Devices, Systems and Methods for Processing of Magnetic Particles
Granted: February 9, 2012
Application Number:
20120034703
Devices, systems and methods for separation of magnetic particles with either hand held devices or automated instruments. Specifically, the production of magnetic fields for the separation of the particles within containers such as microtiter plates with a magnetic field that is substantially consistent for each well. Certain embodiments produce a magnetic field that is substantially uniform across each well bottom, while other embodiments produce a magnetic field that is stronger toward…
Methods and Compositions for Analysis of Nucleic Acids
Granted: February 2, 2012
Application Number:
20120028826
Compositions and methods for analysis of nucleic acids are disclosed. Targets are hybridized to arrays having features that include pairs of co-localized probes within features. The probe pairs may include a first probe type that is oriented so that the 5? end is free and the 3? end is attached to the support and a second probe type that is oriented so that the 3? end is free for extension and the 5? end is attached to the support. The probes of a feature are complementary to different…
Method for detecting transcription factor-protein interactions
Granted: January 26, 2012
Application Number:
20120021938
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.
Cleaning Solution
Granted: January 19, 2012
Application Number:
20120015862
Disclosed are cleaning solutions. More particularly, non-toxic solutions of base, water, alcohol and detergent, that effectively and surprisingly eliminate contaminating aliphatic acids in aqueous solutions. When present as a foam or even a contaminating film remaining on various parts and surfaces, aliphatic acid contaminants can be present a large and costly problem in manufacturing operations, cleaning tasks, personal hygiene. The need to remove such contaminants arises in a myriad…
Methods for Genotyping
Granted: January 12, 2012
Application Number:
20120010087
Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers. The capture probes may be locus specific and allele-specific. The amplified sample may be hybridized to an array…
Use of Acid Scavengers for the Synthesis of Standard Lenght and Long-Mer Nucleic Acid Arrays
Granted: January 12, 2012
Application Number:
20120010108
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…
Detection of Nucleic Acids Through Amplification of Surrogate Nucleic Acids
Granted: January 12, 2012
Application Number:
20120009577
Methods for detecting and optionally quantitating one or more target nucleic acids are provided, in which a surrogate nucleic acid is captured to each target nucleic acid, amplified, and detected. Compositions, kit, and systems related to the methods are also described.
Detection of Nucleic Acids and Proteins
Granted: January 5, 2012
Application Number:
20120004132
Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system…
Signal Multiplexing and Signal Amplification
Granted: January 5, 2012
Application Number:
20120003648
Disclosed are methods, compositions and kits for amplifying signals for detecting the presence, quantity and/or sequence of nucleic acids and proteins, as well as methods, compositions and kits for increasing the number of such targets simultaneously detectable in a sample. Detection may be, for instance, in vivo, in cellulo or in situ. Amplification of signal is achieved by way of hybridization of nucleic acid label probe systems and structures. Increase in target multiplex capacity is…
Methods of analysis of allelic imbalance
Granted: December 29, 2011
Application Number:
20110319273
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…
SYSTEMS AND METHODS FOR PROCESSING SENSOR MODULES
Granted: December 15, 2011
Application Number:
20110303027
The invention provides methods and components for assembly of arrays of sensors from modular units containing component sensors of the array. The methods are particularly useful for forming arrays of microarrays. The sensor modules can readily be assembled in different combinations thereby allowing many different modular sensor arrays to be assembled from the same building blocks. Such modular sensor arrays offer advantages of economies of scale for a manufacturer of the modular units…
Multiplex Amplification Methods
Granted: December 1, 2011
Application Number:
20110294689
Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential…
Complexity Management of Genomic DNA
Granted: November 24, 2011
Application Number:
20110287491
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 amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of…
Methods, systems and computer software for designing and synthesizing sequence arrays
Granted: November 17, 2011
Application Number:
20110281772
Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene…
Feature Intensity Reconstruction of Biological Probe Array
Granted: November 10, 2011
Application Number:
20110274328
The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
System and Method for Making Lab Card by Embossing
Granted: November 3, 2011
Application Number:
20110268832
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.
Amplification and Analysis of Selected Targets on Solid Supports
Granted: November 3, 2011
Application Number:
20110269631
Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. Targets are circularized by hybridization to probes followed by ligation of the ends of the target to form a closed circle. The targets are then used as template for extension of an array bound probe resulting in…
Differential Filtering of Genetic Data
Granted: October 20, 2011
Application Number:
20110257896
Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and…
System, method, and computer software for linked window interfaces
Granted: October 20, 2011
Application Number:
20110258525
Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more…
Methods and Computer Software Products for Identifying Transcribed Regions of a Genome
Granted: October 13, 2011
Application Number:
20110250602
Methods and computer software products are provided for transcriptional annotation. In one embodiment of the invention, a region of the genome where the intensity of hybridization of all the probes are above a threshold value (usually the level of non-specific hybridization) is identified. The region may be identified by aligning the probes against the genome; walking through the genome to find regions where all consecutive probes have intensities above the threshold value.
