Methods of genetic analysis of mouse
Granted: July 31, 2007
Patent Number:
7250289
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of mouse genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. In one embodiment the nucleic acid sequences provided are present as an array of probes that may be used to measure gene expression of at least 30,000 mouse genes. As such, the invention relates to diverse fields impacted by the nature of molecular interaction,…
System, method, and product for dynamic noise reduction in scanning of biological material
Granted: May 22, 2007
Patent Number:
7222025
Systems and methods are described for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam, such as a laser beam. As one example, a scanning system is described that includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization…
Splicing factor target identification
Granted: May 15, 2007
Patent Number:
7217521
Methods for identifying transcripts and genes whose splicing is regulated by a selected splicing factor are disclosed. Unprocessed or partially processed transcripts are bound to an array of probes and contacted with one or more splicing factors. The identities of transcripts bound to splicing factors are determined.
Method of target enrichment and amplification
Granted: May 8, 2007
Patent Number:
7214490
The presently claimed invention provides methods and kits for amplifying a target sequence from within a nucleic acid population. The presently claimed invention provides selection probes which are complementary to at least a portion of said target sequence and mechanisms for adding a probe sequence to the 3? end of a target sequence that is hybridized to a selection probe. The added 3? probe sequence and a probe sequence added at the 5? end of the target by adaptor ligation allow for…
Method and apparatus for providing a bioinformatics database
Granted: May 8, 2007
Patent Number:
7215804
System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.
Multiplex oligonucleotide addition and target amplification
Granted: April 24, 2007
Patent Number:
7208295
Methods for appending oligonucleotides directly to nucleic acid templates, particularly to defined sites internal to single-stranded templates, are described. Appending first and second common priming sites to each of a plurality of templates of distinct sequence allows the subsequent stoichiometric amplification of a plurality of templates of distinct sequence.
Complexity management of genomic DNA
Granted: April 10, 2007
Patent Number:
7202039
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the…
System and computer software products for comparative gene expression analysis
Granted: March 27, 2007
Patent Number:
7197400
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, methods, systems and computer software are provided for comparative gene expression analysis using intensity dependent normalization factors.
Nucleic acid labeling compounds
Granted: February 20, 2007
Patent Number:
7179905
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
Photoactivatable silane compounds and methods for their synthesis and use
Granted: February 13, 2007
Patent Number:
7176297
In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS-SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a…
Tag nucleic acids and probe arrays
Granted: January 2, 2007
Patent Number:
7157564
The invention provides a unique set of nucleic acid sequences which is appropriate for use for a wide variety of applications requiring nucleic acid tags. As such, the sequence tags of the presently claimed invention may be used, for example, to label biological and nonbiological materials, in genotyping applications and in a variety of other analyses.
Optically active substrates
Granted: January 2, 2007
Patent Number:
7158224
A device for optical examination of biological materials using radiation of a selected wavelength includes a substrate having a first surface and a second surface opposite to the first surface. The first surface includes a dense array of micro-optical elements arranged to provide increased intensity radiation or evanescent radiation. The first surface is in close proximity to the biological material being examined.
System, method, and product for providing a wavelength tunable excitation beam
Granted: December 12, 2006
Patent Number:
7148492
A method for scanning a probe array is described. The method comprises tuning an excitation light to a plurality of wavelengths each within an excitation range of a fluorescent label associated with one or more target molecules; and directing the tuned excitation light of each wavelength at the probe array.
Iterative resequencing
Granted: December 5, 2006
Patent Number:
7144699
The invention provides iterative methods of analyzing a target nucleic acid that represents a variant of a reference nucleic acid. An array of probes is designed to be complementary to an estimated sequence of a target nucleic acid. The array of probes is then hybridized to the target nucleic acid. The target sequence is reestimated from hybridization pattern of the array to the target nucleic acid. A further array of probes is then designed to be complementary to the reestimated…
Photolithographic solid-phase polymer synthesis
Granted: December 5, 2006
Patent Number:
7144700
Methods, employing a polycyclic hydrocarbon or a polycyclic heteroaromatic compound as sensitizers, are provided to increase the efficiency of removing, by irradiation, photolabile protecting groups that mask reactive sites on synthesis intermediaries. Preferred groups of photolabile protecting moieties include: ((?-methyl-2-nitropiperonyl)-oxy)carbonyl (MeNPOC), ((Phenacyl)-oxy)carbonyl (PAOC), O-(9-phenylxanthen-9-yl) (PIXYL), and ((2-methylene-9,10-anthraquinone)-oxy)carbonyl (MAQOC).…
Identification of molecular sequence signatures and methods involving the same
Granted: November 14, 2006
Patent Number:
7135285
Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature,…
Computer software for automated annotation of biological sequences
Granted: November 7, 2006
Patent Number:
7133780
Methods, software products and systems are provided for automated high throughout gene characterization. In one exemplary embodiment, HMM models are used to characterize genes. Biological sequences are classified according to their hit with different HMM models using a curve analysis.
Functionalized silicon compounds and methods for their synthesis and use
Granted: October 31, 2006
Patent Number:
7129307
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thiol, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Functionalized silicon compounds and methods for their synthesis and use
Granted: October 31, 2006
Patent Number:
7129308
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thiol, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Computer software system, method, and product for scanned image alignment
Granted: October 31, 2006
Patent Number:
7130458
A computer program analyzes an image including features that correspond to emissions detected from a biological probe array. The program aligns one or more grids, each having one or more grid cells, with all or portions of the image; selects one or more grid cells to be associated with features based on distributions of pixel intensity values within the grid cells; locates a shape, such as a circle, in each selected grid cell based on distributions of pixel intensity values within the…
