Methods, computer software products and systems for gene expression cluster analysis
Granted: June 17, 2004
Application Number:
20040117128
In some embodiment of the invention, methods are provided to classify genes based upon biological knowledge. The methods are useful for analyzing biological data such as gene expression data.
Methods, computer software products and systems for clustering genes
Granted: June 17, 2004
Application Number:
20040117127
In some embodiment of the invention, methods are provided to classify genes based upon biological knowledge. The methods are useful for analyzing biological data such as gene expression data.
Functionated photoacid generator and functionated polymer system for biological microarray synthesis
Granted: June 10, 2004
Application Number:
20040109935
In some embodiment of the invention, methods are provided for the synthesis of polymer arrays. In one embodiment, a reactive polymer and a photo acid generator is used for the photodirected polymer array synthesis.
Method for concentrate nucleic acids
Granted: June 10, 2004
Application Number:
20040110132
In some embodiments of the invention, methods are provided for concentrating nucleic acid samples. In some embodiments, nucleic acid samples are concentrated using a nucleic acid impermeable membrane.
Functionated photoacid generator for biological microarray synthesis
Granted: June 10, 2004
Application Number:
20040110133
In some embodiment of the invention, methods are provided for the synthesis of polymer arrays. In one embodiment, a chemically amplified polymer matrix is used for the synthesis of polymer arrays.
Compleixity management of genomic DNA by semi-specific amplification
Granted: June 10, 2004
Application Number:
20040110153
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample. In one embodiment specific fragments are amplified. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.
Substrate preparation process
Granted: June 3, 2004
Application Number:
20040105932
The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
Bioarray chip reaction apparatus and its manufacture
Granted: June 3, 2004
Application Number:
20040106130
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Reagents and methods for solid phase synthesis and display
Granted: June 3, 2004
Application Number:
20040106728
New compounds, compositions and methods which find application in solid phase synthesis including the preparation of high-density arrays of diverse polymer sequences such as diverse peptides and oligonucleotides as well as in preparation of arrays of small ligand molecules. The compounds of the present invention are those which are typically referred to as linking groups, linkers or spacers and include unsymmetrical disulfide linking groups, and 1,3-diol derivatives capable of providing…
Nucleic acid labeling compounds
Granted: May 27, 2004
Application Number:
20040101892
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.
Non-contiguous oligonucleotide probe arrays
Granted: May 20, 2004
Application Number:
20040096837
In some embodiments of the invention, non-contiguous oligonucleotide probe arrays are provided for gene expression, genotyping and resequencing applications.
Scanned image alignment systems and methods
Granted: May 20, 2004
Application Number:
20040096883
Systems and methods for aligning scanned images are provided. A pattern is included in the scanned image so that when the image is convolved with a filter, a recognizable pattern is generated in the convolved image. The scanned image may then be aligned according to the position of the recognizable pattern in the convolved image. The filter may also act to remove the portions of the scanned image that do not correspond to the pattern in the scanned image.
Products and methods for analyzing nucleic acids including identification of substitutes, insertions and deletions
Granted: May 13, 2004
Application Number:
20040091930
Systems and methods for detecting monomer changes in a sample when an unknown quantity of expected monomers may also be present. Homogeneous and heterogeneous samples are exposed to polymer probes for hybridization. The hybridization affinities of the polymer probes to the samples are then compared to determine differences between the polymers in the samples. Accordingly, deletion, substitution and insertion mutations may be detected in a heterogeneous sample of nucleic acids.
Combinatorial strategies for polymer synthesis
Granted: May 13, 2004
Application Number:
20040092032
A method and device for forming large arrays of polymers on a substrate (401). According to a preferred aspect of the invention, the substrate is contacted by a channel block (407) having channels (409) therein. Selected reagents are delivered through the channels, the substrate is rotated by a rotating stage (403), and the process is repeated to form arrays of polymers on the substrate. The method may be combined with light-directed methodolgies.
Porous silica substrates for polymer synthesis and assays
Granted: May 13, 2004
Application Number:
20040092396
Methods are provided for making and using thin films of porous silica substrates to synthesize arrays of polymers. Methods are also provided for assaying such polymers on porous silica substrates. The porous silica substrates offer an increase in array density and signal enhancement over conventional flat glass substrates. Examples of polymers that can be synthesized and assayed include biological polymers such as nucleic acids, polynucleotides, polypeptides, and polysaccharides. Arrays…
Nucleic acid labeling methods
Granted: May 6, 2004
Application Number:
20040086914
In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one embodiment, T4 RNA ligase is used to attach a 3′-biotinylated AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-biotin is used as donor molecule.
Systems and method for examination of microarrays using scanning electron microscope
Granted: April 29, 2004
Application Number:
20040081985
The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further…
Methods for testing oligonucleotide arrays
Granted: April 22, 2004
Application Number:
20040076987
Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids
Methods of analysis of linkage disequilibrium
Granted: April 15, 2004
Application Number:
20040072217
Methods and kits for analyzing a collection of target sequences in a nucleic acid sample are provided. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. Methods are also provided for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or…
Complexity management of genomic DNA
Granted: April 8, 2004
Application Number:
20040067493
The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for…
