Complexity management and anaylysis of genomic data
Granted: March 23, 2006
Application Number:
20060063158
The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to…
Analytical biochemistry system with robotically carried bioarray
Granted: March 16, 2006
Application Number:
20060057029
An analytical biochemistry system featuring a substrate with reactants immobilized thereon at fixed, known locations, a holder supporting the substrate and a manipulator for transporting the holder to a fixed sample and to an inspection station. The reactants are binding agents for a target biomolecule in a sample which forms a bound substance having a detectable characteristic. The holder may be a standard pipettor, optionally carried by a robot arm or hand as the manipulator to contact…
Methods of genetic analysis of E. coli
Granted: March 9, 2006
Application Number:
20060051769
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of E. coli genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. In one embodiment the nucleic acid sequences provided are present as an array of probes that may be used to measure gene expression of at least 20,000 E. coli genes and at least 500 intragenic regions. As such, the invention relates to diverse fields impacted by…
Methods of genetic analysis of yeast
Granted: March 9, 2006
Application Number:
20060051770
Arrays of oligonucleotide probes which are complementary to a plurality of S. cerevisisae and S. pombe genes are disclosed. The arrays may be used to measure the expression levels of a plurality of genes simultaneously.
Analytical biochemistry system with robotically carried bioarray
Granted: March 2, 2006
Application Number:
20060045812
An analytical biochemistry system featuring a substrate with reactants immobilized thereon at fixed, known locations, a holder supporting the substrate and a manipulator for transporting the holder to a fixed sample and to an inspection station. The reactants are binding agents for a target biomolecule in a sample which forms a bound substance having a detectable characteristic. The holder may be a standard pipettor, optionally carried by a robot arm or hand as the manipulator to contact…
Methods for screening polypeptides
Granted: February 23, 2006
Application Number:
20060040314
In one aspect of the invention, methods are provided for the creation and screening of polypeptides that eliminates bacterial cloning and individual screening In preferred embodiments, the method involves partnering each protein with a unique DNA oligonucleotide tag that directs the protein to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array
Bioarray chip reaction apparatus and its manufacture
Granted: February 23, 2006
Application Number:
20060040380
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.
Apparatus and method for aligning a microarray printing head
Granted: February 16, 2006
Application Number:
20060034725
An alignment apparatus and method are described for accurately and reliably depositing biological materials on a microscope slide or other substrate. A preferred implementation includes a first mounting assembly that enables rotation of deposit elements around a first axis perpendicular to the substrate surface using one or more bearing surfaces concentric with the first axis. A second mounting assembly enables rotation of the deposit elements around a second axis parallel to the…
Methods for identifying DNA copy number changes
Granted: February 16, 2006
Application Number:
20060035258
Methods and computer software products for identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. Genomic DNA is amplified generically and amplified sample is hybridized to an expression array. The expression array comprises probes to regions of genes that are expressed. The probes are complementary to genomic sequences found in mRNAs. Signal intensity is correlated to copy number. The methods…
Complexity management of genomic DNA
Granted: February 16, 2006
Application Number:
20060035274
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 the…
Methods for genotyping polymorphisms in humans
Granted: February 2, 2006
Application Number:
20060024715
Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are…
Methods and compositions for dicing through lithographic micro-machining
Granted: January 26, 2006
Application Number:
20060016782
In one aspect of the invention, a photolithographic method is employed to dice a microarray wafer. In some preferred embodiment, a photoresist that is sensitive to two different radiation sources is employed.
Substrate preparation process
Granted: January 12, 2006
Application Number:
20060008840
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.
Expression monitoring for human cytomegalovirus (HCMV) infection
Granted: January 5, 2006
Application Number:
20060003321
Certain human genes have been found to be induced or repressed in host cells infected with HCMV. A large set of such genes has been identified. These have diagnostic use in determining the extent of tissue damage caused by the infection as well as in determining the stage of disease progression of the HCMV infection. Such genes are likely those involved in mediating the pathology of the infected tissues. Thus by identifying agents which are able to reverse the induction or repression of…
System and method for improved genotype calls using microarrays
Granted: December 29, 2005
Application Number:
20050287575
An embodiment of a method for calling the genotype of a biological sequence is described that comprises receiving sets of intensity data each comprising an intensity value for each probe feature associated with a probe set disposed on a probe array; independently applying filters to the intensity values of a probe set associated with a forward strand and of a probe set associated with a reverse strand, where the probe sets interrogate the same sequence position; independently applying…
Methods for examination of microarrays using surface reflectance measuring tool
Granted: December 22, 2005
Application Number:
20050280826
The present invention provides methods to inspect biomolecules on a solid support using a reflectance measuring tool. In one embodiment of the invention, in-process methods are provided that analyzes wafers after specific steps of the microarray manufacturing process. In another embodiment, probe defects from handling or particulates during manufacturing of microarrays are detected by analyzing wafers and chips.
Method and apparatus for imaging a sample on a device
Granted: December 22, 2005
Application Number:
20050281708
In accordance with various embodiments of the invention, an apparatus is provided for hybridizing a nucleic acid microarray immobilized on a surface of a solid substrate. The apparatus comprises at least one assembly for securing the solid substrate during hybridization, the assembly comprising a carrier and a cover having a surface facing the carrier. The carrier and the cover can be dimensioned to receive the solid substrate between the carrier and the surface of the cover so that the…
Methods for making a device for concurrently processing multiple biological chip assays
Granted: December 22, 2005
Application Number:
20050282156
Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells, subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a…
Molecular genetic profiling of gleason grades 3 and 4/5 prostate cancer
Granted: December 8, 2005
Application Number:
20050272052
Many genes are affected in prostate cancers which have not been previously identified. This includes genes that have been up-regulated or down-regulated. Monitoring the expression levels of these genes is useful to identify the existence of prostate cancer. Also, monitoring the expression levels of these genes is useful to predict the effectiveness of treatment, outcome, use of therapeutics, and screening drugs useful for the treatment of prostate cancer.
Methods of analysis of degraded nucleic acid samples
Granted: December 8, 2005
Application Number:
20050272080
The invention provides arrays for analysis of compromised nucleic acid samples, for example, nucleic acids obtained from formalin fixed paraffin embedded samples and methods to analyzed these compromised samples. Arrays are disclosed in which the probe selection region used to select probes for the array is the 300 bases of the target MRNA that are immediately upstream of the start of the poly(A) tail of the mRNA. The probes selected for the array are more biased toward the 3? end of the…
