Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

Abstract: The invention relates to a composition, method and apparatus for determining the sequence of a nucleic acid strand utilizing a pH-sensing agent.

Abstract: Provided is a reaction device for nucleic acid analysis wherein microparticles, which carry a nucleic acid to be detected having been immobilized thereon, are aligned in a lattice form on a substrate according to the pixel size of a two-dimensional sensor. By this reaction device for nucleic acid analysis which is provided with a channel-forming reaction chamber on the substrate (101), the nucleic acid having been immobilized on the microparticles (103) on the substrate (101) is detected. The microparticles (103), which carry the nucleic acid to be detected having been immobilized thereon, are arranged by microstructures (102) aligned on the substrate (101).

Abstract: Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.

Abstract: The present invention provides methods and kits for determining which microRNAs bind to a target mRNA where the methods comprise the steps of (a) creating a bait sequence from the target mRNA, where the bait sequence comprises a label that binds to a binding agent; (b) adding a mixture of microRNAs to the bait sequence; (c) separating the microRNAs that bind to the bait sequence from those microRNAs that do not bind; and (d) identifying the microRNAs that bind to the bait sequence, wherein the microRNAs identified are those that bind to the target mRNA.

Abstract: A system for holding at least one of sample and reagent for analysis. The system includes a pair of parallel covers, at least one of which is light transmissive, of which pair a light transmissive cover forms a top, and of which pair the other forms a bottom. A frame is disposed between the covers to define, in relation to the covers, an interior volume. The frame and the covers are associated with one another to form a case, the case being substantially tight to liquids. A microfluidic array is disposed in the interior volume. The array includes a sheet of material having a pair of opposed surfaces, a thickness, and a plurality of through-holes running through the thickness between the surfaces, the through-holes containing at least one of sample and reagent.

Abstract: Disclosed herein are systems and methods for the assignment of therapeutic pathways to members of a network of oncology. The systems and methods allow for storage of disparate information in a database and determine a uniform semantics for all of the stored information. In addition, the systems and methods allow for the calculation of treatment pathways based on patient information as well as publicly-available information relating to particular diseases, and for the refinement of those treatment pathways as new information is added. Robot-assisted genomic labs permit automated genetic testing, which is integrated with the system.

Abstract: A fluorescence analyzing method includes the steps of irradiating a board, to which oligonucleotide is fixed, with light for fluorescence measurement; focusing produced fluorescence to form an image; and detecting the fluorescence with a two-dimensional sensor. Here, the board is provided with plural regions to which the oligonucleotide is fixed, and the plural regions are spaced apart from one another on the board substantially equidistantly in the vertical and horizontal directions. A fluorescent image is detected in a condition where the following equation is satisfied: dd=ds×M/n where ds denotes the interval between the regions, M denotes the imaging magnification of an optical focusing/imaging system, dd denotes the pixel pitch of the two-dimensional sensor, and n denotes an integer (n=1, 2, 3, 4, 5).

Abstract: An automated machine for transferring solution from a source microwell plate to a destination microwell plate. A plurality of pins is used for transferring the solution. The pins are attached to pin assemblies. The pin assemblies are attached to the circumference of a circular dial that is rotatably connected to the automated machine. The circular dial rotates the pins form a solution removal position to a solution transfer position and then to a pin cleaning position. Solution is removed from individual wells at the solution removal position and the solution is transferred to individual wells at the solution transfer position. The pins are cleaned at the pin cleaning position. A computer is programmed to control the automated machine and the transfer of solution. In a preferred embodiment, the computer is programmed to: 1) execute a saved transfer list, 2) accept a customized input list from an operator, 3) execute the customized input list, and 4) save the customized input list for later execution.

Abstract: The invention relates to a method for acquisition of genetic information, in particular for personalized medicine.

Abstract: The present invention provides a tool for analysis of expression of Macaca fascicularis gene expression analysis tool containing a set of nucleic acids containing base sequences the same or substantially the same as two or more base sequences selected from the group consisting of the base sequences shown by SEQ ID NOs:1-14, or partial sequences thereof, and a method of analyzing the expression of Macaca fascicularis gene, including measuring a gene transcription product in a Macaca fascicularis sample using the tool.

Abstract: The present invention relates among others to a method of pooling samples to be analyzed for a categorical variable, wherein the analysis involves a quantitative measurement of an analyte, said method of pooling samples comprising providing a pool of n samples wherein the amount of individual samples in the pool is such that the analytes in the samples are present in a molar ratio of x0:x1:x2:x(n?1), and wherein x is equal to a positive value other than 1 representing the pooling factor.

