Highly multiplexed particle-based assays
Granted: February 14, 2012
Patent Number:
8114681
Methods are provided for detecting and optionally quantitating multiple analytes, including nucleic acid and/or polypeptide analytes, in particle-based assays that can be highly multiplexed. Compositions, systems, and kits related to the methods are also featured.
Methods for genotyping selected polymorphism
Granted: February 14, 2012
Patent Number:
8114978
Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some…
Antireflective coatings for high-resolution photolithographic synthesis of DNA array
Granted: February 14, 2012
Patent Number:
8114584
The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a…
Silane mixtures
Granted: January 31, 2012
Patent Number:
8105821
Silanation compositions containing a mixture of two or more silanation reagents, where at least one silanation reagent includes a functional group capable of supporting polymer synthesis and at least one silanation reagent includes no functional group capable of supporting polymer synthesis are useful in modulating the active site density and hydrolytic stability of a surface. These compositions are particularly useful in silanating a surface prior to preparation of a polymer array and…
Parallel preparation of high fidelity probes in an array format
Granted: January 24, 2012
Patent Number:
8101737
The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
Polymorphism detection
Granted: January 10, 2012
Patent Number:
8095323
The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker,…
Multiple step printing methods for microbarcodes
Granted: January 3, 2012
Patent Number:
8088555
A system and method for forming encoded microparticles is described. One embodiment includes a method of forming an encoded microparticle, the method comprising: depositing and patterning a plurality of layers on a substrate so as to form a plurality of microparticles, each microparticle comprising a plurality of separate segments aligned along an axis and representing a code; and releasing the microparticles in order to separate the microparticles from the substrate.
Identification of molecular sequence signatures and methods involving the same
Granted: December 27, 2011
Patent Number:
8084197
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,…
Screening methods involving the detection of short-lived proteins
Granted: December 13, 2011
Patent Number:
8076083
A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting…
Nucleic acid labeling compounds
Granted: December 13, 2011
Patent Number:
8076072
Nucleic acid labeling compounds including the following are disclosed: These compounds are useful for attaching a detectable label to a nucleic acid.
System and method for bubble removal
Granted: December 13, 2011
Patent Number:
8075852
In one aspect of the invention, systems, methods, and devices are provided for handling liquid. In some embodiments, such systems, methods, and devices are used to combine fluids while removing gaseous bubbles.
Water soluble cholesterol derivatives
Granted: December 6, 2011
Patent Number:
8071759
Four novel water soluble cholesterol derivative compounds are disclosed. These compounds have various applications in studies of membrane proteins, including drug screening and studies of receptor stability and folding. In one aspect the water soluble cholesterol derivatives disclosed may be used to replace cholesterol in micelle-solubilized membrane protein preparations.
Substrate preparation process
Granted: November 29, 2011
Patent Number:
8067578
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.
Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays
Granted: November 22, 2011
Patent Number:
8062844
Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase…
System, method, and product for imaging probe arrays with small feature sizes
Granted: November 8, 2011
Patent Number:
8055098
An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.
Parallel preparation of high fidelity probes in an array format
Granted: October 11, 2011
Patent Number:
8034912
The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
Methods of analysis of allelic imbalance
Granted: October 4, 2011
Patent Number:
8029997
Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for…
Complexity management of genomic DNA
Granted: October 4, 2011
Patent Number:
8029999
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…
Nucleic acid labeling compounds
Granted: September 27, 2011
Patent Number:
8026057
Nucleic acid labeling compounds are disclosed. The 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.
System and method for making lab card by embossing
Granted: August 30, 2011
Patent Number:
8007267
In one aspect of the invention, systems, methods, and devices are provided for creating microfluidic and nanofluidic structures. In some embodiments, such systems, methods, and devices are used to create features with high aspect ratios in lab cards.
