Modified Nucleic Acid Probes
Granted: April 21, 2011
Application Number:
20110092382
Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.
Poly(A) Tail Length Measurement by PCR
Granted: March 10, 2011
Application Number:
20110059453
Methods and kits for measuring the length of the poly(A) tail of selected target mRNA are disclosed herein. In preferred aspects the mRNA population is modified by addition of a tail comprising guanosine and inosine (G/I tailing). The added tail is used as a priming site for reverse transcription. The resulting cDNA is then amplified using one or more target specific primers and a universal primer that recognizes the tailed region. The products are separated according to size and the…
Computer Software for Visualizing Genotyping Data
Granted: March 10, 2011
Application Number:
20110060768
A computer system for visualizing recombination events in a group of individuals is provided. According to one aspect of the invention, high-density SNP genotype data is obtained from related individuals in a family. A pedigree is created, haplotypes are reconstructed and likely recombination breakpoints are identified with the use of publicly available computer programs. A software tool is then used facilitate the visualization of the recombination events in the family.
Primer Array Synthesis and Validation
Granted: February 24, 2011
Application Number:
20110046343
Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.
PARALLEL PREPARATION OF HIGH FIDELITY PROBES IN AN ARRAY FORMAT
Granted: February 24, 2011
Application Number:
20110046344
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 for Identifying DNA Copy Number Changes
Granted: February 3, 2011
Application Number:
20110029251
Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to…
Combinatorial Affinity Selection
Granted: February 3, 2011
Application Number:
20110028342
In one aspect of the invention, methods for analyzing nucleic acid sample are provided. In a preferred embodiment, nucleic acids are selected using affinity matrices prior hybridization with a microarray.
PHOTOCLEAVABLE PROTECTING GROUPS
Granted: February 3, 2011
Application Number:
20110028350
Novel compounds are provided, which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein Y is a chemical structure as shown in FIG. 5. Also provided is a method of forming, from component molecules, a plurality of compounds…
HYBRIDIZATION DEVICE, METHODS, AND SYSTEM USING MIXING BEADS
Granted: February 3, 2011
Application Number:
20110028352
A method, device and system for hybridizing a target oligonucleotide to at least one array comprising a plurality of mixing beads are provided. A target solution is mixed by agitating the mixing beads while the target oligonucleotides are hybridizing to the complementary probes on the array. In another embodiment, a permeable barrier contains the mixing beads, thereby preventing them from contacting the array surface.
USE OF ACID SCAVENGERS FOR THE SYNTHESIS OF STANDARD LENGTH AND LONG-MER POLYMER ARRAYS
Granted: January 20, 2011
Application Number:
20110015098
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…
Consumable elements for use with fluid processing and detection systems
Granted: January 13, 2011
Application Number:
20110009297
One embodiment describes an automated and flexible system to analyze probe arrays. It comprises a plurality of arrays mounted on pegs that are moved by an instrument handling robot to liquid reaction stations.
Methods for Genotyping Selected Polymorphism
Granted: January 13, 2011
Application Number:
20110009294
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…
METHODS OF USING AN ARRAY OF POOLED PROBES IN GENETIC ANALYSIS
Granted: January 13, 2011
Application Number:
20110009289
The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger…
ANTIREFLECTIVE COATINGS FOR HIGH-RESOLUTION PHOTOLITHOGRAPHIC SYNTHESIS OF DNA ARRAY
Granted: January 6, 2011
Application Number:
20110003716
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…
PHOTOACID GENERATORS FOR THE SYNTHESIS OF OLIGO-DNA IN A POLYMER MATRIX
Granted: December 30, 2010
Application Number:
20100331218
Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
SUBSTRATE PREPARATION PROCESS
Granted: December 30, 2010
Application Number:
20100331217
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.
Photocleavable Protecting Groups
Granted: December 23, 2010
Application Number:
20100324266
Novel compounds are provided, which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds…
Enzymatic Methods for Genotyping on Arrays
Granted: December 23, 2010
Application Number:
20100323914
Disclosed are methods for enzymatic genotyping of polymorphisms on solid supports. In one aspect the method includes hydrolysis of a nucleotide comprising a label on an array-bound probe by a 5? to 3? exonuclease activity specific for single-stranded DNA. If there is target-probe sequence mismatch at the polymorphic position (the labeled nucleotide in the probe), the labeled nucleotide is hydrolyzed from the probe by the exonuclease. The presence of a detectable signal on the array is…
METHOD OF OLIGONUCLEOTIDE SYNTHESIS
Granted: December 9, 2010
Application Number:
20100311128
Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.
Parallel Preparation of High Fidelity Probes in an Array Format
Granted: December 2, 2010
Application Number:
20100305006
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).
