Microarray Genomic Fingerprinting

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Authors
  1. Ford, B.N.
  2. Shei, Y.
  3. Bamforth, J.
Corporate Authors
Defence R&D Canada - Suffield, Ralston ALTA (CAN)
Abstract
Using current molecular biology, it is possible to create novel microbial forms which have never existed in nature. Current methods for identifying and characterizing microbes depend on some prior assumptions about the genetic content of the organism. Recombinant organisms containing novel genetic material by definition fall outside of the range of prior sequence data. Thus new methods which do not require such assumptions are required to screen and identify the strains, and to detect the presence of novel genetic material. Using an oligonucleotide microarray, we have executed a proof of concept of an array-based genomic fingeprinting technology. The test organisms for this work were Escherichia coli (4 strains), Bacillus anthracis (2 strains), and Yersina enterocolitica. Using standard molecular biology methods, we isolated genomic DNA, digested the DNA to reduce complexity, labelled it with fluorescent dyes, and hybridized the labelled DNA to microarrays containing 21,000 unique olignucleotide features. From a single grid of 484 features, or from a filtered subset of the hybridization data, species could be readily discriminated with high confidence. Strain differentiation may require analysis of the entire feature map, or refinement of the array sequences features, the analysis model, or the analysis software. The next phase of this work will be a test system for rapid species identification in addition to the oligonucleotide fingerprint, leading to a finalized design for

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Keywords
microarray;genomic fingerprint;recombinant;biowarfare;microorganism;DNA fingerprinting;Oligonucleotide analysis
Report Number
DRDC-SUFFIELD-TM-2005-244 — Technical Memorandum
Date of publication
01 Dec 2005
Number of Pages
36
DSTKIM No
CA026740
CANDIS No
524675
Format(s):
Electronic Document(PDF)

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