Abstract: Methods for making and using reagents and adapters for use in nucleic acid sequencing applications are disclosed herein. In several embodiments, adapters and reagents and the methods of making such adapters and reagents can be used for Duplex Sequencing applications.

Abstract: Methods for characterizing genome editing, clonal expansion and associated reagents for use in such methods are disclosed herein. Some embodiments of the technology are directed to characterizing a population of cells following an engineered genomic editing event, that includes in some embodiments characterizing genomic alterations occurring at both intended and unintended genomic loci within the genome of the populations of cells. Other embodiments are directed to utilizing Duplex Sequencing for assessing a clonal selection in mixed cell populations and/or cell populations following a genomic editing event. Further examples of the present technology are directed to methods for detecting and assessing clonal expansion of cells following a genomic editing event.

Abstract: The present technology relates generally to methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications. In some embodiments, highly accurate, error corrected and massively parallel sequencing of nucleic acid material is possible using a combination of uniquely labeled strands in a double-stranded nucleic acid complex in such a way that each strand can be informatically related to its complementary strand, but also distinguished from it following sequencing of each strand or an amplified product derived therefrom. In various embodiments, this information can be used for the purpose of error correction of the determined sequence.

Abstract: Methods for making and using reagents and adapters for use in nucleic acid sequencing applications are disclosed herein. In several embodiments, adapters and reagents and the methods of making such adapters and reagents can be used for Duplex Sequencing applications.

Abstract: Methods for characterizing genome editing, clonal expansion and associated reagents for use in such methods are disclosed herein. Some embodiments of the technology are directed to characterizing a population of cells following an engineered genomic editing event, that includes in some embodiments characterizing genomic alterations occurring at both intended and unintended genomic loci within the genome of the populations of cells. Other embodiments are directed to utilizing Duplex Sequencing for assessing a clonal selection in mixed cell populations and/or cell populations following a genomic editing event. Further examples of the present technology are directed to methods for detecting and assessing clonal expansion of cells following a genomic editing event.

Abstract: The present technology relates generally to methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications. In some embodiments, highly accurate, error corrected and massively parallel sequencing of nucleic acid material is possible using a combination of uniquely labeled strands in a double-stranded nucleic acid complex in such a way that each strand can be informatically related to its complementary strand, but also distinguished from it following sequencing of each strand or an amplified product derived therefrom. In various embodiments, this information can be used for the purpose of error correction of the determined sequence.

Abstract: Disclosed herein are adapter nucleic acid sequences, double-stranded complexed nucleic acids, compositions, and methods for sequencing a double-stranded target nucleic acid with applications to error correction by duplex sequencing.

Abstract: The present technology relates generally to the methods and associated reagents for providing error-corrected nucleic acid sequences. In particular, several embodiments are directed to adapter molecules comprising a hairpin shape and methods of use of such adapters in Duplex Sequencing and other sequencing applications. In some embodiments, physically-linked nucleic acid complexes comprising both the first strand and the second strand can be amplified and independently sequenced in a same clonal cluster on a sequencing surface.

Abstract: Disclosed herein are adapter nucleic acid sequences, double-stranded complexed nucleic acids, compositions, and methods for sequencing a double-stranded target nucleic acid with applications to error correction by duplex sequencing.

Abstract: Methods and associated reagents for efficient genotyping of large numbers of samples via pooling are disclosed herein. Some of the embodiments of the technology are directed utilizing Duplex Sequencing for efficient genotyping of large numbers of samples (e.g., nucleic acid samples, patient samples, tissue samples, blood samples, etc.) and associated applications. Various aspects of the present technology have many applications in both pre-clinical and clinical disease assessment, screening large sample numbers where relatively infrequent variants are being sought, and others.

Abstract: Methods, systems, and kits with reagents for assessing genotoxicity, are disclosed herein. Genotoxicity and their mechanisms of action can be determined within a few days of a subjects exposure. Some embodiments of the technology are directed to utilizing Duplex Sequencing for assessing a genotoxic potential of a compound (e.g., a chemical compound) in an exposed subject. Other embodiments of the technology are directed to utilizing Duplex Sequencing for determining a mutation signature associated with a genotoxic agent; and/or a safe threshold level of genotoxin exposure. Additional embodiments of the technology are directed to identifying one or more genotoxic agents a subject may have been exposed to by comparing the subjects DNA mutation spectrum to the mutation spectra of known mutagenic compounds. Once a genotoxin exposure in a subject is identified, or confirmed, then a prophylactic, and/or inhibitory therapeutic course of treatment is provided.

Abstract: Methods and associated reagents for assessing and resolving nucleic acid mixtures and/or mixed cell populations are disclosed herein. Some embodiments of the technology are directed to utilizing Duplex Sequencing for assessing and resolving nucleic acid mixtures (e.g., multichimeric mixtures, mixtures of nucleic acids from more than one source, etc.) in a sample and associated applications. Other embodiments are directed to detecting and quantifying a donor source of nucleic acid from a mixture.

Abstract: Methods for characterizing genome editing, clonal expansion and associated reagents for use in such methods are disclosed herein. Some embodiments of the technology are directed to characterizing a population of cells following an engineered genomic editing event, that includes in some embodiments characterizing genomic alterations occurring at both intended and unintended genomic loci within the genome of the populations of cells. Other embodiments are directed to utilizing Duplex Sequencing for assessing a clonal selection in mixed cell populations and/or cell populations following a genomic editing event. Further examples of the present technology are directed to methods for detecting and assessing clonal expansion of cells following a genomic editing event.

Abstract: The present technology relates generally to methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications and other nucleic acid sequence interrogations. In some embodiments, provided methods provide non-amplification based targeted enrichment strategies compatible with the use of molecular barcodes for error correction. Other embodiments provide methods for non-amplification based targeted enrichment strategies compatible with direct digital sequencing (DDS) and other sequencing strategies (e.g., single molecule sequencing modalities and interrogations) that do not use molecular barcoding.

Abstract: Methods for making and using reagents and adapters for use in nucleic acid sequencing applications are disclosed herein.

Abstract: The present technology relates generally to methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications. In some embodiments, highly accurate, error corrected and massively parallel sequencing of nucleic acid material is possible using a combination of uniquely labeled strands in a double-stranded nucleic acid complex in such a way that each strand can be informatically related to its complementary strand, but also distinguished from it following sequencing of each strand or an amplified product derived therefrom. In various embodiments, this information can be used for the purpose of error correction of the determined sequence.

Abstract: Disclosed herein are adapter nucleic acid sequences, double-stranded complexed nucleic acids, compositions, and methods for sequencing a double-stranded target nucleic acid with applications to error correction by duplex sequencing.