In some aspects, the present disclosure provides methods for identifying sequence variants, as well as methods of determining copy number of a genetic locus in a sample. Systems and kits for performing methods of the disclosure, as well as compositions produced by or useful in methods of the disclosure are also provided. In some embodiments, methods comprise extending 3′ ends of polynucleotides by adding one or more pre-determined nucleotides. In some embodiments, methods comprise use of a strand-tagging sequence.

In some aspects, the present disclosure provides methods for identifying sequence variants, as well as methods of determining copy number of a genetic locus in a sample. Systems and kits for performing methods of the disclosure, as well as compositions produced by or useful in methods of the disclosure are also provided. In some embodiments, methods comprise extending 3′ ends of polynucleotides by adding one or more pre-determined nucleotides. In some embodiments, methods comprise use of a strand-tagging sequence.

Embodiments of the present disclosure, pertaining to the technical field of high-throughput sequencing, relate to a method for high-throughput sequencing based on an internal reference with a known index. The method includes: generating a random DNA sequence, adding a single-ended adapter DNA sequence containing the known index at both ends of the random DNA sequence to obtain an internal reference sequence, and synthesizing a sequencing quality control sequence based on the internal reference sequence; performing, based on the sequencing quality control sequence, high-throughput sequencing on a library of samples to be tested to obtain sequencing data; and performing result analysis on the sequencing data to obtain a sample error distribution rate of the library of samples to be tested, and ending the high-throughput sequencing. According to the present disclosure, index hopping in the process of sequencing may be monitored based on the internal reference.

Embodiments of the present disclosure, pertaining to the technical field of high-throughput sequencing, relate to a method for high-throughput sequencing based on an internal reference with a known index. The method includes: generating a random DNA sequence, adding a single-ended adapter DNA sequence containing the known index at both ends of the random DNA sequence to obtain an internal reference sequence, and synthesizing a sequencing quality control sequence based on the internal reference sequence; performing, based on the sequencing quality control sequence, high-throughput sequencing on a library of samples to be tested to obtain sequencing data; and performing result analysis on the sequencing data to obtain a sample error distribution rate of the library of samples to be tested, and ending the high-throughput sequencing. According to the present disclosure, index hopping in the process of sequencing may be monitored based on the internal reference.

The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.

The present invention discloses methods and compositions for modulating the quality of an immune response to a target antigen in a mammal, which response results from the expression of a polynucleotide that encodes at least a portion of the target antigen, wherein the quality is modulated by replacing at least one codon of the polynucleotide with a synonymous codon that has a higher or lower preference of usage by the mammal to confer the immune response than the codon it replaces.