Decision Biomarkers Incorporated

Gsi Group Corporation

Perkinelmer Las, Inc.

Courtagen Life Sciences, Inc.

Roger Dowd

Jean I Montagu

David Root

Jonathan S Ehrmann

Donald J Svetkoff

Donald Victor Smart

James J Cordingley

Mack J Schermer

Joohan Lee

Joseph J Griffiths

Herman Deweerd

Peter Maimonis

Jun Yang

Natalia Rodionova

Nathan Tyburczy

Jeffrey G Donahue

Cassette () performs assays, e.g. multiplexed protein biomarker assays. Wide, bubble-free, slow flows are produced from liquids stored on cassette (), flowing over wide array () of ligand receptors on a capture surface. Flows of Reynolds Number less than about 1, preferably 1&#xd7;10to 5&#xd7;10, are heated in region () preceding and including bubble removal system (). Analyte is introduced through compressed septum (). External actuations of displacement pumps () and valves (A, B, and C) produce flows in response to flow-front optical sensors (). Elastic sheet provides pump and valve diaphragms and resilient expansion of mixing volume (). Break-away cover portions are pistons. Heating is by conduction through cassette from external contact heater. Planar cassette body, when tilted from horizontal, enables upward flow from pumped storage () to reaction () to waste (), with buoyancy bubble removal before reaction. Reading of fluorescence is by external reader, employing calibration, control and reference features on capture surface. Extensive set of calibration features of differing intensities enables self-calibration.

Assays based on liquid flow over arrays

The invention features a method of adjusting the concentration of at least one but not all of a plurality of analytes in a fluid sample to match a known working range of detection of an analyte assay system, where each of the plurality of analytes may or may not be present within an expected initial concentration range having a high end and a low end, and at least one analyte has a high end expected concentration range that exceeds the high end of the working range of the assay system. The expected concentration of the high concentration analyte is adjusted by a proportional scaling constant, &#x3b1;, so that the high end of the adjusted expected concentration range is less than or equal to the high end of the working range, without adjusting the expected concentration range of at least one other of the plurality of analytes. Adjustment is preferably accomplished by adding to the solution phase of the assay one or more scaling agents, each scaling agent binding with specificity to an analyte and thereby preventing it from being detected by the assay system, e.g., by competing with binding to immobilized capture agent. This scaling method contrasts with prior methods, in which a concentration of available analyte is offset by a fixed amount to adjust the detectable threshold of the assay. Here, the amount of scaling agent is proportional to a scaling coefficient, and the scaling agent is present in the solution phase of the assay at high concentrations relative to analyte. Due to the equilibrium conditions established by the laws of mass transfer, the amount of free analyte remaining in solution in the presence of scaling agent is predictable and finite, and can be measured as a quantitative indicator of the initial concentration of the analyte in the sample.

Method of adjusting the working range of a multi-analyte assay

An immobilizing device for biological material comprises a rigid support () carrying a substrate layer () of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers () having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and micro-porous, ultra-thin substrate layers () having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (), round disc (), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube. Fluorescence or luminescence intensity and geometric calibration spots () are shown. Reading is enhanced by the intensity calibration spots () to enable normalization of readings under uneven illumination conditions, as when reading by dark field, side illumination mode. The reference spots are shown being printed simultaneously with printing an array of biological spots or with the same equipment Methods of forming layers of the device include controlled drawing from a bath of coating composition and drying, and spinning of C-D shaped substrates. Post-forming treatment is shown by corona treatment and radiation. Adherent metal oxides (), silica-based materials and other materials are used to unite layers of the composite. In multi-well plates the oxide promotes joining of a bottom plate () and upper, well-defining structure () of dissimilar material. The oxides () also provide beneficial opacity to prevent light entering the glass support, for applying potential to the substrate, etc.

Substrates for isolating reacting and microscopically analyzing materials

An immobilizing device for biological material comprises a rigid support () carrying a substrate layer (') of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers (&#x2032;) having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and micro-porous, ultra-thin substrate layers (&#x2032;) having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (), round disc (), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube. Fluorescence or luminescence intensity and geometric calibration spots () are shown. Reading is enhanced by the intensity calibration spots. () to enable normalization of readings under uneven illumination conditions, as when reading by dark field, side illumination mode. The reference spots are shown being printed simultaneously with printing an array of biological spots or with the same equipment. Methods of forming layers of the device include controlled drawing from a bath of coating composition and drying, and spinning of C-D shaped substrates. Post-forming treatment is shown by corona treatment and radiation. Adherent metal oxides (), silica-based materials and other materials are used to unite layers of the composite. In multi-well plates the oxide promotes joining of a bottom plate (&#x2032;) and upper, well-defining structure () of dissimilar material. The oxides () also provide beneficial opacity to prevent light entering the glass support, for applying potential to the substrate, etc.

Substrates for isolating, reacting and microscopically analyzing materials

A method and system are disclosed for automatically creating crosstalk-corrected data of a microarray utilizing calibration dye spots each of which comprises a single pure dye. A microarray scanner, such as a confocal laser microarray scanner, generates dye images, each of which contains at least one of the calibration dye spots for each of the output channels of the scanner. For each of the calibration dye spots, an output of each of the output channels is measured to obtain output measurements. A set of correction factors is computed from the output measurements to correct the data subsequently gathered from the microarray scanner. In other words, the correction factors are applied to quantitation or measurement data obtained from microarray images which contain spots having dyes of known or unknown excitation or emission spectra to obtain crosstalk-corrected data.

Method and system for automatically creating crosstalk-corrected data of a microarray

A method and system for locally processing a predetermined microstructure formed on a substrate without causing undesirable changes in electrical or physical characteristics of the substrate or other structures formed on the substrate are provided. The method includes providing information based on a model of laser pulse interactions with the predetermined microstructure, the substrate and the other structures. At least one characteristic of at least one pulse is determined based on the information. A pulsed laser beam is generated including the at least one pulse. The method further includes irradiating the at least one pulse having the at least one determined characteristic into a spot on the predetermined microstructure. The at least one determined characteristic and other characteristics of the at least one pulse are sufficient to locally process the predetermined microstructure without causing the undesirable changes.

Methods and systems for processing a device, methods and systems for modeling same and the device

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Natick, MA, United States of America

Roger Dowd