Abstract: A method of preparing an at least partially randomly sheared library of nucleic acids is provided. The method includes the steps of providing a source of nucleic acids, randomly incorporating modified bases into the nucleic acids, and digesting the modified nucleic acids with one or more modification-dependent restriction endonucleases to produce the nucleic acid library. The practice of the method can be facilitated using a kit for performing the method. The method can be used to form nucleic acid libraries and as part of a method of next generation sequencing.

Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Abstract: The present invention provides a system and method for assessing a synthetic peptide population including interrogating a population of peptide features in the presence of a receptor having an affinity for a binder sequence. The population of peptide features is synthesized over a plurality of synthesis periods and includes a plurality of control peptide features synthesized to have an amino acid sequence including the binder sequence. The control peptide features include a first feature synthesized beginning with a first one of the synthesis periods, and a second feature synthesized beginning after the first one of the synthesis periods such that synthesis of the second control peptide feature is delayed by at least one synthesis period. The method further includes detecting a signal output characteristic of an interaction of the receptor with the control peptide features, the signal output indicative of the fidelity of synthesis of the population of peptide features.

Abstract: Provided herein are methods and devices for accurate sequencing and detection of epigenetic information from template polynucleotides. Also provided are methods for long-range strand displacement amplification of polynucleotides, microfluidic devices with selectively permeable barriers for multistep processing, and methods for polynucleotide amplification using the microfluidic devices.

Abstract: The present invention relates to a method of identifying a nucleotide at a defined position and determining the sequence of a target polynucleotide using an electro-switchable biosensor, as well as devices comprising an electro-switchable biosensor and uses thereof.

Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

Abstract: The invention relates to the field of multiplex amplification. In particular, the invention relates to methods for assaying a sample for one or more nucleic acid targets in a single reaction based on the distinct melting temperatures or melting profiles of primers and/or probes. The invention also provides probes and kits for use in such methods.

Abstract: A method for constructing a sequencing library based on a single-stranded DNA molecule is provided comprising: (1) forming a poly(C)n tail at a 3?-terminus of the single-stranded DNA molecule, to obtain a single-stranded DNA molecule with the poly(C)n tail with n representing a number of base C, and n being an integer ranging from 5 to 30; (2) obtaining a double-stranded DNA molecule by using an extension primer based on the single-stranded DNA molecule with the poly(C)n tail, with the extension primer comprising a H(G)m unit at a 3?-terminus thereof, H being base A, base T or base C, m being a number of base G, and m being an integer ranging from 5 to 15; and (3) ligating an adapter to one terminus of the double-stranded DNA molecule remote from the H(G)m unit, and amplifying the resulting ligation product to obtain an amplification product forming the sequencing library.

Abstract: The present invention relates to the discovery of a method for identifying a treatment regimen for a patient diagnosed with cancer, predicting patient resistance to therapeutic agents and identifying new therapeutic agents. Specifically, the present invention relates to the use of an algorithm to identify a mutation in a kinase, determine if the mutation is an activation or resistance mutation and then to suggest an appropriate therapeutic regimen. The invention also relates to the use of a pattern matching algorithm and a crystal structure library to predict the functionality of a gene mutation, predict the specificity of small molecule kinase inhibitors and for the identification of new therapeutic agents.

Abstract: Compositions of nucleic acid hybridization probes for detecting a nucleic acid target sequence and methods for their production are described. In one preferred embodiment, the nucleic acid hybridization probe includes a hybridization domain, an adaptor, a linker, and a signaling domain. The hybridization domain includes a nucleic acid sequence having complementarity to the nucleic acid target sequence. The adaptor is a nucleic acid sequence. The linker includes a moiety having at least one abasic site, such that the moiety blocks extension by an elongating polymerase on a nucleic acid template containing the moiety. The signaling domain comprises a nucleic acid having at least one label or a nucleic acid having at least one nucleic acid domain for binding at least one additional nucleic acid.

