Abstract: The invention is a novel method of sequencing nucleic acids involving making and sequencing a library of double stranded target nucleic acids containing a linear partially single-stranded adaptor.

Abstract: An improved peptide library preparation method is described for constructing complete virtual peptide libraries such as a complete virtual tripeptide library, tetrapeptide library, pentapeptide library, hexapeptide library, heptapeptide library, or a complete octapeptide library, etc. The method includes constructing an expression vector for the expression of cyclic peptides. Each cyclic peptide displays an array of peptides of different sizes and sequences, and the number of cyclic peptides needed for constructing a complete virtual peptide library can be dramatically reduced compared with conventional chemical peptide synthesis. Furthermore, the cyclic peptide libraries can be readily reproduced by the expression and purification of the cyclic peptides using the constructed gene libraries.

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: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.

Abstract: Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

Abstract: The invention provides barcode libraries and methods of making and using them including obtaining a plurality of nucleic acid constructs in which each construct comprises a unique N-mer and a functional N-mer and segregating the constructs into a fluid compartments such that each compartment contains one or more copies of a unique construct. The invention further provides methods for digital PCR and for use of barcode libraries in digital PCR.

Abstract: Methods of preparing a next generation sequencing (NGS) library from a ribonucleic acid (RNA) sample are provided. Aspects of the methods include combining the RNA sample with a first strand cDNA primer and a template switch oligonucleotide under first strand cDNA synthesis conditions, where one of the first strand cDNA primer and the template switch oligonucleotide includes a first post-tagmentation amplification primer binding domain. The resultant product is subjected to amplification conditions sufficient to produce a double stranded cDNA, which is then tagmented with a transposome that includes a second post-tagmentation amplification primer binding domain. The tagmented sample is then subjected to amplification conditions using first and second post-tagmentation amplification primers that include sequencing platform adapter constructs to produce a NGS library. Aspects of the invention further include compositions produced by the methods and kits that find use in practicing the methods.

Abstract: Novel engineered compositions, reagents, and methods are described that facilitate NGS analysis of both random and specific nucleic acid sequences in a sample by providing high efficiency target enrichment and improved error suppression. Specifically, the design and use of engineered NGS dual adapter molecules with homology regions (HRs) targeted at the 5? and 3? regions of a double-stranded DNA target, unique molecule identifiers (UMIs), and NGS adapters allows target libraries to be created for subsequent NGS analysis.

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 generally relates to performing sandwich assays in droplets. In certain embodiments, the invention provides methods for detecting a target analyte that involve forming a compartmentalized portion of fluid including a portion of a sample suspected of containing a target analyte and a sample identifier, a first binding agent having a target identifier, and a second binding agent specific to the target analyte under conditions that produce a complex of the first and second binding agents with the target analyte, separating the complexes, and detecting the complexes, thereby detecting the target analyte.

Abstract: Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.

Abstract: Methods of amplifying and determining a target nucleotide sequence are provided. The method of amplifying the target nucleotide sequence includes the following steps. A first adaptor and a second adaptor are linked to two ends of a double-stranded nucleic acid molecule with a target nucleotide sequence respectively to form a nucleic acid template, in which the first adaptor includes a Y-form adaptor or a hairpin adaptor and the second adaptor is a hairpin adaptor. Then, a PCR amplification cycle is performed on the nucleic acid template to obtain a PCR amplicon of the target nucleotide sequence.

Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

Abstract: The present invention relates to methods, kits and systems for the prognosis of the disease outcome of breast cancer, said method comprising: (a) determining in a tumor sample from said patient the RNA expression levels of at least 2 of the following 9 genes: UBE2C, BIRC5, RACGAP1, DHCR7, STC2, AZGP1, RBBP8, IL6ST, and MGP (b) mathematically combining expression level values for the genes of the said set which values were determined in the tumor sample to yield a combined score, wherein said combined score is indicative of a prognosis of said patient; and kits and systems for performing said method.

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.

Abstract: Disclosed herein, inter alia, are nanoarrays and methods of use thereof.

Abstract: The invention relates to new methods for synthesising polynucleotide molecules according to a predefined nucleotide sequence. The invention also relates to methods for the assembly of synthetic polynucleotides following synthesis, as well as systems and kits for performing the synthesis and/or assembly methods.

Abstract: The invention provides methods for assessment of risk for genetic conditions using target-enriched multiplexed parallel analysis, for example fetal risk for genetic conditions in prenatal testing. The methods of the invention utilize Target Capture Sequences (TACS) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The methods of the disclosure can be used to determine carrier status of inheritable genetic abnormalities associated with genetic conditions and from this information the fetal risk of inheriting the genetic condition can be determined. Kits for carrying out the methods of the invention are also provided.

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial-proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

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.