Affymetrix Patent Applications

SYSTEM, METHOD, AND PRODUCT FOR IMAGING PROBE ARRAYS WITH SMALL FEATURE SIZES

Granted: February 26, 2015
Application Number: 20150057167
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.

ANALYSIS OF METHYLATION USING NUCLEIC ACID ARRAYS

Granted: February 5, 2015
Application Number: 20150038352
Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Complexity Management of Genomic DNA

Granted: January 15, 2015
Application Number: 20150017632
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…

METHODS FOR SYNTHESIZING POOLS OF PROBES

Granted: January 1, 2015
Application Number: 20150004600
Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.

Systems and Methods For Probe Design to Detect the Presence of Simple and Complex Indels

Granted: September 18, 2014
Application Number: 20140274728
Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.

Detection of Nucleic Acids

Granted: September 18, 2014
Application Number: 20140274756
This invention provides compositions, methods, and systems for characterizing, resolving, and quantitating single stranded and double stranded DNA and RNA in-situ. Paired sense and anti-sense probes can signal the presence of double stranded nucleic acids. DNA and RNA can be distinguished in cell and tissue samples by hybridizing with probe sets adapted to highlight differences in these targets in-situ.

Multiplex Capture of Nucleic Acids

Granted: July 10, 2014
Application Number: 20140194296
Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also…

Nucleic Acid Labeling Compounds

Granted: July 3, 2014
Application Number: 20140187434
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.

Method for Detecting Transcription Factor-Protein Interactions

Granted: May 1, 2014
Application Number: 20140121122
A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Miniaturized microparticles

Granted: February 27, 2014
Application Number: 20140057809
A system and method for forming encoded microparticles is described. One embodiment includes an encoded microparticle, the microparticle comprising a plurality of segments aligned along an axis, wherein the plurality of segments define a code for the microparticle; and an outer cuboid encapsulating the plurality of segments, wherein the plurality of segments are detectable through the outer cuboid.

Multiple Step Printing Methods for Microbarcodes

Granted: February 20, 2014
Application Number: 20140051027
A system and method for forming encoded microparticles is described. One embodiment includes a method for forming a microparticle, the method comprising providing a pattern, wherein the pattern defines a code element, printing the pattern on a substrate to form a first code element within a microparticle region, printing the pattern on the substrate to form at least one successive code element, such that the first code element and the at least one successive code element are within the…

MANUFACTURING AND PROCESSING POLYMER ARRAYS

Granted: January 16, 2014
Application Number: 20140018266
The invention provides methods to process multiple microarrays by providing a microarray plate and processing plates. In an embodiment of the invention, methods for assembling microarray plates by using wafers are described for high throughput microarray processing.

Recombinant Colwellia Psychrerythraea Alkaline Phosphatase and Uses Thereof

Granted: December 26, 2013
Application Number: 20130344493
A heat labile alkaline phosphatase enzyme and methods of using the same and kits including the same are disclosed. Specifically, a nucleotide sequence of, peptide sequence of, methods of using, and kits comprising, a heat labile alkaline phosphatase isolated from Colwellia psychrerythraea are provided. Methods of over-expression and purification of the recombinant alkaline phosphatase and mutants thereof are also disclosed. Methods of over-expressing and purifying commercially useful…

Analysis of Data Obtained from Microarrays

Granted: September 5, 2013
Application Number: 20130230221
Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and…

Biological Assays Using Microparticles

Granted: August 15, 2013
Application Number: 20130210028
Encoded microparticles described are useful in the study of many different biological agents in multiplex assays. For instance, the encoded microparticles may be employed in various co-precipitation assays to purify and/or isolate various analytes of interest. Encoded microparticles may also be used as real-time detectors in many different situations whereby binding of a secreted analyte or contaminating analyte may be detected using various labeling techniques. Further, encoded…

Parallel Preparation of High Fidelity Probes in an Array Format

Granted: August 1, 2013
Application Number: 20130197208
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: July 25, 2013
Application Number: 20130190199
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…

Microfluidic Methods, Devices, and Systems for Fluid Handling

Granted: July 25, 2013
Application Number: 20130190213
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 process reagent biochemical reactions.

COMPUTER-AIDED VISUALIZATION OF EXPRESSION COMPARISON

Granted: July 4, 2013
Application Number: 20130169645
Innovative systems and methods for visualizing information collected from analyzing samples are provided. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is…

SURFACE LINKERS FOR ARRAY SYNTHESIS

Granted: June 27, 2013
Application Number: 20130165350
The present invention provide several methods of derivatizing a surface of a support with one or more linkers thus providing a suitable platform for synthesis of a polymer array, particular a nucleic acid array. Some methods derivatize a surface with a self-assembled monolayer (SAM) of a linker. The SAM confers advantages of hydrolytic stability, broad compatibility with synthesis and detection chemistries, and reduced emergence of latent functional groups during polymer array synthesis.…