Available Technology

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.
Patent Abstract: 
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.
Benefits 
Efficient and accurate microarray signal analysis -Improved detection of weak targets and improved local background estimation for microarray spots
applications 
Inventors: 
Yidong Chen
Patent Number: 
PCT/US03/01784 US Application No. 10/501,848
Internal Laboratory Ref #: 
E-089-2003/0
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