and the intensive search for new drugs leads to the identification and structure determination of many novel compounds from these organisms [46].…”