Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: An array-based method for performing SNP analysis is provided. In certain embodiments, the method may comprise: a) contacting a labeled genomic sample with an array comprising a first SNP-detecting oligonucleotide and a second SNP-detecting oligonucleotide that differ from each other by a single nucleotide, under hybridization conditions that provide binding equilibrium; and b) evaluating a SNP of said labeled genomic sample by comparing: i. binding of the labeled genomic sample to the first SNP-detecting oligonucleotide and ii. binding of the labeled genomic sample to said second SNP-detecting oligonucleotide.

Abstract: A test system includes an optical medium, a binding agent capable of capturing a target complex, and a light detector. The optical medium provides a light path, and the binding agent is positioned to hold the target complex in an evanescent field created by propagation of light along the light path. The complex interacts with the evanescent field and emits light that the detector positioned to detect. The optical medium and the detector can be included in an optical integrated circuit where detected light passes through the optical medium transverse to the direction of the light path.

Abstract: The invention relates to novel methods for reducing background fluorescence of arrays. In particular embodiments, the invention provides a method of treating an array by exposing the array to light wherein the array receives at least a specified dosage of light. In various embodiments the invention also provides a device for exposing an array to light, wherein the device includes: (a) a light source capable of producing light; and (b) an array holder configured to hold the array, the array holder disposed to permit the array to receive the light from the light source.

Abstract: Methods, systems and computer readable media for analysis of comparative genomic hybridization data analysis, including creating a centralization curve from log ratio data values for DNA copy numbers of a genome of a test sample relative to a genome of a reference sample, wherein the reference sample has a known ploidy, and the test sample has a same copy number as the reference sample in normal, non-aberrant genomic regions; identifying a peak corresponding to regions of normal copy number in the centralization curve; centralizing the log ratio data so that the peak corresponding to regions of normal copy number is centered at a log ratio value of zero; calculating a mathematical measurement that is a function of the width of the peak corresponding to regions of normal copy number; calculating a tolerance value as a function of the mathematical measurement; and outputting the tolerance value.

Abstract: A measurement inside a specimen is performed by providing a nanoscale FET probe comprising a cantilever element and a nanowire extending from the cantilever element. The nanowire is electrically connected to the cantilever element at at least one of the ends of the nanowire. The nanowire is coated along at least part of the length thereof with molecules of a capture agent. The cantilever element is moved to insert the nanowire onto the specimen. An electrical property of the nanoscale FET probe is monitored to detect binding events between the capture agent molecules and an analyte of interest inside the specimen.

Abstract: A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

Abstract: A method and system for estimating the background signal over an arbitrarily-sized region of a scanned image of a molecular array, including a background region surrounding the ROI corresponding to the feature. A bit mask is generated, based on a molecular-array, feature-based data set that includes pixel-based intensities and a list of features, including feature coordinates and feature ROI radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and ROIs. An integrated intensity for a background region of arbitrary size and shape can be efficiently determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask.

Abstract: Automated methods and systems for determining an in-focus-distance for a position on the surface of a molecular array substrate using a molecular array scanner are provided. A signal from a first position of an array substrate is detected and noise is filtered out of the detected signal using a symmetrical filter to produce an in-focus-distance. In one embodiment, the in-focus-distance is utilized as an estimated in-focus-distance at a second position of the array substrate. The method finds use in maintaining the focus of a light source while scanning the array by the scanner. Also provided are methods of assaying a sample using the methods and systems of the invention, and kits for performing the invention. The subject invention finds use in a variety of different applications, including both genomics and proteomics applications.

Abstract: A maximum sensitivity optical scanning system is disclosed. It finds use in a variety of applications, including the reading of biopolymeric arrays. It operates by scanning sample at a setting selected to result in signal saturation for some, but not all available data. Subsequent scans of the same area are taken at lower sensitivity settings (in terms of detector gain and/or excitation light source gain or attenuation) and data from at least the previously saturated regions is obtained. If system sensitivity is set too low to produce useful results, optional features may adjust sensitivity upward and follow with an increased sensitivity scan as a remedial measure. Full signal sensitivity is better preserved as most needed in taking data for the weakest signals first with the high-level scan. Data for sample producing stronger signals that can better tolerate photobleaching is then taken in one way or another.

