Abstract: Disclosed are a method and a device for labelling single nucleotide polymorphism site in a genome. The above-mentioned method comprises: the single-end RAD sequences from the genomes of two individuals are obtained; the single-end RAD sequences are filtered to remove unqualified sequences; the sequencing depth of the sequences from the genomes of two individuals is aligned in pairs and without gaps to determine the SNP sites.

Abstract: Provided herein are methods for accurately determining the alleles present at a locus that is broadly applicable to any locus, including highly polymorphic loci such as HLA loci, BGA loci and HV loci. Embodiments of the disclosed methods are useful in a wide range of applications, including, for example, organ transplantation, personalized medicine, diagnostics, forensics and anthropology.

Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases.

Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases.

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 for identifying ribonucleotide sequences, in vitro, using the ribosome-mediated translation, are provided.

Abstract: Technologies are described herein for noise adaptive training to achieve robust automatic speech recognition. Through the use of these technologies, a noise adaptive training (NAT) approach may use both clean and corrupted speech for training. The NAT approach may normalize the environmental distortion as part of the model training. A set of underlying “pseudo-clean” model parameters may be estimated directly. This may be done without point estimation of clean speech features as an intermediate step. The pseudo-clean model parameters learned from the NAT technique may be used with a Vector Taylor Series (VTS) adaptation. Such adaptation may support decoding noisy utterances during the operating phase of a automatic voice recognition system.

Abstract: A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.

Abstract: A method, computer program product and system of minimizing epigenetic surprisal data either by comparing epigenetic surprisal data to a fixed baseline epigenetic data, so that all of the comparisons were made to the same baseline epigenetic data or by comparing epigenetic surprisal data to a rolling baseline of epigenetic surprisal data—that is, after each comparison the baseline is changed to the data from the time point which had been compared previously.

Abstract: Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant.

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: A method and apparatus for diagnosing cancer by using genetic information, the method comprising acquiring first gene expression data of a subject, for whom cancer is to be diagnosed, for a gene marker set including at least one gene marker; and determining a possibility of a presence of the cancer of the subject by using the acquired first gene expression data and pre-stored second gene expression data of a normal person group and a cancer patient group, wherein the gene marker set includes gene markers such as pyrroline-5-carboxylate reductase 1 (PYCR1), phosphoglycerate dehydrogenase (PHGDH), glutaminase 2 (liver, mitochondrial) (GLS2), and glutaminase (GLS) among others.

Abstract: A novel method for prediction of the degree of heterotic phenotypes in plants is disclosed. Structural variation analyzes of the genome are used to predict the degree of a heterotic phenotype in plants. In some examples, copy number variation is used to predict the degree of heterotic phenotype. In some methods copy number variation is detected using competitive genomic hybridization arrays. Further, methods for optimizing the arrays are disclosed, together with kits for producing such arrays, as well as hybrid plants selected for development based on the predicted results.

Abstract: The present disclosure provides peptide amino acid sequencing and identification methods and kits for performing such methods. For example, single-molecule detection of fluorophore-labeled peptides is disclosed using multiple rounds of standard Edman degradation or using digestion by chemicals or enzymes. Different fluorophores covalently attached to each of a specific type of amino acid side chain of a peptide provide for the derivation of the peptide's encoded amino acid sequence following image alignments of multiple Edman cycles or following digestion by chemicals or enzymes. The amino acid sequence of a peptide and/or the identity of the peptide can be determined by bioinformatic analysis based on the encoded amino acid sequence. The present disclosure further provides peptide derivatization and immobilization strategies to enable the sequencing and identification of a single peptide or a plurality of peptides.

Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.

Abstract: A method for sequencing a polynucleotide sample having a barcode sequence includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined order of nucleotide flows; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-correcting code that is (i) designed based on and adapted for use with the predetermined order of nucleotide flows, and (ii) capable of distinguishing any codeword in the error-correcting code from the other codewords in the error-correcting code in the presence of zero, one, and two errors.

Abstract: Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.

Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

Abstract: The invention generally relates to tools for genomic analysis and particularly to a pipeline editor that can turn pipelines into standalone tools for use in other pipelines. The invention provides systems and methods for genomic analysis in which individual analytical tools can be arranged into analytical pipelines that can then be “collapsed” into standalone tools, which themselves can be put into the pool of individual tools for use in further building of pipelines. Aspects of the invention provide a system that includes a server computer system operable to present to a user a plurality of genomic tools, receive input from the user arranging the tools into a pipeline, create a new tool that includes the pipeline, and offer the new tool along with the plurality of genomic tools.

Abstract: Provided are a system and method for sequence alignment. The system for sequence alignment includes an exact matching module configured to perform exact matching of an input read to a reference sequence, a secondary matching module configured to map the read to the reference sequence in consideration of mismatches between the read and the reference sequence when the read does not exactly match the reference sequence, and a global alignment module configured to perform global alignment operation of the read with the reference sequence when the read is not mapped to the reference sequence by the secondary matching module.

Abstract: The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.

