1875-5488/12 $58.00+.00 ©2012 Bentham Science Publishers Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facili- tate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

Abstract: Despite their non-diseased nature, healthy human tissues may show a surprisingly large fraction of aneusomic or aneuploid cells. We have shown previously that hybridization of three to six non-isotopically labeled, chromosome-specific DNA probes reveals different proportions of aneuploid cells in individual compartments of the human placenta and the uterine wall. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes. Chromosome losses in placental or uterine tissues, on the other hand, were detected infrequently. A more thorough numerical analysis of all possible aneusomies oc-curring in these tissues and the investigation of their spatial as well as temporal distribution would further our understand-ing of the underlying biology, but it is hampered by the high cost of and limited access to DNA probes. Furthermore, mul-tiplexing assays are difficult to set up with commercially available probes due to limited choices of probe labels. Many laboratories therefore attempt to develop their own DNA probe sets, often duplicating cloning and screening efforts un-derway elsewhere. In this review, we discuss the conventional approaches to the preparation of chromosome-specific DNA probes followed by a description of our approach using state-of-the-art bioinformatics and molecular biology tools for probe identification and manufacture. Novel probes that target gonosomes as well as two autosomes are presented a