Abstract: The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes, or their co-expressed genes, from a biological sample obtained from a prostate cancer patient. The genes may be grouped into functional gene subsets for calculating a quantitative score useful to predict a likelihood of a clinical outcome for a prostate cancer patient.

Abstract: The present invention provides a method for producing a circular DNA molecule having a specific structure that enables to distinguish circular DNA formed from a single DNA molecule (single-molecule circular DNA), from circular DNA formed from multiple DNA molecules (multiple-molecule circular DNA) and also from single-molecule circular DNA derived from the circular DNA formed from multiple DNA molecules. According to the present invention, only single-molecule circular DNA that is not derived from multiple-molecule circular DNA can be selected in the production of circular DNA.

Abstract: The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, pcr, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.

Abstract: The present invention is characterized by a D-Aptamer-Like Peptide (D-Aptide) or retro-inverso Aptide which specifically binds to a target comprising: (a) a structure stabilizing region comprising parallel, antiparallel or parallel and antiparallel D-amino acid strands with interstrand noncovalent bonds; and (b) a target binding region I and a target binding region II comprising randomly selected n and m D-amino acids, respectively, and coupled to both ends of the structure stabilizing region. The D-Aptide or retro-inverso Aptide has the sequence of the same or opposite direction to L-Aptide, wherein the stability to proteases is improved while maintaining the affinity to a target compared with L-Aptide. The D-Aptide of the present invention has substantially the same target affinity and a remarkably improved stability compared with L-Aptide which is different from a general technical knowledge.

Abstract: The invention is concerned with a method of predicting a patient's susceptibility to developing hypertension associated with an anti-angiogenesis treatment, such as bevacizumab, by determining the genotype of KDR gene and/or EGF gene. The invention further relates to a pharmaceutical composition comprising an angiogenesis inhibitor, such as bevacizumab, for the treatment of a patient suffering from cancer based on the genotype of KDR gene and/or EGF. The invention further relates to a method for reducing the risk of hypertension associated with an anti-angiogenesis therapy, such as bevacizumab, in a patient suffering from cancer by determining the genotype of KDR gene and/or EGF gene.

Abstract: An analysis instrument comprises plural modules connected together over a data network, each module comprising an analysis apparatus operable to perform biochemical analysis of a sample. Each module comprises a control unit that controls the operation of the analysis apparatus. The control units are addressable to select an arbitrary number of modules to operate as a cluster for performing a common biochemical analysis. The control units communicate over the data network, repeatedly during the performance of the common biochemical analysis, to determine the operation of the analysis apparatus of each module required to meet the global performance targets, on the basis of measures of performance derived from the output data produced by the modules. The arrangement of the instrument as modules interacting in this manner provides a scalable analysis instrument.

Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.

Abstract: The present invention relates to a method for screening, predicting or prognosing esophageal adenocarcinoma/high grade dysplasia in a subject.

Abstract: Methods for creating a library of recurrently mutated genomic regions and for using the library to analyze cancer-specific and patient-specific genetic alterations in a patient are provided. The methods can be used to measure tumor-derived nucleic acids in patient blood and thus to monitor the progression of disease. The methods can also be used for cancer screening.

Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.

Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.

Abstract: Provided are a sub-totipotent stem cell product and epigenetic modification label thereof, a method for inducing the generation of the sub-totipotent stem cell product and identification for the epigenetic modification label of the differentiation potential of stem cells. Also provided is a use of histone modification states of sub-totipotent genes and/or differentiation related genes to predict the epigenetic modification label of the differentiation potentials of stem cells.

Abstract: The instant application provides methods and related compositions pertaining to the identification of resistance to anticancer treatment in. a patient. In a particular embodiment, the invention provides biomarkers for the identification of resistance to anticancer treatment in a breast cancer patient, wherein a reduced expression of a MEDIATOR and/or SWI/SNF complex gene in the breast cancer cells of the patient indicates that the breast cancer cells in the patient may be successfully treated with a PI3K and/or mTOR inhibitor.

Abstract: The present invention relates to processes for characterizing and screening for the existence or predisposition to X-linked disorders associated with changes in X-chromosome inactivation. The present invention also relates to processes of reducing a disease phenotype associated with an X-linked disorder in a female subject.

Abstract: The present invention relates to a noninvasive method for quantifying Fel d 1 cat allergen expression levels—the major allergen responsible for cat allergies—in individual cats (Felis catus).