Abstract: Methods and compositions are provided for the identification of a molecular diagnostic test for cancer. The test defines a novel DNA damage repair deficient molecular subtype and enables classification of a patient within this subtype. The present invention can be used to determine whether patients with cancer are clinically responsive or non-responsive to a therapeutic regimen prior to administration of any chemotherapy. This test may be used in different cancer types and with different drugs that directly or indirectly affect DNA damage or repair, such as many of the standard cytotoxic chemotherapeutic drugs currently in use. In particular, the present invention is directed to the use of certain combinations of predictive markers, wherein the expression of the predictive markers correlates with responsiveness or non-responsiveness to a therapeutic regimen.

Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Abstract: The present invention relates a composition, including an RNA probe which contains a fluorescence material absorbed in graphene oxide, for detecting a nucleic acid, and to a method for detecting a nucleic acid using the composition. By means of the composition and the method, the presence and expression pattern of a target nucleic acid in a sample or a cell can be observed in real time, and a plurality of target nucleic acids can be detected in multitude.

Abstract: The invention provides methods for the diagnosis and prognosis of cardiovascular disease, and for monitoring of the treatment of cardiovascular disease, including heart failure and cardiomyopathy. The invention further provides methods for identifying an agent for treating cardiomyopathy or heart failure, for identifying a cardiotoxic agent, and for identifying a rescue agent to reduce or prevent drug-induced toxicity, by using one or more biomarkers selelcted from the group consisting of CCDC47, HMOX1, PTX3, PAI1, IL27, IGFBP7, Emmprin, CFL2, EDIL3, NUCB1, PE D18:0-20:3/D18:1-20:2/D16:0-22:3; PE D18:0-22:5/D18:1-22:4; PE D16:1-22:6; PE P18:1-18:1/P18:0-18:2/P16:0-20:2; LPC 20:3; and PC-LI-183-D18:22-22:6, or any of the other biomarkers provided herein. The invention further provides kits for practicing the methods of the invention.

Abstract: Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data.

Abstract: The present invention provides for a system, method, and device for analyzing, localizing and/or identifying tissue types. The method includes analyzing, localizing and/or identifying one or more tissue samples, characterized in that the method comprises: (a) generating gaseous tissue particles from a site in the one or more tissue samples, (b) transporting the gaseous tissue particles from the site to an analyzer, (c) using the analyzer for generating tissue-related data based on the gaseous tissue particles, and (d) analyzing, localizing and/or identifying the one or more tissue samples based on the tissue-related data. The invention can either be used in close conjunction with a surgical procedure, when one or more surgical tools are an integrated part of ionization, or as a separate mass spectrometric probe for the analysis of one or more tissue parts.

Abstract: A diagnostic reagent or device comprises at least one ligand capable of specifically complexing with, binding to, or quantitatively detecting or identifying the biomarker chloride intracellular channel protein 4 (CLIC4) or an isoform, pro-form, modified molecular form including posttranslational modification, or unique peptide fragment or nucleic acid fragment thereof. An alternative diagnostic reagent or device comprises ligand or ligands capable of specifically complexing with, binding to, or quantitatively detecting or identifying multiple tropomyosin biomarkers. Optionally, such reagent or device includes a signaling molecule and/or a substrate on which the ligand is immobilized. Other reagents and methods of diagnosing ovarian cancer include use of CLIC4 ligands and/or multiple tropomyosin ligands with an additional ovarian cancer biomarker. For example, CLIC4 combined with one or more of CLIC1 and/or one or multiple members of the tropomyosin family, e.g.

Abstract: The present invention relates a kit for detecting a nucleic acid and a method of detecting a nucleic acid for enabling a multiplexed-detection and real-time detection of a target nucleic acid by using properties of a graphene oxide.

Abstract: The present invention relates to a composition comprising a plurality of cDNA molecules for use in methods of detecting changes in expression of genes encoding proteins that are associated with mental illnesses and which are differentially expressed in patients with mental illnesses, such as bipolar I disorder, bipolar II disorder, unipolar disorder, schizophrenia, attention deficit hyperactive disorders, obsessive compulsive disorders, anxiety disorders or other related mood disorders. The composition and the cDNA molecules may be used in their entirety or in part as to diagnose, to stage, to treat, and/or to monitor the treatment of a subject with mental illness.

Abstract: The present application relates to the field of cancer, particularly to mismatch repair (MMR?) deficient tumors. New markers are presented herein that have a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods are provided for diagnosing microsatellite instability of a tumor, comprising determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.