Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.

Abstract: The redundancy in genomic sequence data is exploited by compressing sequence data in such a way as to allow direct computation on the compressed data using methods that are referred to herein as “compressive” algorithms. This approach reduces the task of computing on many similar genomes to only slightly more than that of operating on just one. In this approach, the redundancy among genomes is translated into computational acceleration by storing genomes in a compressed format that respects the structure of similarities and differences important to analysis. Specifically, these differences are the nucleotide substitutions, insertions, deletions, and rearrangements introduced by evolution. Once such a compressed library has been created, analysis is performed on it in time proportional to its compressed size, rather than having to reconstruct the full data set every time one wishes to query it.

Abstract: A method includes identifying, at a processor, a set of communication lines from a plurality of communication lines, the set of communication lines including a first communication line and a second communication line. A first crosstalk characteristic of the first communication line is correlated with a second crosstalk characteristic of the second communication line. The method also includes modifying, at the processor, a first signal corresponding to the first communication line based on a second signal corresponding to the second communication line.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: Haplotypes of one or more portions of a chromosome of an organism from sequencing information of DNA or RNA fragments can be determined. Heterozygous loci (hets) can be used to determine haplotypes. One allele on a first het can be connected (likely to be on the same haplotype) to an allele on a second het, thereby defining a particular orientation between the hets. Haplotypes can be assembled through these connections. Errors can be identified through redundant connection information, particularly using a confidence value (strength) for a particular connection. The connections among a set of hets can be analyzed to determine likely haplotypes for that set, e.g., an optimal tree of a graph containing the hets. Furthermore, haplotypes of different contiguous sections (contig) of the chromosome can be matched to a particular chromosome copy (e.g., to a particular parental copy). Thus, the phase of an entire chromosome can be determined.

Abstract: DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vectors, the second number being smaller than the first number. Each basis vector represents a specific combination of predetermined nucleotide segments. For each of the nucleotide sequences, an approximate representation of the nucleotide sequence is determined based on a combination of the basis vectors. For each pair of nucleotide sequences, a distance between the pair of nucleotide sequences is determined according the distance between the approximate representation of the pair of nucleotide sequences. The set of nucleotide sequences are classified based on the distances between the pairs of nucleotide sequences.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.

Abstract: A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.

Abstract: The invention relates to methods of diagnosing susceptibility to cardiovascular disease, including coronary artery disease. MI, abdominal aorta aneurysm, intracranial aneurysm restenosis and peripheral arterial disease, by assessing the presence or absence of alleles of certain polymorphic markers found to be associated with cardiovascular disease. The invention further relates to kits encompassing reagents for assessing such markers, and methods for assessing the probability of response to therapeutic agents and methods using such markers.

Abstract: The present invention provides a highly-safe information processing system that is capable of effectively using nucleotide sequence information differences between individual organisms to offer semantic information useful for each individual organism while properly preventing leakage and illegal use of nucleotide sequence information. Further, the present invention includes steps a and b. Step a is performed to acquire either encrypted nucleotide sequence-related information or cryptographic key that corresponds to positional information indicating a position within a nucleotide sequence.

Abstract: A comprehensive strategy is used to determine valid reference time-concentration curves (TCCs) from image data. The image data corresponds to a series of image scans acquired over time for an area of interest of a patient to which a contrast agent was previously administered. The image scans are initially registered to a common coordinate system. Then, observed potential reference TCCs in the image scans are compared to modeled reference TCCs to determine if the potential reference TCCs are plausible reference TCCs. Thereafter, any plausible reference TCCs are evaluated to determine if they contain residual, isolated motion artifacts. If a plausible reference TCC does not include any motion artifacts, the plausible reference TCC is considered a valid reference TCC. If a plausible reference TCC is determined to include motion artifacts, the plausible reference TCC is modified to a valid reference TCC by removing the motion artifacts, or otherwise the plausible reference TCC is rejected.

Abstract: The present disclosure provides systems and methods for nucleic acid sequence analysis. A system for processing raw nucleic acid sequence data from a genomic sequencer comprises a data processing server having a housing contained therein one or more processing modules. The one or more processing modules can each comprise an electronic control unit programmed to align nucleic acid sequence data from a genomic sequencing device and perform one or more of variant analysis and structural variant analysis on the nucleic acid sequence data. The system can further comprise a computer server in communication with the processing server. The computer server can be programmed or otherwise configured to process and/or analyze the aligned nucleic acid sequence data.

Abstract: Genetic data in row-wise flat files, such as VCF and VCF-like files, comprising a plurality of data elements of different types is analyzed using a parallel framework in an MPP shared-nothing distributed database having a plurality of distributed segments by first parsing the data into groups of data elements of the same types, converting the data into entry-wise genetic data such that the same types of data elements are in a column, and distributing and storing the entry-wise genetic data in the distributed segments. SQL database queries are used to analyze the genetic data, including locating probable significant associations between genotype and phenotype data.

