Assays for determining telomere length and repeated sequence copy number
Granted: December 3, 2009
Application Number:
20090298709
Methods of detecting copy number of a repeated sequence element, including methods of determining telomere length, are provided. The methods can be multiplexed for detection of repeated sequence element copy number on two or more nucleic acid targets simultaneously. Compositions, kits, and systems related to the methods are also described.
Modified Nucleic Acid Probes
Granted: November 19, 2009
Application Number:
20090286690
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.
ARRAY-BASED TRANSLOCATION AND REARRANGEMENT ASSAYS
Granted: September 24, 2009
Application Number:
20090239764
Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations…
RESEQUENCING METHODS FOR IDENTIFICATION OF SEQUENCE VARIANTS
Granted: September 17, 2009
Application Number:
20090233809
Methods for detection of variant alleles are disclosed. In preferred aspects variants are detected by hybridization patterns to arrays of probes that are contain a single mismatch to a reference sequence, thus reducing the number of probes needed for resequencing by hybridization. The target capture method used is Target Amplification by Capture and Ligation (TACL), and is capable of amplifying many thousands of loci together. Mismatch Repair Detection (MRD) is used as an allele…
Silane Mixtures
Granted: August 27, 2009
Application Number:
20090215652
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: July 30, 2009
Application Number:
20090192050
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).
BIOARRAY CHIP REACTION APPARATUS AND ITS MANUFACTURE
Granted: June 4, 2009
Application Number:
20090143249
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Sequencing of surface immobilized polymers utilizing microfluorescence detection
Granted: May 28, 2009
Application Number:
20090137419
Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents which specifically recognize terminal monomers are used to label polymers at defined positions on a solid substrate.
Methods for Genotyping Polymorphisms
Granted: May 21, 2009
Application Number:
20090131268
The invention provides method for genotyping specific sets of polymorphisms in a single multiplex reaction. The polymorphisms are selected to be of interest in detecting genetic variation that alters individuals' metabolism, distribution, extretion and transport of pharmacological compounds. In preferred aspects the genotyping employs a multiplex hybridization-based assay. In some aspects combinations of methods are employed to allow the combination of polymorphisms to be interrogated.…
Locus specific amplification using array probes
Granted: May 7, 2009
Application Number:
20090117573
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. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.
Methods for Identifying DNA Copy Number Changes Using Hidden Markov Model Based Estimations
Granted: April 16, 2009
Application Number:
20090098547
Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
Methods for Genotyping with Selective Adaptor Ligation
Granted: March 19, 2009
Application Number:
20090075345
The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. This selective adaptor ligation allows for…
PHOTOCLEAVABLE PROTECTING GROUPS
Granted: March 19, 2009
Application Number:
20090076295
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…
Substrate preparation process
Granted: March 5, 2009
Application Number:
20090062148
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.
PHOTOACID GENERATORS FOR THE SYNTHESIS OF OLIGO-DNA IN A POLYMER MATRIX
Granted: March 5, 2009
Application Number:
20090062149
Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
Nucleic Acid Labeling Methods
Granted: February 26, 2009
Application Number:
20090054258
In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3?-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3?-AppN-3?-linker-detectable moiety is used as donor molecule. In another aspect of the present invention, a method of detecting the presence of an RNA of interest in a sample is provided, the…
IDENTIFICATION OF MOLECULAR SEQUENCE SIGNATURES AND METHODS INVOLVING THE SAME
Granted: January 29, 2009
Application Number:
20090029865
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,…
METHODS AND APPARATUS FOR DETECTION OF FLUORESCENTLY LABELED MATERIALS
Granted: January 8, 2009
Application Number:
20090010524
Fluorescently marked targets bind to a substrate 230 synthesized with polymer sequences at known locations. The targets are detected by exposing selected regions of the substrate 230 to light from a light source 100 and detecting the photons from the light fluoresced therefrom, and repeating the steps of exposure and detection until the substrate 230 is completely examined. The resulting data can be used to determine binding affinity of the targets to specific polymer sequences.
Multiplex oligonucleotide addition and target amplification
Granted: January 1, 2009
Application Number:
20090004701
Methods for appending oligonucleotides directly to nucleic acid templates, particularly to defined sites internal to single-stranded templates, are described. Appending first and second common priming sites to each of a plurality of templates of distinct sequence allows the subsequent stoichiometric amplification of a plurality of templates of distinct sequence.
System and method for multiplex liquid handling
Granted: December 18, 2008
Application Number:
20080311585
The present invention generally relates to microfabricated devices for carrying out and controlling chemical reactions and analysis. In particular, the present invention provides systems, methods, devices and computer software products related to multiplex liquid handling systems utilizing lab cards related to biological assays.
