Method and system for accurate alignment and registration of array for DNA sequencing
First Claim
1. A method for use in performing biochemical experiments comprising:
- providing a microarray comprising a solid planar substrate having a surface;
preparing a substrate for imaging to establish location and registration of biochemical sites on the substrate by providing a predetermined two-dimensional spatial pattern of biochemical sites in periodic distance between adjacent sites on the substrate;
detecting image field spots in a spatial two-dimensional array on the substrate corresponding to biochemical sites in an image on the substrate;
aligning a spatial two-dimensional grid with image field spots of biochemical sites on the substrate to determine a grid offset in order to permit alignment using Moiré
patterns;
the surface further comprising a regular two-dimensional array of optically resolvable surface sites, the optically resolvable surface sites comprising;
(a) attachment sites configured for attachment of biomolecules and (b) sites in a plurality of preselected deletion patterns configured to prevent attachment of the biomolecules, wherein each deletion pattern is configured to cross-correlate to at least one mask pattern,capturing an image of the microarray;
registering the image comprising cross correlating the deletion patterns to the mask pattern to determine absolute location within a field.
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Accused Products
Abstract
In a genome sequencing system and methodology, a protocol is provided to achieve precise alignment and accurate registration of an image of a planar array of nanoballs subject to optical analysis. Precise alignment correcting for fractional offsets is achieved by correcting for errors in subperiod x-y offset, scale and rotation by use of minimization techniques and Moiré averaging. In Moiré averaging, magnification is intentionally set so that the pixel period of the imaging element is a noninteger multiple of the site period. Accurate registration is achieved by providing for pre-defined pseudo-random sets of sites, herein deletion or reserved sites, where nanoballs are prevented from attachment to the substrate so that the sites of the array can be used in a pattern matching scheme as registration markers for absolute location identification. Information can be extracted with a high degree of confidence that it is correlated to a known location, while at the same time the amount of information that can be packed on a chip is maximized.
47 Citations
36 Claims
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1. A method for use in performing biochemical experiments comprising:
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providing a microarray comprising a solid planar substrate having a surface; preparing a substrate for imaging to establish location and registration of biochemical sites on the substrate by providing a predetermined two-dimensional spatial pattern of biochemical sites in periodic distance between adjacent sites on the substrate; detecting image field spots in a spatial two-dimensional array on the substrate corresponding to biochemical sites in an image on the substrate; aligning a spatial two-dimensional grid with image field spots of biochemical sites on the substrate to determine a grid offset in order to permit alignment using Moiré
patterns;the surface further comprising a regular two-dimensional array of optically resolvable surface sites, the optically resolvable surface sites comprising;
(a) attachment sites configured for attachment of biomolecules and (b) sites in a plurality of preselected deletion patterns configured to prevent attachment of the biomolecules, wherein each deletion pattern is configured to cross-correlate to at least one mask pattern,capturing an image of the microarray; registering the image comprising cross correlating the deletion patterns to the mask pattern to determine absolute location within a field. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method for use in performing biochemical experiments comprising:
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providing a solid, planar substrate having an array of sites on which biochemical experiments are performed, the array characterized by a predetermined two-dimensional spatial pattern in periodic distance between adjacent sites; observing light emitted by the biochemical experiments using an imaging system having an array of pixels, the array characterized by constant distances between pixels; and light emitted by the biochemical experiments being focused in spots on the array of pixels, each said spot corresponding to a biochemical experiment; wherein distance between said spots not being an integer multiple of distance between said pixels, for observing and identifying the biochemical experiments. - View Dependent Claims (17, 36)
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18. A method for use in performing biochemical experiments comprising:
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providing a solid, planar substrate having discrete surface sites, the surface sites being configured to support biochemical experiments, the sites being located at spots in a predetermined two-dimensional spatial periodic array of spots on a surface of the substrate, and a fraction of the sites that would otherwise exist being deleted from the array according to a preselected deletion pattern; performing biochemical experiments at the sites; obtaining images of the biochemical experiments at the sites; cross-correlating representations of the images with representations of the deletion pattern to determine absolute location of the spots; and observing and identifying the images with subpixel accuracy. - View Dependent Claims (19, 20, 21, 22, 23)
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24. A system comprising:
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a preprocessor for preparing a planar substrate for imaging to establish location and registration of biochemical sites on the substrate according to a predetermined two-dimensional pattern; a detector for detecting image field spots corresponding to biochemical sites in an image on a substrate; a first subsystem for aligning a two-dimensional grid with said image field spots; and a second subsystem for registering grid points with said image field spots;
the registering subsystem including a first cross correlator for cross correlating representations of the image field spots with representations of a first known deletion pattern of image field spots on the substrate to determine absolute location within a two-dimensional field. - View Dependent Claims (25, 26, 27)
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28. A device for analysis of biomolecules comprising
a solid planar substrate having a surface, the surface having thereon a regular two-dimensional array of optically resolvable surface sites, the optically resolvable sites comprising: -
(a) attachment sites for attachment of the biomolecules, and (b) sites in a preselected known deletion pattern to which the biomolecules do not attach, wherein the deletion pattern is configured to cross-correlate to a mask pattern for registration of the array in order to allow accurate location and analysis of the biomolecules at the attachment sites. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35)
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Specification