Bioinformatics tools allow targeted selection of chromosome enumeration probes and aneuploidy detection.

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  • Author(s): O'Brien B;O'Brien B; Zeng H; Polyzos AA; Lemke KH; Weier JF; Wang M; Zitzelsberger HF; Weier HU
  • Source:
    The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society [J Histochem Cytochem] 2013 Feb; Vol. 61 (2), pp. 134-47. Date of Electronic Publication: 2012 Nov 29.
  • Publication Type:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Validation Study
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: SAGE Publications Country of Publication: United States NLM ID: 9815334 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1551-5044 (Electronic) Linking ISSN: 00221554 NLM ISO Abbreviation: J Histochem Cytochem Subsets: MEDLINE
    • Publication Information:
      Publication: <2011->: Thousand Oaks, CA : SAGE Publications
      Original Publication: Baltimore : Williams & Wilkins Co., c1953-
    • Subject Terms:
      Aneuploidy*; Computational Biology/*methods ; Cytogenetics/*methods ; In Situ Hybridization, Fluorescence/*methods; Cell Line, Tumor ; Chromosomes, Human, Pair 10/genetics ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; DNA Probes/genetics ; Data Mining ; Female ; Gene Library ; Humans ; Interphase ; Placenta/metabolism ; Polyploidy ; Pregnancy ; Reproducibility of Results
    • Abstract:
      Accurate determination of cellular chromosome complements is a highly relevant issue beyond prenatal/pre-implantation genetic analyses or stem cell research, because aneusomy may be an important mechanism by which organisms control the rate of fetal cellular proliferation and the fate of regenerating tissues. Typically, small amounts of individual cells or nuclei are assayed by in situ hybridization using chromosome-specific DNA probes. Careful probe selection is fundamental to successful hybridization experiments. Numerous DNA probes for chromosome enumeration studies are commercially available, but their use in multiplexed hybridization assays is hampered due to differing probe-specific hybridization conditions or a lack of a sufficiently large number of different reporter molecules. Progress in the International Human Genome Project has equipped the scientific community with a wealth of unique resources, among them recombinant DNA libraries, physical maps, and data-mining tools. Here, we demonstrate how bioinformatics tools can become an integral part of simple, yet powerful approaches to devise diagnostic strategies for detection of aneuploidy in interphase cells. Our strategy involving initial in silico optimization steps offers remarkable savings in time and costs during probe generation, while at the same time significantly increasing the assay's specificity, sensitivity, and reproducibility.
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    • Grant Information:
      CA136685 United States CA NCI NIH HHS; R01 CA136685 United States CA NCI NIH HHS; CA123370 United States CA NCI NIH HHS; HD45736 United States HD NICHD NIH HHS; R21 CA132815 United States CA NCI NIH HHS; R21 CA123370 United States CA NCI NIH HHS; CA132815 United States CA NCI NIH HHS; CA132815-02S1 United States CA NCI NIH HHS; R01 HD045736 United States HD NICHD NIH HHS
    • Accession Number:
      0 (DNA Probes)
    • Publication Date:
      Date Created: 20121204 Date Completed: 20130325 Latest Revision: 20211021
    • Publication Date:
      20231215
    • Accession Number:
      PMC3636690
    • Accession Number:
      10.1369/0022155412470955
    • Accession Number:
      23204113