Abstract: Profiling data includes accessing multiple collections of records to store quantitative information for each particular collection including, for at least one selected field of the records in the particular collection, a corresponding list of value count entries, each including a value appearing in the selected field and a count of the number of records in which the value appears. Processing the quantitative information of two or more collections includes: merging the value count entries of corresponding lists for at least one field from each of a first collection and a second collection to generate a combined list of value count entries, and aggregating value count entries of the combined list of value count entries to generate a list of distinct field value entries identifying a distinct value and including information quantifying a number of records in which the distinct value appears for each of the two or more collections.

Abstract: The present invention concerns markers of resistance of HER2 expressing tumors to treatment with HER2 inhibitors, such as HER2 antibodies, including trastuzumab.

Abstract: A method and apparatus for determining hemoglobin concentration is provided. A method aspect includes the steps of: a) depositing an unlyzed, substantially undiluted blood sample into an analysis chamber adapted to quiescently hold the sample for analysis; b) imaging the sample in a region of the analysis chamber where the height of the chamber is no more than about twenty microns (20?) or no less than about two microns (2?), to produce image signals representative of the optical density of the imaged region; c) determining a sample representative optical density value using the image signals representative of the optical density of the imaged region; and d) determining the hemoglobin concentration of the sample using the sample representative optical density value.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

Abstract: Systems and methods for displaying measured values of a complete blood count (“CBC”) parameter include displaying the measured values of the CBC parameter obtained from a plurality of samples from a first lot of a quality control composition, where the displaying includes displaying a marker corresponding to each measured value from the first lot on a plot that includes a two dimensional coordinate system, and where the two dimensional coordinate system includes a first dimension corresponding to a time at which measured values of the CBC parameter were obtained, and a second dimension corresponding to a numerical value of the CBC parameter.

Abstract: Embodiments of a method and/or system of transmitting and/or receiving data is disclosed.

Abstract: Provided are fragments of human p97 (melanotransferrin) polypeptides having blood-brain barrier (BBB) transport activity, including variants and combinations thereof, conjugates comprising the p97 fragments, and related methods of use thereof, for instance, to facilitate delivery of therapeutic or diagnostic agents across the BBB.

Abstract: The present disclosure relates to apparatus, systems, compositions, and methods for analyzing a sample containing particles. In some aspects the system comprises an analyzer which may be a visual analyzer. In one aspect, this disclosure relates to a particle imaging system comprising a flowcell through which a sample containing particles is caused to flow, and a high optical resolution imaging device which captures images for image analysis of samples. Other compositions, methods and features of this disclosure are disclosed herein.

Abstract: The present invention provides a method of diagnosing the existence of a kidney disorder in a feline comprising measuring the level of expression of one or more biomarkers selected from the group consisting of lumican; collagen alpha 1 (111) chain, variant 12; decorin; secreted frizzled-related protein 2; retinol binding protein 5; MMP-2; MMP-7; and MMP-19, in a biological sample from the feline, wherein differences in expression of the one or more biomarkers in the sample relative to a control value for expression in a sample from a normal animal indicate the existence of a kidney disorder; a method of treating a feline so diagnosed; and compositions, reagents and kits for carrying out the specified methods.

Abstract: Embodiments of methods, apparatuses, devices and/or systems for manipulating hierarchical sets of data are disclosed. In particular, methods, apparatus devices and or/or systems for analyzing hierarchical data are disclosed.

Abstract: Methods and systems for identifying a quantitation cycle (Cq) for a PCR reaction that includes fitting a line having a plurality of line segments to data points associated with a PCR amplification reaction. The data points include a cycle value associated with a PCR cycle and a product value associated with a PCR product. A baseline is identified and reaction segment associated with an exponential region of the PCR reaction is also identified. The reaction segment includes a subset of the plurality of line segments having a slope not less than a steepness criterion. A reaction line is fit to the data points associated with the reaction segment. The Cq is identified by calculating the cycle value for a data point defining the intersection of the baseline and reaction line.

Abstract: An object of the disclosure of the present specification is to provide a method for detection of a target nucleic acid which allows construction of an effective detection system of a target nucleic acid. For this purpose, in the disclosure of the present specification, a first primer comprising an identification sequence complementary to a target sequence in a target nucleic acid and a tag addition sequence, and a second primer having a label are prepared. The first primer and the second primer are used for the target nucleic acid in a sample to amplify a chimeric DNA having a tag sequence and the label. The chimeric DNA is hybridized with a detection probe on a solid phase to obtain signal intensity information based on the label, and the target nucleic acid is detected based on the signal intensity information.

Abstract: A method, software, database and system for determining an optimal treatment for an illness in an individual and for determining the impact (e.g., side effects and intended benefits) of the treatment in the individual are presented in which an attribute profile of the individual containing genetic and non-genetic attributes is compared against a database containing combinations genetic and non-genetic attributes that are statistically associated with successful treatment of the illness in other individuals.