Abstract: This invention is directed in part to methods, assays and/or kits for identifying an individual who has an autoimmune disease (such as rheumatoid arthritis), or who has an altered risk for having or developing the autoimmune disease. The methods in one aspect comprise determining the presence or absence of a nucleic acid variant within the somatostatin receptor type 2 (sstr2) gene in the individual's nucleic acids, wherein the presence of the nucleic acid variant is correlated with having the autoimmune disease or the altered risk. The nucleic acid variant may, for example, be a single nucleotide polymorphism (SNP).

Abstract: The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).

Abstract: A method for nucleic acid sequencing includes: (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; (b) exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands; and (d) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing erro

Abstract: The present invention relates to the field of genomic mutation detection, and in particular, to the detection of the copy number variation (CNV) in cellular chromosomal DNA fragments. The present invention also relates to the detection of diseases related to the copy number variation in the cellular chromosomal DNA fragments.

Abstract: Provided herein is technology relating to enzymatic modification of nucleic acids and particularly, but not exclusively, to methods and compositions relating to using uracil-DNA-N-glycosylase for minimizing or eliminating errors in a DNA sequence due to deamination of cytosine residues.

Abstract: In some embodiments, methods of determining that a subject is likely to have cancer are provided. Such methods may include amplifying a microbial DNA sample in a test sample obtained from the subject to determine an amount of microbial DNA in the test sample, wherein the amount of microbial DNA is determined by an amplification or sequencing technique; and determining that the subject is likely to have breast cancer when there is a significantly decreased level of microbial DNA in the test sample when compared to a level of microbial DNA in a control sample. In other embodiments, methods of treating cancer (e.g., breast cancer) are provided. In one aspect, such methods include administering a therapeutically effective dose of a probiotic organism via ductal lavage to a subject suffering from the breast cancer.

Abstract: The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

Abstract: Means and methods of predicting future dental problems are disclosed. Molecular tests use biological matter from a patient to obtain information regarding various genes. The tests and methods generate displays and reports regarding genetic risk pertaining to cavities, tooth decay and other disorders.

Abstract: The present invention is directed to methods, devices, compositions and systems for obtaining sequence data from nucleic acid templates by utilizing electronic sensing elements.

Abstract: The present invention provides methods of determining the breeding value of an individual or determining the best pair of individuals to mate based on additive and non-additive factors. The invention further provides methods of breeding an individual selected by using a molecular marker-derived matrix comprising additive and non-additive effects. The invention also provides a kit for determining the Estimated Breeding Value of an individual.

Abstract: Flow chambers are provided. In some embodiments, the flow chambers include an inner panel having at least one flow channel having an inlet/outlet opening on each end thereof formed therein, wherein the inlet/outlet openings are adapted to releasably receive a septum; one or more ports adapted to releasably receive a plug and for at least liquid communication with the at least one flow channel, and an outer frame that defines an outer portion of the at least one flow channel and that defines a perimeter of the flow chamber. In some embodiments, the flow chamber has overall dimensions of a standard multiwell plate and the at least one flow channel is located in a position that corresponds to a column location of the standard multiwell plate. Also provided are methods for producing the presently disclosed flow chambers and employing the same to assay biological features of cultured cells and/or tissues.

Abstract: Methods and techniques to identify carcinogenesis pathways and markers for early cancer diagnosis. Cell sampling is performed on a single tumor with multiple samples being taken from the tumor and outward toward the periphery and beyond. Large scale analysis is performed, such as whole genomic sequencing, to identify the differences between the cells of the various samples. The differences are evaluated to determine which differences represent a change along the carcinogenesis pathway.

Abstract: Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing sensors to monitor changes in solutions or bound molecules contained in the reaction regions. Additional embodiments provide devices and methods for sequencing DNA using arrays of reaction regions that allow for optical monitoring of solutions in the reaction regions. Chemical amplification schemes that allow DNA to be sequenced in which multiple nucleotide addition reactions are performed to detect the incorporation of a base are disclosed. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced.

Abstract: The present invention provides methods of sequencing a large fragment of DNA by hybridizing a set of specifically designed probes to the DNA, shearing the DNA, and sequencing the DNA with Next Generation Sequencing. The probes are designed to target genes of interest at intervals to allow the capture of relatively large DNA fragments. The present invention also provides methods of diagnosing a neuromuscular disease (NMD) comprising detecting mutations in one or more of SCML2, CHRND, OFD1, DYNC1H1, COL6A3, EMD, ARHGAP4, FLNA, MID1IP1, MID1, and CFP.

