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 introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

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 introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

Disclosed are systems and methods for detecting genetic alterations comprising androgen receptor gene splice variants (AR-Vs), mutations, indel, copy number changes, fusion and combination thereof, in a biofluid sample from the patient. The systems and methods are similarly applicable to the detection of gene alterations comprising gene splicing variants, mutations, indel, copy number changes, fusion and combination thereof of other genes of interest. The streamlined methods improve the consistency and simplicity of non-invasive detections of biomarkers.

The invention relates to control compositions for sequencing and for chemical analyses, such as analytical chemistry analyses. More particularly, the invention relates to control compositions for sequencing and for chemical analyses having at least one barcode sequence fragment and at least one universal sequence fragment, and to methods of their use.

The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

The present disclosure provides methods and kits for tracking nucleic acid target origin by barcode tagging of the targets when they break into smaller fragments. Nucleic acid targets are captured in vitro by clonally localized nucleic acid barcode templates on a solid support. Millions of nucleic acid targets can be processed simultaneously in a massively parallel fashion without additional partition. These captured targets are broken into small fragments, and a target specific barcode sequence is tagged on each fragment as an identification of their original target. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing.

Food distributed to consumers through a distribution chain may be traced by tagging the food with DNA tags that identify the origin of the food, such as the grower, packer and other points of distribution, and their attributes. This makes it much quicker and easier to trace the food in case of food contamination or adulteration. Preferably these attributes indicate the field, location, crew and machine used to grow and process the food, and the dates of the various steps of food harvesting, processing and distribution. Natural or synthetic DNA pieces may be used to tag items, including food items. Multidigit binary or other types of bar codes may be represented by multiple types of DNA. Each digit of the bar code may be represented by one, two or more unique DNA pieces.

Food distributed to consumers through a distribution chain may be traced by tagging the food with DNA tags that identify the origin of the food, such as the grower, packer and other points of distribution, and their attributes. This makes it much quicker and easier to trace the food in case of food contamination or adulteration. Preferably these attributes indicate the field, location, crew and machine used to grow and process the food, and the dates of the various steps of food harvesting, processing and distribution. Natural or synthetic DNA pieces may be used to tag items, including food items. Multidigit binary or other types of bar codes may be represented by multiple types of DNA. Each digit of the bar code may be represented by one, two or more unique DNA pieces.

The present disclosure provide compositions, methods and kits for generating a set of combinatorial barcodes, and uses thereof for barcoding samples such as single cells or genomic DNA fragments. Some embodiments disclosed herein provide compositions comprising a set of component barcodes for producing a set of combinatorial barcodes. The set of component barcodes can comprise, for example, n×m unique component barcodes, wherein n and m are integers, each of the component barcodes comprises: one of n unique barcode subunit sequences; and one or two linker sequences or the complements thereof, wherein the component barcodes are configured to connect to each other through the one or two linker sequences or the complements thereof to produce a set of combinatorial barcodes.