Abstract: The invention features a method of diagnosing an iron disorder, e.g., hemochroatosis, or a genetic susceptibility to developing such a disorder in a mammal by determining the presence of a mutation in exon 2 or in an intron of an HFE nucleic acid.

Abstract: A system for optimising the cycling conditions used to control a polymerase chain reaction assigns membership values for denaturation, annealing and extension events in order to determine the relative contribution of each event during the reaction, and using genetic algorithms to determine the optimum times required to complete each event.

Abstract: The present invention relates to a composition comprising a plurality of polynucleotide sequences. The composition can be used as probes or array elements.

Abstract: The invention is directed to purified and isolated novel DAKAR (death associated kinase containing ankyrin repeat) polypeptides, the nucleic acids encoding such polypeptides, processes for production of recombinant forms of such polypeptides, antibodies generated against these polypeptides, fragmented peptides derived from these polypeptides and the uses of the above.

Abstract: Methods and compositions are provided for analyzing differences in the RNA profiles between a plurality of different physiological samples. In the subject methods, a set of a representational number of distinct gene specific primers is used to generate labeled nucleic acids from each of the different physiological samples. The labeled nucleic acids are then compared to each other and differences in the RNA profiles are determined. The subject methods find use in methods of identifying differential gene expression.

Abstract: Compositions and methods for the therapy and diagnosis of cancer, such as breast cancer, are disclosed. Compositions may comprise one or more breast tumor proteins, immunogenic portions thereof, or polynucleotides that encode such portions. Alternatively, a therapeutic composition may comprise an antigen presenting cell that expresses a breast tumor protein, or a T cell that is specific for cells expressing such a protein. Such compositions may be used, for example, for the prevention and treatment of diseases such as breast cancer. Diagnostic methods based on detecting a breast tumor protein, or mRNA encoding such a protein, in a sample are also provided.

Abstract: An apparatus and method for identifying and/or quantifying a charged biological substance in a conductive liquid medium.

Abstract: Techniques for facilitating the identification of candidate genes from a plurality of DNA sequences. According to an embodiment of the present invention, techniques are provided for extracting and integrating information from various information sources and results of various analyses, and storing the integrated information in a form which is conducive to identification of candidate genes. The stored information may include results of a homology search for the plurality of DNA sequences, annotative information for the plurality of DNA sequences indicating the biochemical functions and physiological roles of the plurality of DNA sequences, gene expression profile data for the plurality of DNA sequences describing behavioral patterns of the plurality of DNA sequences, results from clustering the plurality of DNA sequences based on time course data as described by the gene expression profile data, and other information.

Abstract: The present invention relates, first, to methods for the synthesis of peptides referred to as T-1249 and T-1249-like peptides. Such methods utilize solid and liquid phase synthesis procedures to synthesize and combine groups of specific peptide fragments to yield the peptide of interest. The present invention further relates to individual peptide fragments which act as intermediates in the synthesis of the peptides on interest (e.g., T-1249). The present invention still further relates to groups of such peptide intermediate fragments which can be utilized together to produce full-length T-1249 and T-1249-like peptides.

Abstract: A family of tumor rejection antigen precursors, and the nucleic acid molecules which code for them, are disclosed. These tumor rejection antigen precursors are referred to as BAGE tumor rejection antigen precursors, and the nucleic acid molecules which code for them are referred to as BAGE coding molecules. Various diagnostic and therapeutic uses of the coding sequences and the tumor rejection antigen precursor molecules are described.

Abstract: Compounds and methods for treating prostate cancer are provided. The inventive compounds include polypeptides containing at least a portion of a prostate tumor protein. Vaccines and pharmaceutical compositions for immunotherapy of prostate cancer comprising such polypeptides, or DNA molecules encoding such polypeptides, are also provided, together with DNA molecules for preparing the inventive polypeptides.

Abstract: Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.

Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In one embodiment of the invention, the test regions (which can be wells) are further subdivided into smaller subregions (indentations, or dimples).

Abstract: Described herein are methods that can be used for diagnosis and prognosis of colorectal cancer. Also described herein are methods that can be used to screen candidate bioactive agents for the ability to modulate colorectal cancer. Additionally, methods and molecular targets (genes and their products) for therapeutic intervention in colorectal cancer are described.

Abstract: A method for displaying results of hybridization experiments using a biochip is provided. In the method, a plurality of control spots spotted in each of a plurality of sections defined on a biochip is measured. The measured data are plotted on a graph for each section, and all of the graphs are simultaneously displayed on a single screen in the same arrangement as that of the sections on the biochip. By simultaneously displaying all of the graphs on a single screen, it is possible to skim the whole biochip to find experimental errors. Also, experimental errors can be quantified with respect to the dispersion of control data on the basis of the linearity of the data points and slope angles defined for each data points on a graph.

Abstract: Cancer associated antigens have been identified by autologous antibody screening of libraries of nucleic acids expressed in renal cancer cells using antisera from cancer patients. The invention relates to nucleic acids and encoded polypeptides which are cancer associated antigens expressed in patients afflicted with renal cancer. The invention provides, inter alia, isolated nucleic acid molecules, expression vectors containing those molecules and host cells transfected with those molecules. The invention also provides isolated proteins and peptides, antibodies to those proteins and peptides and cytotoxic T lymphocytes which recognize the proteins and peptides. Fragments of the foregoing including functional fragments and variants also are provided. Kits containing the foregoing molecules additionally are provided. The molecules provided by the invention can be used in the diagnosis, monitoring, research, or treatment of conditions characterized by the expression of one or more cancer associated antigens.

Abstract: A sensor for identifying molecular structures within a sample solution is disclosed. The sensor comprises an insulating layer with a plurality of interspaced channels therein having essentially the same direction. The channels furthermore have submicron dimensions. A method of fabricating a sensor for identifying molecular structures within a sample solution is also disclosed.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: Methods of providing shuffling libraries that include codon-varied oligonucleotide sequences are described. Codon-varied oligonucleotides are synthesized using trinucleotide or mononucleotide phosphoramidite sequences, and are derived from homologous or non-homologous nucleic acid sequences, or combinations of such sequences. Various methods of recombining codon-varied oligonucleotide sequences to expedite artificial evolution are also described. The present invention additionally relates to various integrated systems that are optionally used to automate these recombination methods.

Abstract: Systems, tools and methods of assaying biological material are used to perform complex sandwich hybridization assays. The tools used comprise biological solution probes that are customized for each assay. The solution probe comprises a first region for hybridizing to a probe, in a generic set of capture probes on a universal assay apparatus, and a second region for hybridizing to a target in a sample. The solution probe assembles the target to the assay apparatus by hybridizing the second region to the target and the first region to the capture probe. In array assays, one or more biological samples, having one or more targets per sample, can be multiplexed on the same universal array comprising the generic set of capture probes in an array pattern of features on the substrate. The customized solution probe addresses and assembles a predetermined target-sample combination onto the array at a corresponding capture probe address location.