Abstract: A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed.

Abstract: The present invention is directed to the identification of a novel repressor located between ˜1.2 kb to ˜1.6 kb from the translation start site of the IFN-?1 promoter. The present invention provides a method of using siRNAs against ZEB1 (binds to the repressor region) and BLIMP-1 (binds outside the repressor region) and increases the promoter activity of IFN-?1 (i.e., increases the production of IFN-?1 protein). siRNAs against ZEB1 mRNA or BLIMP-1 mRNA increase IFN-?1 gene activity. There is provided a therapeutic application of siRNAs against ZEB1 and BLIMP-1 mRNAs in treating a mammal (including a human) by increasing the production of IFN-?1 protein that promotes an anti-viral response as well as treats asthma diseases.

Abstract: The present invention relates to a self-amplifying folded oligonucleotide structure for sensitive oligonucleotide sensing without polymerase chain reaction (PCR). A self-amplifying folded oligonucleotide structure comprise a target sensing sequence having stem loop structure, a signaling molecule and signal modifying molecule labeled two stems wherein the two stems include oligonucleotide sequence that is complementary to a target sensing sequence of another self-amplifying folded oligonucleotide structure.

Abstract: A method for identifying a risk factor for diseases, disorders or conditions, such as those caused by human immunodeficiency virus, using the polymerase chain reaction and specific primers. Methods for treating patients having these diseases, disorders or conditions by antimicrobial treatment of the risk factor by combined antiviral and antibacterial treatment or by sustaining or stimulating the subject's immune system. Methods for screening biological products including red blood cell preparations. Primers and methods for detecting nucleic acids or microbial agents associated with red blood cells, such as those associated with red blood cells in subjects infected with HIV and undergoing antiretroviral therapy.

Abstract: The invention relates to double-stranded ribonucleic acid (dsRNA) compositions targeting the ALAS1 gene, and methods of using such dsRNA compositions to alter (e.g., inhibit) expression of ALAS1.

Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

Abstract: Methods are disclosed for resolving measurement problems such problems in measuring chromosomal copy number. Some disclosed methods involve first selecting a primary assay element characteristic to partition. Such characteristic may be a source of experimental variability such as the GC content of measured DNA sequences. Additionally, the disclosed methods may employ an abundance or copy number function to transform the assay element frequencies into an abundance, dose, copy number score, or the like. In some cases, the disclosed methods estimate an amount of certain fetal DNA in a sample. The methods can further compare the estimated amount to a measured amount of fetal DNA in the sample. The comparison can be used to determine the fetal sex or aneuploidy.

Abstract: Provided are techniques for locating one or more genome patterns. One or more lexical annotators that each identifies a sequence of nucleotides are created. One or more parsing rule annotators are created using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators. The one or more parsing rule annotators are used to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.

Abstract: Provided are techniques for locating one or more genome patterns. One or more lexical annotators that each identifies a sequence of nucleotides are created. One or more parsing rule annotators are created using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators. The one or more parsing rule annotators are used to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.

Abstract: A nucleotide leader sequence 5?-UTR comprises elements favorable to gene expression, such as repeated CAA trinucleotide elements in combination with repeated CT dinucleotide elements.

Abstract: A dynamic diagnostic plan generator arranges diagnostic test procedures related to a vehicle/power tool/patient symptom or operational problem in a sequence based on a probabilistic Failure Mode and Effects Analysis (FMEA). The diagnostic plan generator also tracks a vehicle/power tool/patient state, and provides instructions for test preparation steps and instructions for performing the diagnostic test procedures. The plan generator further generates schematic illustrations of the diagnostic test procedures, and creates a diagnostic data structure containing information related to the diagnostic test procedures. In addition, the diagnostic plan generator sends and receives information regarding actual failure mode occurrences, for example, to and from a central database. Furthermore, the diagnostic plan generator facilitates the creation of failure mode tests by an expert diagnostics author.

Abstract: Embodiments of a method and/or system of transmitting and/or receiving data is disclosed.

Abstract: In embodiments of compression match enumeration, a trie structure can be searched to enumerate data sequence matches after the trie structure is generated. The trie structure can be generated by overwriting a suffix array of data sequences stored in a memory buffer, where the suffix array includes an array of buffer positions sorted alphabetically by a data string that begins a data sequence at a respective buffer position. The trie structure can then be traversed to determine the data sequence matches from nodes in the trie structure. The trie structure can also be updated while being traversed to bypass multiple enumerations of the data sequence matches that have the same match length.

Abstract: The invention is directed to methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect, the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence tree representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated.

Abstract: RNA sequencing techniques provide rapid base-calling and resequencing for improved bio-informatics. Exemplary embodiments of computer-implemented systems and methods can be provided, as applied to RNA sequence interpretation, enumeration and classification, etc.

Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.

Abstract: Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).