A Parameterized Model for Simulating Microarrays

The current invention describes a simulation procedure in which several parameters can be used to model microarray image formation. Over 20 model parameters, each governed by a probability distribution, control the signal intensity, spot geometry, spot drift, background effects, and the many kinds of noise that affect microarray images as a result of the manner in which they are formed. In practice, a simulated microarray image is generated according to a number of defined parameters and can be compared to a known value. An imaging procedure is then applied to the simulated microarray image to generate observed values. The known values can then be compared to the observed values to evaluate the imaging procedure.

The model can be used to measure the performance of imaging procedures designed to measure the true intensity of spots on microarrays. Modeling and simulation of microarray image formation is a key to benchmarking various signal processing tools being developed to estimate cDNA signal spots. Using a model to describe the true signal intensity not only helps in evaluating these tools, but also facilitates the understanding of various process interactions. The simulation program has been used extensively in the design of the microarray image-analysis program used at the National Human Genome Research Institute (NHGRI). This has been done by testing the accuracy of the analysis program on simulated images exhibiting troublesome noise conditions and then tuning the program to achieve better results.

The simulation procedure can be incorporated into hardware/software for ease of use. The levels of foreground noise, background noise, and spot distortion can be set, and algorithms can be evaluated under varying conditions.

Potential Commercial Applications: Competitive Advantages:
  • Microarray imaging
  • Evaluation of gene expression
  • Efficient and accurate microarray signal analysis
  • Improved detection of weak targets and improved local background estimation for microarray spots

Development Stage:
Late stage


Yidong Chen (NHGRI)  ➽ more inventions...

Intellectual Property:
U.S. Pat: 7,363,169 issued 2008-04-22
PCT Application No. PCT/US03/01784
US Application No. 10/501,848

Y Balagurunathan, ER Dougherty, Y Chen, ML Bittner, JM Trent. Simulation of cDNA microarrays via a parameterized random signal model. J Biomed Opt. 2002 Jul;7(3):507-523. PubMed abs

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OTT Reference No: E-089-2003/0
Updated: Feb 2, 2009