Abstract: In one aspect, described herein are field effect chemical sensor devices useful for chemical and/or biochemical sensing. Also provided herein are methods for single molecule detection. In another aspect, described herein are methods useful for amplification of target molecules by PCR.

Abstract: A method and an array filling system for loading a plurality of disparate sample containers, the sample containers comprising an integral structure. Each receptacle is characterized by a hydrophilic surface, and the receptacles are separated by a hydrophobic surface. The system has a liquid transfer device capable of holding liquid and adapted for motion to cause sequential communication of liquid held in the liquid transfer device with successive receptacles of the array by dragging the liquid across the hydrophobic surface.

Abstract: A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention.

Abstract: Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal.

Abstract: In a genome sequencing system and methodology, a protocol is provided to achieve precise alignment and accurate registration of an image of a planar array of nanoballs subject to optical analysis. Precise alignment correcting for fractional offsets is achieved by correcting for errors in subperiod x-y offset, scale and rotation by use of minimization techniques and Moiré averaging. In Moiré averaging, magnification is intentionally set so that the pixel period of the imaging element is a noninteger multiple of the site period. Accurate registration is achieved by providing for pre-defined pseudo-random sets of sites, herein deletion or reserved sites, where nanoballs are prevented from attachment to the substrate so that the sites of the array can be used in a pattern matching scheme as registration markers for absolute location identification.

Abstract: The present invention includes composition and methods for making and using a combinatorial library to identify modified thioaptamers that bind to, and affect the immune response of a host animal, transcription factors such as IL-6, NF-?B, AP-1 and the like. Composition and methods are also provided for the treatment of viral infections, as well as, vaccines and vaccine adjuvants are provided that modify host immune responses.

Abstract: A copy number variations detecting apparatus and method according to at least one embodiment of the present invention compare column vectors adjacent to each other on array comparative genomic hybridization data (aCGH data) and compartmentalize the aCGH data into a plurality of segments according to the comparison results, compare row vectors within the segments for each segment and reconfigure the segments into a predetermined number of clusters according to the comparison results, selectively determine the segments as a candidate copy number variation zone corresponding to a distribution form of the clusters for each segment, detect the CNVs within the candidate CNVZ for each sample, and perform merging and pruning on the candidate CNVZ(s) to obtain a final CNVZ(s).

Abstract: Multiplexed affinity purification and thermal dissociation prior to biochip hybridization simplifies uncharacterized sample admixtures, thereby minimizing or eliminating sample interferents, improving hybridization specificity on a microarray detector, and minimizing or eliminating the need for post-hybridization thermal dissociation analysis. An integrated thermo-affinity sample preparation sub-circuit for sample purification and enrichment is described that is consistent with a field-portable form factor and analytical processes. Thermo-affinity sample preparation on model admixtures of varying complexity was efficacious.

Abstract: A portable plasma based diagnostic apparatus comprising a plasma source for producing energy projectiles atmospheric pressure, a mass analyzer, a sampling interface for receiving direct sample to be analyzed, the sampling interface being positioned between the plasma source and the mass analyzer, a database containing a library of biomarkers with their associated mass spectra, a processor operatively connected to the plasma source, the mass analyzer and the database. The processor is so configured so as to obtain from the mass analyzer a sample mass spectrum of parent and fragment ions resulting form the collision between the energetic projectiles and the sample, compare the sample mass spectrum with mass spectra in the reference library in order to identify at least one indicator and provide a report based on the at least one identified indicator.

Abstract: The sequence of a target polynucleotide can be determined by: (i) contacting the target polynucleotide with a polymerase enzyme and one of the nucleotides A, T(U), G and C under conditions suitable for the polymerase reaction to proceed; (ii) measuring the time taken for the polymerase to bind to and subsequently dissociate from the target polynucleotide, to thereby determine whether the polymerase has incorporated the nucleotide onto the target polynucleotide; (iii) optionally repeating steps (i) and (ii) with additional nucleotides, to thereby identify the sequence of the target polynucleotide.

Abstract: System, including apparatus and methods, for performing droplet-based assays. The system may comprise a droplet transporter configured to pick up droplets from each emulsion of an array of reacted emulsions and to drive flow of the droplets through a detection region. The system also may comprise a detector configured to collect data related to one or more analytes from individual droplets of the reacted emulsions as such individual droplets travel through the detection region. The system further may comprise a controller programmed to determine, based on the data collected, an aspect of the one or more analytes in one or more samples included in droplets of the emulsions.

Abstract: Individual patient- and disease-specific test results are obtained from a mixture of one or more distinct tests from multiple combined and distinct patient samples or reactions. In an especially preferred aspect, multiple reaction products from oligonucleotides having unique identifier portions are prepared or received from a clinician and combined for hybridization on a chip. Test results are deconvoluted using a deconvolution table in which associative data are employed to provide access to the individual patient- and disease-specific test results.

Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.

Abstract: The present invention relates to a method for identifying proteins in one or more samples based on the isolation and analysis of their C-terminal peptides. The isolated peptides are purified and analysed by Mass spectroscopy. Identification of the parent protein is based on the mass of the C-terminal peptide in combination with additional physicochemical parameters. The present invention further relates to an annotated database of C-terminal peptides of in silico cleaved proteins comprising the masses of C-terminal peptides and one or more physicochemical properties thereof.

Abstract: BioMEMS/NEMS appliance biologically monitors an individual, using biosensors to detect cellular components. Data is simulated or analyzed using systems-biology software, which provides diagnostic or therapeutic guidance.

Abstract: The present invention provides a sensor apparatus based on 2D films or 3D assemblies of cubic nanoparticles capped with an organic coating. The apparatus is used to determine the composition and preferably measure the concentration of volatile and non-volatile compounds in a sample, with very high sensitivity. Methods for use of the apparatus in applications such as diagnosis of disease, food quality and environmental control are disclosed.

Abstract: Integrated universal chemical detector in a micro-optical chip in which chemical/bio-sensitive micro/nano-pixels are aligned to create diffraction patterns that can be visually or instrumentally categorized in order to identify a substantial plurality of agents. By using a diffraction method to create a macroscopic diffraction image, a single small array can effectively detect hundreds or even thousands of different chemicals. The apparatus can be further automated by analyzing the diffraction patterns electronically.

Abstract: The present invention provides a biological finger-print system for botanics and/or herbal medicine by using the overall gene expression profiling in peripheral white blood cells. Besides, the present invention further provides clinical application in humans for monitoring the potential adverse or side effects of botanics and/or herbal medicine.

Abstract: The present invention relates to a device for the isolation and/or purification of nucleic acid molecules suitable to bind and/or inactivate inhibitors of the activity of reagents or enzymes used for DNA manipulation and to separate a plurality of nucleic acid molecules with respect to their size. Moreover, the invention relates to a method for the isolation of a nucleic acid molecule comprising applying a sample to the device of the invention wherein said nucleic acid molecule preferably represents a fraction of the metagenome of a given habitat. Furthermore, the invention relates to a method for the generation of at least one gene library comprising nucleic acid molecules isolated by the method of the invention and to a nucleic acid molecule isolated by the method of the invention.

Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: A method and system for sequencing polypeptides utilizing acid and base labile xanthates.

Abstract: The present invention aims to improve detecting accuracy and reproducibility of a biomolecule sensor. The biomolecule sensor of the present invention includes single probe molecules orderly aligned and fixed on grid points on the surface of a substrate. Accordingly, in the biomolecule sensor of the present invention: probe molecules for detecting a biomolecule are orderly aligned and separately fixed; blocking for preventing non-specific adsorption is applied to a region other than the region of the probe molecules for detecting a biomolecule; and fluorescence enhancement is achieved by metal microparticles.

Abstract: A system and methods of sequencing a nucleic acid by detecting the identity of a fluorescent nucleotide analogue incorporated at the 3? end of a growing nucleic acid strand are provided.

Abstract: A multi-well system is described which is comprised of a tray comprising a plurality of wells which may include thousands, tens of thousands or even hundreds of thousands of wells or more. Each of the wells has a unique address. The system includes a tray top comprised of a plurality of areas wherein each of the areas corresponds uniquely to each of the wells and includes a unique address. The system may include a second tray top also comprised of a plurality of areas with unique addresses which uniquely correspond to each of the wells. The areas on the tops have compounds bound to those areas which compounds bind to components present in the wells and are used to obtain specific material in each well for analysis.

Abstract: A total forensic DNA casework management system and method for the deconvolution of mixed DNA samples using a novel, 3-rule algorithm to determine the proportional allele sharing of the sample's contributors. The process is fully document, can assess and process DNA anomalies and artifacts, and transforms raw STR data to produce final DNA profile types, peak height ratios, proportions, fitting criteria and associated graphs.

Abstract: The invention relates to microstructures and the use thereof for the directed evolution of biomolecules.

Abstract: It is intended to provide a method whereby a plural number of antibodies against cell surface antigens are quickly classified and to provide a method whereby antigens of the thus classified antibodies are quickly identified. Further, it is intended to provide a method of promoting the utilization of the useful data obtained by the above methods. Furthermore, it is intended to provide an antibody which is effective in treating or diagnosing cancer.