Abstract: A graphical user interface (GUI) type model helps application designers create error free graphical user interface applications (GAPs). The GUI type model provides a reference set of GUI element types. The application designer assigns a selected GUI element type to each GUI element in a GAP design. The GUI element types help ensure consistent and proper treatment of the GUI element types at every stage in the development of the application, from initial planning and design, to compilation and execution.

Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.

Abstract: Techniques perform de novo assembly. The assembly can use labels that indicate origins of the nucleic acid molecules. For example, a representative set of labels identified from initial reads that overlap with a seed can be used. Mate pair information can be used. A sequence read that aligns to an end of a contig can lead to using the other sequence read of a mate pair, and the other sequence read can be used to determine which branch to use to extend, e.g., in an external cloud or helper contig. A kmer index can include labels indicating an origin of each of the nucleic acid molecules that include each kmer, memory addresses of the reads that correspond to each kmer in the index, and a position in each of the mate pairs that includes the kmer. Haploid seeds can also be determined using polymorphic loci identified in a population.

Abstract: A system for determining the quality of predicted DNA base identifications is disclosed, the system comprising a processor configured to receive a training data set, the training data set comprising a plurality of predicted DNA base identifications, define a group of subsets, compare the predicted DNA base identifications with actual DNA base identifications for training data within each subset of the group, determine a sampling characteristic for each subset of the group based on training data within the respective subset, and determine a quality characterization for predicted DNA base identifications within at least one of subset of the group based on the comparison and determined sampling characteristic, wherein the sampling characteristic comprises a confidence value comprising a binomial proportion confidence interval value.

Abstract: An apparatus having within or as part of a housing; a sample port; a microarray port; a lysis module; a purification module for containing a solid phase for binding of oligonucleotides; a thermocycling module for containing a polymerase chain reaction; a fragmentation module; and a microarray module for holding a microarray and a liquid in contact with the microarray. The apparatus is configured to be coupled to a device for: pumping a liquid through, in order, the lysis, purification, thermocycling, fragmentation, and microarray modules; sonicating any contents of the lysis module; thermocycling the thermocycling module to perform the polymerase chain reaction; heating the fragmentation module to fragment any oligonucleotides contained therein; circulating a fluid over the surface of the microarray; and performing one or more washing or staining steps on the microarray.

Abstract: Short Tandem Repeats are currently used by law enforcement and others, for example, for the identification of individuals by DNA matching. A method is described herein that uses WPD to classify and identify repeating sequences in nucleotide sequences from the position and frequency information contained within nucleotide sequences. This decomposition allows for the quick classification of nucleotide sequences (i.e., reads) into two different classes, including, for example, one class that contains sequencer reads that contain a repeat motif with non-repeat sequence on either flank, and another class that contains sequencer reads that do not contain any repeat sequence.

Abstract: By driving molecules electrophoretically through a nanopore, single molecule detection can be achieved. To enhance translocational control, functionalized and non-functionalized electrodes are strategically placed around or above a nanopore. Changes in transmission spectra and input voltage detected by electrodes allow accurate identification of single molecules as they pass through a nanopore.

Abstract: In at least one illustrative embodiment, a method may comprise selecting a first plurality of text strings that each represent a nucleotide sequence that was read by a massively parallel sequencing instrument, where the nucleotide sequences represented by the selected first plurality of text strings each correspond to a first target locus, comparing the selected first plurality of text strings to one another to determine an abundance count for each unique text string included in the selected first plurality of text strings, identifying a first number of unique text strings included in the selected first plurality of text strings as representing noise responses, and determining a method detection limit as a function of the abundance counts for the first number of unique text strings identified as representing noise responses.

Abstract: Methods, libraries, and kits for nucleotide sequencing are provided.

Abstract: The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.

Abstract: A method for identifying people involves breathing respired air into a collector unit, trapping condensate from the respired air in the collector unit, introduction of the condensate by a same introduction to a DNA sensor unit, analysis of the condensate after a cell disruption, comparison of the result the data from a databank and output of the comparison result with analysis of the identity of a person.

Abstract: Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.

Abstract: A sequencing application implements a multi-stage search technique in order to identify locations where a sequence of elements occurs within a much longer reference sequence of elements. The sequencing application breaks the sequence of elements into multiple, possibly overlapping seeds, used to determine all potential occurrences of the sequence in the reference. In order to determine the occurrences of each of the seeds in the reference, the application breaks the seeds into multiple sub-seeds and implements a different search stage for each different short sub-seeds. If a given search stage produces a small number of search results, then the sequencing application determines that each of the occurrences can be tested for a complete match between the entire short read and the reference string, for example using a Smith-Waterman or Needleman-Wunsch algorithm. Otherwise the application attempts to further restrict the determined number of potential occurrences proceeding to the next search stage.

Abstract: The present disclosure provides methods for diagnosis of interstitial lung diseases (ILDs). The present disclosure provides methods for differential diagnosis of idiopathic pulmonary fibrosis from other ILDs. Compositions and kits useful in carrying out a subject method are also provided.