Abstract: The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provide methods for the sensitive and specific detection of target gene sequences and gene expression profiles.

Abstract: The present disclosure provides methods, arrays and kits for assessing the quality of genomic DNA samples, especially those obtained from formalin-fixed paraffin-embedded (FFPE) samples. The methods, arrays and kits provided herein use primer pairs specific to regions in the genomes of the organisms from which genomic DNA samples are obtained that have identical or nearly identical copies distributed across multiple chromosomes.

Abstract: The invention provides methods and compositions, including kits, for the construction of directional nucleic acid libraries. The invention further provides methods and compositions for the amplification and sequencing of directional cDNA libraries.

Abstract: The present invention relates to systems and methods for performing multiplex amplification reactions. In particular, the present invention relates to multiplex methylation-specific amplification systems and methods.

Abstract: The invention includes methods and apparatus for isolating and recovering mutations, especially rare and unknown mutations, without amplifying the sample. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

Abstract: Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.

Abstract: The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe.

Abstract: The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample.

Abstract: The disclosure provides methods and kits for preparing sequencing library to detect chromosomal abnormality using cell-free DNA (cfDNA) without the need of first isolating the cfDNA from a liquid fraction of a test sample. In some embodiments, the method involves reducing the binding between the cfDNA and nucleosomal proteins without unwinding the cfDNA from the nucleosomal proteins. In some embodiments, the reduction of binding may be achieved by treating with a detergent or heating. In some embodiments, the method further involves freezing and thawing the test sample before reducing the binding between the cfDNA and the nucleosomal proteins. In some embodiments, the test sample is a peripheral blood sample from a pregnant woman including cfDNA of both a mother and a fetus, wherein the methods may be used to detect fetal chromosomal abnormality such as copy number variation.

Abstract: The methods provided herein relate to the identification of novel DNA biomarkers and the use of the aberrant methylation patterns of the DNA biomarkers to diagnose small cell lung cancer (SCLC). Such methods may include diagnosing SCLC when there is an increase in methylation of one or more DNA biomarkers in a test sample compared with that in a normal sample. DNA methylation patterns of DNA biomarkers on a genome-wide scale may be determined using a variety of methods including the methylated-CpG island recovery assay (MIRA). In some embodiments, methods of treating a subject for SCLC or monitoring the treatment are also provided. Methods may include measuring the methylation levels of one or a combination of DNA biomarkers and administering chemotherapy to a subject when there is an increase in the methylation levels of the test sample in relation to that of the normal sample or standard sample.

Abstract: The present invention relates to methods of identifying gene targets, including methods of using ribonucleoprotein (RNP) immunoprecipitation-microarrays to identify cancer gene targets, such as subsets of RNP-associated mRNAs in breast cancer cell lines. Also presented, are ribonucleotide binding protein-associated biomarkers, panels or sets of ribonucleotide binding protein-associated biomarkers, methods and compositions comprising ribonucleotide-binding protein, associated nucleotides, nucleotide arrays, and kits, plus methods of using HuR-associated biomarkers to facilitate the diagnosis of, monitoring the disease status of, and the progression of treatment of breast cancers to facilitate the diagnosis of and monitoring the disease status or progression of treatment of breast cancers, including drug-resistant breast cancers.

Abstract: The present invention relates to a new class of nucleic acid tagging molecules which are essentially free of homopolymer stretches. Such tagging molecules are helpful for effectively tagging a plurality of individual target molecules and detecting said tags with a high degree of accuracy.

Abstract: A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells.

Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.

Abstract: Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

Abstract: Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.

Abstract: A nucleic acid patch method for amplifying target nucleic acid sequences in circulating free DNA or residual DNA samples where the defining ends of the target nucleic acid sequences are unknown.

Abstract: Described are methods for early noninvasive or minimally invasive detection of pathological changes in organ systems/organs/tissues/cells by quantifying organ system-/organ-/tissue-/cells type-enriched miRNA in bodily fluids.

Abstract: Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.

Abstract: The invention generally relates to methods for sample multiplexing. In certain embodiments, methods of the invention obtaining a plurality of different reactant molecules, attaching a unique identifier to the reactant molecules, and forming a droplet including the reactant molecules.

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.