Abstract: Optical scanner system approaches are described in which novel focusing approaches are provided. A control algorithm accounts for geometric variation of successive scans in opposite directions across a microarray slide or substrate in order to provide optimized focus. The feedback approach taught may involve PI or PID terms. In either type of control approach, a projected slope of the slide is calculated and followed back and forth outside a scan region of the array in exiting and entering fully adaptive focusing zones, respectively. During turn-around, the system may track a setpoint between the periods of following the extrapolated slope. Also provided are methods of using the subject system in a biopolymer array based application, including genomic and proteomic applications.

Abstract: A maximum sensitivity optical scanning system is disclosed. It finds use in a variety of applications, including the reading of biopolymeric arrays. It operates by scanning sample at a setting selected to result in signal saturation for some, but not all available data. Subsequent scans of the same area are taken at lower sensitivity settings (in terms of detector gain and/or excitation light source gain or attenuation) and data from at least the previously saturated regions is obtained. If system sensitivity is set too low to produce useful results, optional features may adjust sensitivity upward and follow with an increased sensitivity scan as a remedial measure. Full signal sensitivity is better preserved as most needed in taking data for the weakest signals first with the high-level scan. Data for sample producing stronger signals that can better tolerate photobleaching is then taken in one way or another.

Abstract: An automated method and system for determining an optimal focus distance for scanning a molecular array scanner. Blocks of rows of a reference array are automatically scanned at successively greater distances of the stage from a light gathering medium, such as an optical fiber, or z-positions, to produce data providing a functional relationship between z-position and measured signal intensities. The data is then processed by a peak-height-based, or window-based, focus-finding routine that selects an optimal focus-distance for data scans.

Abstract: Optical scanner system approaches are described in which novel focusing approaches are provided. A control algorithm accounts for geometric variation of successive scans in opposite directions across a microarray slide or substrate in order to provide optimized focus. The feedback approach taught may involve PI or PID terms. In either type of control approach, a projected slope of the slide is calculated and followed back and forth outside a scan region of the array in exiting and entering fully adaptive focusing zones, respectively. During turn-around, the system may track a setpoint between the periods of following the extrapolated slope. Also provided are methods of using the subject system in a biopolymer array based application, including genomic and proteomic applications.

Abstract: Automated methods and systems for determining an in-focus-distance for a position on the surface of a molecular array substrate using a molecular array scanner are provided. A signal from a first position of an array substrate is detected and noise is filtered out of the detected signal using a symmetrical filter to produce an in-focus-distance. In one embodiment, the in-focus-distance is utilized as an estimated in-focus-distance at a second position of the array substrate. The method finds use in maintaining the focus of a light source while scanning the array by the scanner. Also provided are methods of assaying a sample using the methods and systems of the invention, and kits for performing the invention. The subject invention finds use in a variety of different applications, including both genomics and proteomics applications.

Abstract: A method and system for estimating the background signal over an arbitrarily-sized region of a scanned image of a molecular array, including a background region surrounding the ROI corresponding to the feature. A bit mask is generated, based on a molecular-array, feature-based data set that includes pixel-based intensities and a list of features, including feature coordinates and feature ROI radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and ROIs. An integrated intensity for a background region of arbitrary size and shape can be efficiently determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask.

Abstract: A method and system for partitioning DNA sequences into sets of sequences. Each set of sequences, or partition, can be fully analyzed in a single CMT/PEA genotyping assay or other type of genotyping assay resulting in a mass spectrum generated form cleaved mass tags or extended oligonucleotide primers. Four different methods for partitioning an initial set of DNA sequences, each containing an SNP, are disclosed. All four methods employ the assignability of bi-allenlic SNP sequence pairs to sequence pair partitions in order to build the partitions sequence-pair-by-sequence-pair. A partition is assignable when there is at least one unique mass spectrum peak generated in a CMT/PEA or analogous genotyping assay for each sequence of each sequence pair within the partition.

Abstract: A maximum sensitivity optical scanning system is disclosed. It finds use in a variety of applications, including the reading of biopolymeric arrays. It operates by scanning sample at a setting selected to result in signal saturation for some, but not all available data. Subsequent scans of the same area are taken at lower sensitivity settings (in terms of detector gain and/or excitation light source gain or attenuation) and data from at least the previously saturated regions is obtained. If system sensitivity is set too low to produce useful results, optional features may adjust sensitivity upward and follow with an increased sensitivity scan as a remedial measure. Full signal sensitivity is better preserved as most needed in taking data for the weakest signals first with the high-level scan. Data for sample producing stronger signals that can better tolerate photobleaching is then taken in one way or another.