Abstract: A method of processing an input sample, as well as related kits and compositions, is provided herein.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

Abstract: Methods and systems for determining a subject's likelihood of responding to a treatment by assessing the subject's cell-free DNA (cfDNA) sample include receiving sequence data gathered from sequencing the cfDNA sample, generating a feature matrix of values that correspond to synonymous and nonsynonymous mutations detected in the sequence data, and predicting, based on analysis of the feature matrix at a TMB prediction model, a tumor mutational burden (TMB) for a tissue of interest at the subject. The predicted TMB is evaluated to determine whether a set of criteria indicating a likely response to treatment is met. The set of criteria can include criterion(s) that are met when the predicted TMB is high, when the predicted TMB corresponds to a predicted tumoral heterogeneity indicative of homogeneous tissue, when the predicted TMB corresponds to a tumor fraction indicative of a positive responder, or any combination thereof.

Abstract: Methods for preparing a sequencing library from a DNA-containing test sample are provided. In some embodiments, the methods involve rescuing a partially ligated DNA fragment to enhance library preparation conversion efficiencies. In some embodiments, the methods involve improving recovery of duplex sequence information from double-stranded DNA.

Abstract: Methods for preparing a sequencing library from a DNA-containing test sample are provided. In some embodiments, the methods involve rescuing a partially ligated DNA fragment to enhance library preparation conversion efficiencies. In some embodiments, the methods involve improving recovery of duplex sequence information from double-stranded DNA.

Abstract: Aspects of the invention include methods for preparing an enriched sequencing library. In some embodiments, the methods involve preparing a sequencing library that is enriched for AT-rich sequences. In certain embodiments, the methods involve determining a presence or an absence of cancer, determining a cancer stage, monitoring cancer progression, and/or determining a cancer classification in a subject by analyzing an enriched sequencing library.

Abstract: Methods for preparing a sequencing library from a DNA-containing test sample are provided, including methods for rescuing one or more partially ligated DNA fragments to enhance library preparation conversion efficiencies. The subject methods can further be used to improve recovery of duplex sequence information from double-stranded DNA.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: a substrate having an inner surface facing a library sequencing region, and an outer surface; a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors in sequence reads, and methods for identifying rare variants in a test sample, are provided.

Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

Abstract: Aspects of the invention include methods for preparing an enriched sequencing library. In some embodiments, the methods involve preparing a sequencing library that is enriched for AT-rich sequences. In certain embodiments, the methods involve determining a presence or an absence of cancer, determining a cancer stage, monitoring cancer progression, and/or determining a cancer classification in a subject by analyzing an enriched sequencing library.

Abstract: Methods for preparing a sequencing library from a DNA-containing test sample are provided. In some embodiments, the methods involve rescuing a partially ligated DNA fragment to enhance library preparation conversion efficiencies. In some embodiments, the methods involve improving recovery of duplex sequence information from double-stranded DNA.

Abstract: Methods for preparing a sequencing library from a DNA-containing test sample are provided, including methods for rescuing one or more partially ligated DNA fragments to enhance library preparation conversion efficiencies. The subject methods can further be used to improve recovery of duplex sequence information from double-stranded DNA.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.