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.
Complexity management of genomic DNA
Granted: August 9, 2011
Patent Number:
7993883
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…
System, method, and computer software for the presentation and storage of analysis results
Granted: August 2, 2011
Patent Number:
7991560
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for…
Methods for high throughput genotyping
Granted: August 2, 2011
Patent Number:
7991564
Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity…
System, method, and computer software product for linked window interfaces
Granted: August 2, 2011
Patent Number:
7992098
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…
Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping
Granted: July 26, 2011
Patent Number:
7985547
The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
System, method, and product for scanning of biological materials
Granted: July 19, 2011
Patent Number:
7983467
An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon…
Photoacid generators for the synthesis of oligo-DNA in a polymer matrix
Granted: June 21, 2011
Patent Number:
7964654
Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
System, method, and computer product for exon array analysis
Granted: June 14, 2011
Patent Number:
7962289
In one embodiment, a method for analyzing data generated by probe arrays is described that comprises receiving user selections of two or more data files and an identification of one or more subsets of intensity values acquired from a biological probe array. The method includes iteratively opening each data file, identifying the selected subset of intensity values associated with each open data file, determining parameters for processing, storing the parameters and the identified…
Methods and computer software for detecting splice variants
Granted: June 14, 2011
Patent Number:
7962291
Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
Hot start nucleic acid amplification
Granted: May 31, 2011
Patent Number:
7951534
Methods and compositions for performing nucleic acid duplication and amplification reactions are provided. A single-stranded nucleic acid binding protein is selected and provided in the reaction mixture which is assembled at a low, nonstringent temperature to include all of the necessary reagents for successful nucleic acid duplication or amplification reactions. By incorporating a single-stranded nucleic acid binding protein into the reaction mixture at low temperature, the generation…
Oxide layers on silicon substrates for effective confocal laser microscopy
Granted: May 31, 2011
Patent Number:
7951601
Methods of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, the method comprising the steps of providing a silicon wafer substrate having a top side and a bottom side, coating the top side of the silicon wafer with an oxide coating to provide an oxide coated wafer, covalently coupling a plurality of probes to the top side of the coated wafer to provide a fixed polymer array, hybridizing the fixed polymer array with a plurality of labeled…
Cell penetrating peptides for intracellular delivery of molecules
Granted: May 17, 2011
Patent Number:
7943581
The present invention concerns cell-penetrating peptides which comprise an amino acid sequence consisting of GLX9WRAX9WRX1LX2RSLX9WX3X4X5X6X7X8(SEQ ID No: 1), wherein X1 is A, L or G, X2 is W or none, X3 is R or K, X4 is K, L or S, X5 is L or K, X6 is R or W, X7 is K or S, and X8 is A, V or Q, and X9 is W, F or Y. These CPPs can be used as vectors for delivering nucleic acids and/or proteins and/or peptides to cells, in vitro or in vivo.
Use of acid scavengers for the synthesis of standard length and long-mer polymer arrays
Granted: March 22, 2011
Patent Number:
7910312
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…
Analysis of methylation using nucleic acid arrays
Granted: March 8, 2011
Patent Number:
7901882
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.
Methods for selecting a collection of single nucleotide polymorphisms
Granted: February 1, 2011
Patent Number:
7881875
The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
System, method, and product for scanning of biological materials
Granted: January 18, 2011
Patent Number:
7871812
An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon…
Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays
Granted: January 4, 2011
Patent Number:
7862996
Protective groups which may be cleaved with an activatable deprotecting reagent 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…
Multiplex targeted amplification using flap nuclease
Granted: January 4, 2011
Patent Number:
7862999
Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are…
Photoacid generators for the synthesis of oligo-DNA in a polymer matrix
Granted: January 4, 2011
Patent Number:
7863344
Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
