Abstract: Methods, polynucleotides, kits, and reaction mixtures are disclosed for the enriching of short polynucleotide molecules that have a length within a desired target length range. A Type IIS or Type III restriction enzyme is used to cleave polynucleotides at cleavage sites located at a distance from the restriction enzyme recognition sites. For example, a mixture of polynucleotides can be formed by inserting DNA molecules between a recognition site for the restriction enzyme and a region of non-naturally-occurring nucleotides that block cleavage by the restriction enzymes. If a polynucleotide contains a DNA molecule with a length within a target range, then the cleavage site will be within the blocking region, and cleavage will not occur. Polynucleotides containing DNA molecules with lengths outside the target range can be cleaved. By selectively enriching, through PCR or other means, polynucleotides that are intact, a concentrated population of polynucleotides of a target length can be formed.

Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.

Abstract: The present invention provides method of classifying a subject into a necrotizing meningoencephalitis (NME) disease risk group. The method may include assessing the presence of one or more marker (e.g., SNPs or risk loci) in a sample from the subject. For example, detection of the presence of one or more markers that are associated with an increased risk of NME can indicate that the subject should be classified into a risk group.

Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.

Abstract: A whole blood measurement method associated to hematocrit (HCT) and a whole blood measurement circuit thereof is applied in the detection of HCT of a whole blood sample to be tested. Herein, a time to digital converting circuit (TDC) is used for counting charging time or discharging time of a fixed capacitor and a to-be-tested sample, and a capacitance difference that is related to HCT is generated according to the charging time or the discharging time, so as to provide a reference for a whole blood feature test.

Abstract: Multimeric barcoding reagents for labelling a target nucleic acid comprise: first and second barcode molecules linked together, wherein each of the barcode molecules comprises a nucleic acid sequence comprising a barcode region; and first and second barcoded oligonucleotides. The multimeric barcoding reagents enable spatial sequencing. A single multimeric barcoding reagent can be used to label sub-sequences of an intact nucleic acid molecule or co-localised fragments of a nucleic acid molecule. The labelled sub-sequences can be sequenced and the sequencing data processed to determine the sequence of sub-sequences from a single intact nucleic acid molecule or from co-localised fragments of a nucleic acid molecule. Corresponding libraries, kits, methods and uses are provided.

Abstract: Method and sample vessels are provided for amplification and sequencing of nucleic acids in a sample.

Abstract: Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.

Abstract: Provided herein are methods, systems, and compositions for seamless nucleic acid assembly. Methods, systems, and compositions as provided herein provide for efficient assembly of nucleic acids without primer removal. Methods, systems, and compositions for seamless nucleic acid assembly comprise use of an endonuclease or exonuclease, optionally in conjunction with additional enzymes to assemble nucleic acids or polynucleotides.

Abstract: Embodiments of a method and/or system (e.g., for microsatellite instability detection associated with at least one cancer condition; etc.) can include: determining a microsatellite-related background model; determining one or more loci associated with microsatellite instability based on the microsatellite-related background model; and/or determining a microsatellite instability characterization (e.g., a binary status determination between microsatellite instability such as MSI-H, and microsatellite stability such as MSS; etc.) for the user. Additionally or alternatively, embodiments of the method and/or system can include facilitating treatment provision for one or more users based on the microsatellite instability characterization.

Abstract: The present invention provides a method of determining integrity and/or quantity of cell free DNA (cfDNA) in a bio logical sample comprising amplifying target sequences with at least a first primer/probe set and at least a second primer probe/set, amplifying the target sequences of differing lengths, and monitoring for detection of the labels of the oligonucleotide probes, and determining the integrity and/or quantity of the cfDNA based on the level of detection of the label of the oligonucleotide probe from the first primer/probe set compared to the level detection of the label of the oligonucleotide probe from the second primer/probe set. The present invention also provides methods for generating a library with the cfDNA for sequencing and analysis.

Abstract: The present invention relates to subtilase variants suitable for use in, e.g., cleaning or detergent compositions, such as laundry detergent compositions and dish wash compositions, including automatic dish wash compositions. The present invention also relates to isolated DNA sequences encoding the variants, expression vectors, host cells, and methods for producing and using the variants of the invention.

Abstract: Provided are methods, compositions, reagents, kits that are useful for detecting a specific nucleic acid region in genome with high efficiency and high sensitivity.