Abstract: A magnetic sensor for identifying small superparamagnetic particles bonded to a substrate contains a regular orthogonal array of MTJ cells formed beneath that substrate. A magnetic field imposed on the particle, perpendicular to the substrate, induces a magnetic field that has a component within the MTJ cells that is along the plane of the MTJ free layer. If that free layer has a low switching threshold, the induced field of the particle will create resistance changes in a group of MTJ cells that lie beneath it. These resistance changes will be distributed in a characteristic formation or signature that will indicate the presence of the particle. If the particle's field is insufficient to produce the free layer switching, then a biasing field can be added in the direction of the hard axis and the combination of this field and the induced field allows the presence of the particle to be determined.

Abstract: Assays can determine multiple analytes in a sample, such as a biological marker and a drug-related compound.

Abstract: Apparatus comprising a surface site comprising a substantially inorganic surface having a chemical composition selected from the group consisting of metals, semiconductors, insulators, and mixtures thereof, the surface positioned within a polypeptide bonding region and having a selective bonding affinity for a polypeptide; a plurality of interlayers between which the surface site is interposed; a distal site end on the surface site and distanced from the interlayers, the surface being provided on the distal site end; the surface site and the interlayers being interposed between first and second supports; first and second conductors provided on the first and second supports and having respective first and second distal conductor ends positioned within the polypeptide bonding region; the conductors being capable of applying an external voltage potential across the polypeptide bonding region.

Abstract: A method and device for digital multiplex PCR assays employ a microfluidic chip for performing real-time, continuous flow PCR within microchannels of the chip. A stream of sample material is introduced into each microchannel and alternating boluses of assay-specific reagents and buffer are introduced into the stream to form sequentially configured test boluses. A PCR procedure is performed on the test boluses followed by a thermal melt procedure. During the thermal melt procedure, fluorescent output is detected and fluorescence vs temperature data is collected and compared to expected normal correlations. The results, positive or negative, are converted to digital format, with positive results designated as “1” and negative results designated as “0”, or vice versa.

Abstract: The present invention relates to methods, microarrays and kits for detecting one or more human astrovirus serotypes in a sample (e.g., a fecal sample) from an individual. The method includes amplifying nucleic acid molecules of the sample with one or more primers, to thereby obtain an amplified nucleic acid product; contacting the amplified nucleic acid product with one or more serotype specific probes having a nucleic acid sequence that is specific for only one astrovirus serotype in the group of astroviruses being assessed, wherein the nucleic acid sequence includes between about 9 and 25 nucleic acid bases (e.g., SEQ ID NO: 5-24); and detecting the hybridization complex. The presence of hybridization complexes with a serotype specific probe indicates the presence of one or more specific astrovirus serotypes, and the absence of hybridization complexes with a serotype specific probe indicates the absence of the specific astrovirus serotype.

Abstract: Methods arrays and systems that facilitate contig assembly during nucleic acid sequencing are provided. Geographical locations of analyte molecules on an array are correlated with subsequence relationships within larger nucleic acids.

Abstract: Potential therapeutic, agent for the prevention, treatment or amelioration of an affective disorder, such as a bipolar disorder, depression or anxiety disorder are identified. Also provided are methods for diagnosing and monitoring affective disorders. The methods are based on changes in expression of one or more genes that are differentially expressed in affective disorders.

Abstract: The present invention relates to an apparatus and method of sorting objects and identifying the objects in a forensics sample, including using holographic optical trapping to sort objects from contaminants, and performing (single cell) PCR-based STR analysis on the objects to determine their identification. In addition, the chip used as a support for sorting the objects can also be used for performing single cell PCR-based STR analysis. In another embodiment, a microfluidics chip is used to stream the sample and sort the objects, before single cell PCR-based STR analysis is performed. The chip used for sorting utilizing HOT in the absence or presence of microfluidic streaming and sorting can also be the same as that used for the single cell PCR-based STR analysis.

Abstract: The present invention relates to novel genetic markers associated with scoliosis, risk of developing scoliosis and risk of scoliosis curve progression, and methods and materials for determining whether a human subject has scoliosis, is at risk of developing scoliosis or is at risk of scoliosis curve progression.

Abstract: Combinatorial processing including stirring is described, including defining multiple regions of a substrate, processing the multiple regions of the substrate in a combinatorial manner, introducing a fluid into a first aperture at a first end of a body to dispense the fluid out of a second aperture at a second end of the body and into one of the multiple regions, and agitating the fluid using an impeller at a second end of the body to facilitate interaction of the fluid with a surface of the substrate.

Abstract: The invention relates to a device comprising a first material (10) and a second material. (20) whereby the first and the second material are so provided towards each other as to form at least one focusing microstructure with a focal point (30) located outside of the first material.