Abstract: A genetic information managing apparatus compares a base sequence of a subject with a standard base sequence to determine a longest common base sequence, and arranges the base sequence of the subject on the standard base sequence in accordance with the longest common base sequence. The genetic information managing apparatus divides the arranged base sequence into a plurality of base code groups, allocates a plurality of identifiers to the plurality of base code groups, respectively, and stores the plurality of base code groups to a plurality of storing units in association with corresponding identifiers.

Abstract: The invention provides methods for determining copy number of the Y chromosome, including, but not limited to, methods for gender determination or Y chromosome aneuploidy of fetus using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein describe a strategy for filtering out (or masking) non-discriminant sequence reads on chromosome Y using representative training set of female samples. In some embodiments, this filtering strategy is also applicable to filtering autosomes for evaluation of copy number variation of sequences on the autosomes. In some embodiments, methods are provided for determining copy number variation (CNV) of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. Also disclosed are systems for evaluation of CNV of sequences of interest on the Y chromosome and other chromosomes.

Abstract: The present invention relates to a method for detecting genetic variation, comprising the following steps: acquiring reads from a test sample; aligning said reads with a reference genome sequence; dividing said reference genome sequence into windows, calculating the number of said reads which are aligned to each window, and acquiring the statistic for each window on the basis of the number of said reads; and for a fragment of the reference genome sequence, acquiring the genetic variation sites on the basis of the change in the statistics of all the windows thereon in the fragment of the reference genome sequence.

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: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Abstract: Provided is a method for detecting DNA methylation based on MspJI cleavage and performing bioinformatics analysis of genomic methylation.

Abstract: Methods for non-random loading of single analyte molecules into array structures are provided. The methods allow for distribution of a population of target molecules into a plurality of size confined regions such as wells. Sizing moieties are linked to individual target molecules. The sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, such that only a selected number of sizing moieties will fit into the size confined regions. The confined regions and the sizing moieties or target molecules comprise a selected charge that allow for controlling the loading of the sizing moities.

Abstract: Gene signatures for determining whether a neoplasm (such as a multiple myeloma neoplasm) is sensitive to mTORi/HDACi combination therapy and/or for determining the prognosis of a neoplasm in a subject are described. Some embodiments include determining whether a neoplasm is sensitive to mTORi/HDACi combination therapy by predicting whether mTORi/HDACi combination therapy will successfully treat the neoplasm, for example increasing survival of the subject with the neoplasm. In some embodiments, determining the prognosis includes predicting the outcome (such as chance of survival) of the subject with a neoplasm. Also disclosed are reagents, for example arrays, for use with the disclosed methods, as well as computer implementation of the disclosed methods.

Abstract: Provided is a method of gap closing in nucleotide sequence. The nucleic acid sequence comprises a first contig at one end of a gap in an unassembled region, and a second contig at the other end of the gap in the unassembled region.

Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.

Abstract: The present invention pertains to a process for automatically analyzing mixed DNA samples. Specifically, the process comprises the steps of obtaining a mixed DNA sample; amplifying the DNA sample to produce a product; detecting the product to produce a signal; and analyzing the signal to determine information about the composition of the mixed DNA sample. This DNA mixture analysis is useful for finding criminals and convicting them. This mixture analysis provides high quality estimates, and can determine genotypes, mixture weights, and likelihood ratios. This analysis provides confidence measures in the results it computes, and generates reports and intuitive visualizations. The process automates a tedious manual procedure, thereby reducing the cost, time, and effort involved in DNA forensic analysis. The system can greatly accelerate the rate of DNA crime analysis, and be used to exonerate innocent people.

Abstract: The present invention belongs to the field of genomics and nucleic acid sequencing. It involves a novel method of sequencing biological material and real-time probabilistic matching of short strings of sequencing information to identify all species present in said biological material. It is related to real-time probabilistic matching of sequence information, and more particular to comparing short strings of a plurality of sequences of single molecule nucleic acids, whether amplified or unamplied, whether chemically synthesized or physically interrogated, as fast as the sequence information is generated and in parallel with continuous sequence information generation or collection.

Abstract: The invention is based, at least in part, on the development of stabilized binding molecules that consist of or comprise a stabilized scFv and methods for making such stabilized molecules.

Abstract: The present invention provides methods for optimizing oligonucleotide hybridization probes for use in basic and clinical research. Specifically, the invention involves hybridizing serially diluted genomic sample to the oligonucleotide probes on the array, such that a signal intensity is produced for each of the probes; computationally identifying optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample and are reproducibly strong relative to non-optimized probes.

Abstract: The conventional DNA sequencers for analyzing nucleotide sequences have no function of detecting minute polymorphisms. Any cross talk in the wavelengths of fluorescent substances for labeled DNA fragments hinders detection of weak-strength signals at the same coordinates, making it difficult to detect genetic mutations with small existence ratios, for example, in somatic mutations. Disclosed is a gene analyzer composed of a plurality of flow channels, each of which is used to electrophorese nucleic acid samples labeled for each of nucleotide types; a chromatogram data creating part for detecting a labeled signal for each of the nucleotide types for each of the nucleic acid samples in each of the plurality of flow channels and creating chromatogram data on signal strengths detected; a peak detection part for the peal values in the chromatogram data for each of the nucleotide types; and a data integrating part for integrating a plurality of chromatogram data.