Abstract: In one implementation, a method is described. The method includes determining an operational characteristic of sensors of a sensor array. The method further includes selecting a group of sensors in the array based on the operational characteristic of sensors in the group. The method further includes enabling readout of the sensors in the selected group. The method further includes receiving output signals from the enabled sensors, the output signals indicating chemical reactions occurring proximate to the sensors of the sensor array.

Abstract: Improved single molecule sequencing methods, compositions, and devices, are provided. In a first aspect, the present invention provides a multi-pass method of sequencing a target sequence using nanopore sequencing, the method comprising: i) providing a non-naturally occurring concatemer nucleic acid molecule comprising a plurality of copies of the target sequence; ii) nanopore sequencing at least three copies of the target sequence in the concatemer, thereby obtaining a multi-pass sequence dataset, wherein the multi-pass sequence dataset comprises target sequence datasets for the at least three copies of the target sequence; and iii) using the multi-pass sequence dataset to determine the target sequence.

Abstract: Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.

Abstract: The invention provides methods for generating a nucleic acid library. Target-specific primer-probes are hybridized to a target nucleic acid fragment to create a hybridization product. Each of the target-specific primer-probes comprises a target-specific sequence and a first adaptor sequence. The target nucleic acid fragment comprises a target genomic region of interest, wherein said target genomic region of interest comprises an exon of a gene and the target-specific primer-probes are tiled across the exon of the gene. The target nucleic acid fragment further comprises a second adaptor sequence different from said first adaptor sequence. Following hybridization, the target-specific primer-probes are extended to create double-stranded extension products and further amplified, thereby generating the nucleic acid library.

Abstract: Presented herein are methods and compositions for enhancing utilization of surface primers during the surface amplification process. The methods are useful for surface amplification at improved densities. The methods and compositions provided herein enable creation of clusters which are brighter, but at the same densities as currently achieved using standard cluster amplification.

Abstract: Disclosed herein are devices, systems and methods for conducting a reaction using electrowetting in a vertical or substantially vertical position. Some embodiments disclosed herein provide fluidic cartridges for use in a substantially vertical position comprising: (a) a front substrate; (b) a back substrate; (c) a droplet operations gap formed between the front substrate and the back substrate; and (d) a plurality of electrodes on the front substrate or the back substrate, wherein the plurality of electrodes are configured to transport a droplet along a substantially vertical plane defined by the front substrate and the back substrate.

Abstract: A pixel circuit acts as a sensing element in a sensing device. The pixel circuit includes a sensing electrode, a first gate electrically connected to the sensing electrode, a second gate in electrical communication with the first gate, and a readout device that is electrically connected to the second gate. An input voltage applied to the sensing electrode is amplified between the first gate and the second gate, the amplification being measured as an output signal from the readout device to perform a sensing operation. For example, the output signal may be relatable to pH, analyte measurements, or other properties of sample liquids analyzed by the sensing device. A sensing device may include multiple pixels disposed on a substrate, each pixel including said pixel circuit. Driver circuits controlled by control electronics are configured to generate signals that selectively address the pixels and to read out voltages at the sensing electrodes.

Abstract: Modified nucleic acid adapters are provided that collectively provide a mixture of nucleotides at the 3? end of 5? adapters and at the 5? end of 3? adapters such that at least one adapter in each set has any given nucleotide at position 1, i.e., the nucleotide position available for ligation to a small RNA, and has any given nucleotide at position 2 adjacent to position 1 for use in overcoming bias during nucleic acid manipulation, such as small RNA characterization and/or profiling by, e.g., deep sequencing, along with methods for use of the modified adapters in small RNA characterization. The modified adapters have at least two mixed nucleotides at the adapter terminus to be ligated to a nucleic acid such as a small RNA.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.

Abstract: Embodiments of the invention provide methods of creating clinical models for different forms of metastatic cancer. The methods may include obtaining samples from subjects with metastatic cancer, determining an allelic status of one or more markers in the samples (e.g., creating a molecular profile of the subject's cancer), and using model organisms with subject-derived xenografts for treatment selection.

