Reading chemical arrays

Abstract

Methods of using an addressable array of biopolymers which has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established. A definition of the shapes of the established regions of each set is saved in a memory. Each region of each set is processed according to a corresponding routine for that set.

Description

FIELD OF THE INVENTION [0001] This invention relates to arrays, particularly biopolymer arrays (such polynucleotide arrays, and particularly DNA arrays) which are useful in diagnostic, screening, gene expression analysis, and other applications. BACKGROUND OF THE INVENTION [0002] Arrays of biopolymers, such as arrays of peptides or polynucleotides (such as DNA or RNA), are known and are used, for example, as diagnostic or screening tools. Such arrays include regions (sometimes referenced as features or spots) of usually different sequence biopolymers arranged in a predetermined configuration on a substrate. The arrays, when exposed to a sample, will exhibit a pattern of binding which is indicative of the presence and / or concentration of one or more components of the sample, such as an antigen in the case of a peptide array or a polynucleotide of particular sequence in the case of a polynucleotide array. The binding pattern can be detected by reading the array, for example, by observ...

AI Technical Summary

Benefits of technology

"The present invention provides a method for using an addressable array of biopolymers on a substrate to detect and analyze samples. The method involves detecting signals from the exposed array, saving the signals as a signal image, and processing the signals to establish the shape of each region in the array. The method can also include retrieving and displaying the saved shapes, as well as reviewing and altering the processed data. The invention also provides an apparatus for using the addressable array and a computer program product for implementing the method. The technical effects of the invention include improved accuracy and efficiency in analyzing samples and faster data processing."

Problems solved by technology

In array fabrication, the quantities of DNA available for the array are usually very small and expensive.

During array fabrication however, the resulting fabricated array may not have an actual layout which is precisely the same as a target layout.

For example, some features actually deposited may have errors in position, dimensions, or presence (and may not be present at all due to intermittent errors in the drop deposition apparatus).

Incorrectly designating regions as features or otherwise incorrectly calculating a total signal value for a feature in a determination of results from the exposed array, can read to serious errors in result interpretation.

However, with thousands of features on each array, such a manual procedure is very slow, and does not lend itself to reproducible results.

For example, a routine which establishes a feature boundary based only on regions of highest signal strength, may fail to recognize a region where features have been smeared due to a scratch or other contact with the array.

The present invention further recognizes that while this can be reproduced by running the same feature extraction program on the raw signal data acquired during array reading such a method is computationally intensive and therefore time consuming.

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