Abstract: The present invention generally relates to spatial and structural genomic analysis compositions, which can be used for the mapping of chromosomes and structural analyses of chromosomal rearrangements, including the entire chromosome, as well as specific portions or regions of interest of the chromosomes. In some embodiments, multiple portions of the genome can be distinguished, for instance, using a first detection entity and a second detection entity different from the first detection entity. The detection entities may be immobilized relative to oligonucleotides, which may be selected to bind to different locations within the chromosome. For instance, the oligonucleotides may be at least substantially complementary to the chromosome, e.g., substantially complementary to a specific location of the chromosome.

Abstract: The present invention generally relates to techniques involving comparative genomic hybridization (CGH) and related techniques, including the validation of assay results. In one aspect, a region of interest of a genome or other target nucleic acid, identified using CGH or similar techniques, may be validated using a probe based on the CGH results. The oligonucleotides, in some embodiments, may bind the genome in some fashion (e.g., to the region of interest, and/or to other predetermined regions), and thus can be used for validation of CGH or other results.

Abstract: Apparatus and methods are disclosed for printing a plurality of biopolymer features on the surfaces of substrates. An apparatus comprises a substrate mount for receiving a substrate, a dispensing device for dispensing reagents for synthesizing a biopolymer on a surface of the substrate, an optical system for positioning the substrate mount along a y-axis and an optical system for positioning the dispensing device along an x-axis. The apparatus may comprise a touch system for positioning the substrate and the dispensing device along a z-axis. One of the substrate mount or the dispensing device is adapted for translation along the y-axis and for rotation about a central axis that is parallel to a z-axis. The other of the above is adapted to move along the x-axis transversely to the direction of, and independently of, movement of the one adapted for translation along the y-axis. The optical systems cooperate to position the substrate mount and the dispensing device relative to one another.

Abstract: A method is described for removing residue from a fluid deposited on the interior surface of an inkjet printhead after the printhead has contained or dispensed the fluid at least once. The method makes use of a reverse flushing technique optionally used in combination with sonication. A cleaning station for flushing an inkjet printhead with a wash fluid, rinse fluid, and/or inert gas is provided as well.

Abstract: Devices, apparatus and methods for conducting hybridization reactions are disclosed. An embodiment of a device comprises two chambers in fluid communication. Each of the chambers has an interior wherein one of the chambers has at least one interior dimension that is larger (larger chamber) than at least one interior dimension of the other of the chambers (smaller chamber). Each of the interiors comprises an array of features.

Abstract: A method and apparatus for fabricating an array of biopolymers on a substrate using a biopolymer or biomonomer fluid, and using a dispensing head. The head has a reservoir chamber and at least one jet which can dispense droplets onto a substrate. The jet includes a capillary delivery chamber communicating with the reservoir chamber, which delivery chamber has an orifice. The jet further includes an ejector which, when activated, causes a droplet to be ejected from the orifice. The method includes loading the head by positioning the head with the orifice adjacent and facing a biomonomer or biopolymer fluid, and providing a load pressure to the reservoir chamber. The load pressure is sufficiently negative such that the fluid is drawn into the reservoir chamber through the orifice and delivery chamber, while simultaneously being insufficient to result in ambient atmosphere entering the delivery chamber through the orifice once the head has been loaded and no further fluid is facing and adjacent the orifice.

Abstract: Systems and methods for optimizing polymer analysis are provided. One such system includes a polymer analysis system having a polymer control system. The polymer analysis system is operative to: apply a set of conditions to a sample being analyzed by the polymer array, the set of conditions correspond to at least one characteristic of the polymer array; analyze the at least one characteristic using the polymer control system; and generate polymer array data.

Abstract: Methods are provided for depositing a quantity of fluid onto the surface of an array. In the subject methods, a thermal inkjet head loaded with the fluid is positioned in opposing relationship to, e.g. over, the array surface. Actuation of the thermal ink-jet results in the expulsion of a quantity of fluid onto the array surface. The subject methods find particular use in array-based binding assays in which an array of binding agents is employed for the detection of an analyte(s), particularly array-based hybridization assays.

Abstract: An apparatus for mixing fluids comprises a housing having at least a portion of its interior, for example, a channel, with capillary dimensions and at least one structural member in the interior adjacent an end of the channel. The dimensions of and placement of the structural member are sufficient such that intermittent application of centrifugal force to the interior of the housing causes movement of the fluid therein. The housing may comprise a mixing chamber or area that is in fluid communication with the interior. The apparatus may comprise a mechanism adapted to generate centrifugal force within the housing to cause movement of fluid in the interior of the housing without exit of fluid therefrom.

Abstract: Apparatus and methods are disclosed relating to linear arrays. An embodiment of an apparatus comprises a rotatable support for one or more linear arrays, a mechanism for rotating the support, and a device for examining the linear arrays for the results of chemical reactions. Each of the linear arrays comprises a plurality of features for conducting the chemical reactions. Optionally, the apparatus may comprise a heater for heating the linear arrays. Optionally, the apparatus may comprise a fluid dispensing device for dispensing processing fluids such as, for example, wash solutions.

Abstract: Apparatus and methods for mixing fluids are disclosed. An apparatus comprises a housing or channel having an interior with capillary dimensions and a pressure activated mechanism in fluid communication with the interior. The pressure activated mechanism is activatable to cause motion of fluid in the interior of the housing thereby mixing the fluid in the interior. An apparatus may comprise an activating mechanism for activating the pressure activated mechanism. Typically, at least a portion of the interior of the housing comprises a linear array of features for conducting chemical reactions. Optionally, an apparatus comprises a fluid dispensing device.

Abstract: Methods and compositions for identifying patient samples are provided. In practicing the subject methods, an SNP profile is determined for a nucleic acid sample, where the determined SNP profile is then employed to identify the source of the sample, e.g., the subject or patient from which the sample was obtained. Also provided are methods of assaying subjects for a condition, e.g., a disease condition, where the assays included an SNP profile based sample source identification step. In addition, compositions and kits for use in practicing the subject methods are provided. The subject methods and compositions find use in a variety of different applications, and are particularly suited for use in clinical assay applications.

Abstract: A method of using a chemical array unit having a chemical array with probes at multiple feature locations. A request for test may be read, which test uses a sub-array of the array. A pattern of the sub-array may be retrieved from a memory using the test request, which memory carries a pattern for the sub-array which is retrievable with the different test request. Also, a method of reading a chemical array unit which has been exposed to a sample, and feature locations of which have been rendered incapable of providing signal data representative of binding of a sample component. Further methods, apparatus, and computer program products are provided.