Abstract: In certain embodiments, the present invention provides a way of “digitally” marking different the alleles of different chromosomes by using a transposase to insert differently barcoded transposons into genomic DNA before further analysis. According to this method, each allele becomes marked with a unique pattern of transposon barcodes. Because each unique pattern of transposon barcodes identifies a particular allele, the method facilitates determinations of ploidy and copy number variation, improves the ability to discriminate among homozygotes, heterozygotes, and patterns arising from sequencing errors, and allows loci separated by uninformative stretches of DNA to be identified as linked loci, thereby facilitating haplotype determinations. Also provided is a novel artificial transposon end that includes a barcode sequence in two or more positions that are not essential for transposition.

Abstract: The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure further provides methods for haplotype phasing and meta-genomics assemblies.

Abstract: This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X?-A?-B?-Z?, wherein sequence A? is complementary to a genomic fragment and sequence B? is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

Abstract: Embodiments of the present invention provide methods, systems, and apparatus for deducing the fetal DNA fraction in maternal plasma without using paternal or fetal genotypes. Maternal genotype information may be obtained from a maternal-only DNA sample or may be assumed from shallow-depth sequencing of a biological sample having both maternal and fetal DNA molecules. Because sequencing may be at shallow depths, a locus may have only few reads and may fail to exhibit a non-maternal allele even if a non-maternal allele is present. However, normalized parameters that characterize non-maternal alleles sequenced can be used to provide an accurate estimate of the fetal DNA fraction, even if the amount of non-maternal alleles is in error. Methods described herein may not need high-depth sequencing or enrichment of specific regions. As a result, these methods can be integrated into widely used non-invasive prenatal testing and other diagnostics.

Abstract: Provided herein are devices and methods for the micro-isolation of biological cellular material. A micro-isolation device described can comprise a photomask that protects regions of interest against DNA-destroying illumination. The micro-isolation device can further comprise photosensitive material defining access wells following illumination and subsequent developing of the photosensitive material. The micro-isolation device can further comprise a chambered microfluidic device comprising channels providing access to wells defined in photosensitive material. The micro-isolation device can comprise a chambered microfluidic device without access wells defined in photosensitive material where valves control the flow of gases or liquids through the channels of the microfluidic device.

Abstract: The present invention resides in a method for the manufacture of a disulphide-requiring biopharmaceutical having an element of at least tertiary structure using wild type E. coli.

Abstract: The present disclosure relates to chemical compounds, methods for their discovery, and their therapeutic and research use. In particular, the present disclosure provides compounds as therapeutic agents against bacterial infections (e.g., biofilms). The present disclosure also provides topical formulations for use in methods for treating bacterial infections.

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 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: An enclosed benchtop analytical device, as well as systems, processes, and techniques related thereto are disclosed. A benchtop analytical device can include an enclosure enclosing a probe and a sample. A compliance component can determine satisfaction of one or more compliance rules, such as a compliance rule relating to an enclosure being in an operable configuration based on a lid of the enclosure being closed. If the compliance rule(s) is determined to be satisfied, the compliance component may enable the release of optical energy for interrogation of the sample via the probe. In some embodiments, the enclosure can enclose a sample plate that can be used to conveniently and accurately retain a sample in a suitable position within the enclosure.

Abstract: Disclosed are methods of identifying a methicillin-resistant Staphylococcus aureus (MRSA) in a sample wherein the methods involve detecting a S. aureus-specific nucleic acid sequence, mecA and mecC, in the sample. Kits for determining the presence of MRSA in a sample are also provided.

Abstract: Methods and systems for determining copy number variants are disclosed. An example method can comprise applying a sample grouping technique to select reference coverage data, normalizing sample coverage data comprising a plurality of genomic regions, and fitting a mixture model to the normalized sample coverage data based on the selected reference coverage data. An example method can comprise identifying one or more copy number variants (CNVs) according to a Hidden Markov Model (HMM) based on the normalized sample coverage data and the fitted mixture model. An example method can comprise outputting the one or more copy number variants.

Abstract: The present invention provides multivalent CD20-binding molecules, and compositions thereof, such as enriched compositions comprising large proportions of multivalent CD20-binding molecule relative to monovalent CD20-binding molecule. Certain multivalent CD20-binding molecules of the present invention comprise 1) two or more CD20 binding regions and 2) one or more Shiga toxin effector polypeptide regions derived from an A Subunit of a member of the Shiga toxin family. Certain multivalent CD20-binding molecules of the present invention, and compositions thereof, have uses for selective killing specific cell types and as therapeutics for the treatment of a variety of diseases, including cancers, tumors, and immune disorders.

Abstract: The present invention provides for methods of measuring levels of micro RNAs for the diagnosis, treatment and/or monitoring the progression of post-traumatic stress disorder (PTSD) or traumatic brain injury (TBI) in a subject having or suspected of having PTSD and/or TBI. The methods, in general comprise measuring levels of at least one of miR-142-5p, miR-19b, miR-1928, miR-223-3p, miR-322*, miR-324, miR-421-3p, miR-463* and miR-674* is a sample from a subject suffering from or suspected of having PTSD and/or TBI.

Abstract: Described herein are methods of measuring, in a genomic sample from an individual, the relative frequency of a target sequence (that is, its copy number) with respect to a control sequence of known copy number at a different genomic locus in the same genome, wherein the target and control sequences differ by at least one single nucleotide variation (SNV). These methods involve both the target sequence and the control sequence in a single reaction/container, using a pair of primers that prime amplification of both the target sequence and the control sequence, or a single downstream primer and two upstream primers (that differs only at the position of the SNV between the target and control sequences), and measuring the abundance of each of the target sequence and the control sequence using SNV-specific labeled probes or primers, or a melting curve analysis that distinguishes between the amplified control and target sequences. The methods are exemplified with various different amplifications process.

Abstract: A method for detecting a low-occurrence mutation in isolated DNA adds a blocking probe to reagents during amplification of the isolated DNA. The blocking probe is an oligonucleotide complementary to wild-type DNA corresponding to the sample. The blocking probe spans a site of a suspected mutation within a region of interest in the isolated DNA. After amplification, fragments of the amplified DNA is sequenced using next generating sequencing and an output is generated to display the sequenced fragments. In some embodiments, the blocking probe is locked nucleic acid (LNA).

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: The invention is directed to methods and compositions for collecting a non-placental biological samples of cells and quantifying and comparing levels of expression of microRNAs to characterize a preeclampsia-related condition. The samples may be collected before or after an intervention or may be collected over a period of time. One of the samples may be a control sample. Patients may then be treated according to their response.

Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.

Abstract: Embodiments of the disclosure encompass methods of amplifying nucleic acid from one or more cells using MALBAC (multiple annealing and looping-based amplification cycles) primers. In particular embodiments, the nucleic acid is amplified as amplicons in a linear manner. Specific embodiments include the removal or effective destruction of nonlinearly produced amplicons.

Abstract: The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

Abstract: Genomic references are structured as a reference graph that represents diploid genotypes in organisms. A path through a series of connected nodes and edges represents a genetic sequence. Genetic variation within a diploid organism is represented by multiple paths through the reference graph. The graph may be transformed into a traversal graph in which a path represents a diploid genotype. Genetic analysis using the traversal graph allows an organism's diploid genotype to be elucidated, e.g., by mapping sequence reads to the reference graph and scoring paths in the traversal graph based on the mapping to determine the path through the traversal graph that best fits the sequence reads.

Abstract: A device and method for imaging fluorescently labeled molecules (e.g., nucleic acids) includes securing a modular attachment device to the mobile phone with a sample containing stretched, fluorescently labeled nucleic acid molecules and illuminating the sample with excitation light to cause the fluorescently labeled nucleic acid molecules to emit fluorescent light. Images of the nucleic acids are captured using a camera of the mobile phone. The images from the mobile phone are transferred to a remote computer for image processing and analysis. The images are processed by the remote computer to generate analysis data of sample, wherein the analysis data includes the length of nucleic acid molecules contained in the sample or the length of molecular sub-region(s). The mobile phone or another computing device receives from the remote computer the analysis data and displays at least some of the analysis data thereon.

Abstract: A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.

Abstract: Accurate variant calling methods for low frequency variants are provided. Sequence reads of targeted ultra-deep sequencing are received and aligned to a reference sequence. Read depths and variant counts for variants of the same class at each location where the reference allele exists on the reference sequence are determined for each sample-amplicon. Based on the read depths and variant counts, a probability value indicating the confidence level that a specific variant at a specific location is a true positive is calculated using methods such as a statistical model based method and a localized method using a reference sample. The probability value is then compared with a threshold level to determine whether the detected variants are true positives.

Abstract: An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.