Abstract: Diagnostic devices and methods are provided for screening for a disease condition, including a cancer condition or a mendelian disease. The diagnostic devices allow for in vivo contact of cell-free nucleic acids or circulating tumor cells. The diagnostic device has a needle with a body and a detection reaction module attached to the body.

Abstract: Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

Abstract: Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.

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: Systems and methods described herein include detecting a presence or absence of HPV in a biological sample having cell-free nucleic acids from a subject and potentially cell-free nucleic acids from an HPV strain. Based on a detection of HPV viral nucleic acids in the biological sample, an HPV-based multiclass classifier that predicts a score for each HPV-associated cancer type is applied. The HPV-based multiclass classifier is trained on a training set of HPV-positive cancer samples. An HPV-associated cancer associated with the biological sample is determined based on the scores predicted by the HPV multiclass classifier.

Abstract: Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process.

Abstract: Methods for determining a disease condition of a subject of a species are provided that comprises obtaining a dataset of fragment methylation patterns determined by methylation sequencing of nucleic acid from a biological sample of the subject. A fragment methylation pattern comprises the methylation state of each CpG site in the fragment. A patch including a channel comprising parameters for the methylation status of respective CpG sites in a set of CpG sites in a reference genome represented by the patch is constructed by populating, for each respective fragment in the plurality of fragments that aligns to the set of CpG sites, an instance of all or a portion of the plurality of parameters based on the methylation pattern of the respective fragment. Application of the patch to a patch convolutional neural network determines the disease condition of the subject.

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: Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared from dsDNA alone.

Abstract: Aspects of the invention relate to methods and compositions for preparing and analyzing a single-stranded sequencing library from a double-stranded DNA (e.g., double-stranded cfDNA) sample. In some embodiments, the sample includes double-stranded DNA (dsDNA) molecules, and damaged dsDNA (e.g., nicked dsDNA) molecules. In some embodiments, the sample includes single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information, including strand-pairing and connectivity information, from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared using conventional methods.

Abstract: Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

Abstract: Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.

Abstract: In comparison to conventional sequencing pileup algorithms, the process described herein generates sequencing pileups that contains additional information not typically reported by conventional algorithms while also consuming fewer computational resources (e.g., time, processing power, and memory). First, each of a FASTA reference genome and BAM sequence read files are converted to an internal representation. This enables the rapid iteration across nucleotide bases of the sequence reads to determine support characteristics that summarize information of nucleic acid molecules corresponding to positions across the reference genome. Next, the support characteristics of positions across the reference genome are stored through a memory allocation process that utilizes a first and a second temporary storage. This enables the convenient freeing of one temporary storage while the other temporary storage is being used.

Abstract: Systems and methods for determining a source of a variant include receiving a plurality of variants obtained from a biological sample, the variants being of unknown source upon receipt, and receiving, for each of the variants, a plurality of values for a plurality of covariates from the biological sample. The variants are input into a source assignment classifier to determine a source for each of the variants, the source being one of a plurality of possible sources. The source assignment classifier includes a plurality of coefficients associated with the plurality of covariates and a function that receives as input the values associated with each variant and the coefficients and outputs the determined source of each of the variants.

Abstract: Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared from dsDNA alone.

Abstract: Methods and systems for detecting positive, neutral, or negative selection at a locus include obtaining a test sample of cell-free nucleic acids from a subject, preparing a sequencing library of the cell-free nucleic acids, sequencing the library to obtain a plurality of sequence reads, analyzing the sequence reads to detect and quantify one or more somatic mutations at the locus, determining a selection coefficient for the locus, and comparing the selection coefficient with a threshold value to detect positive, neutral, or negative selection at the locus.

Abstract: In various aspects, the present disclosure provides methods, compositions, reactions mixtures, kits, and systems for sequencing both RNA and DNA from a single source sample. In some embodiments, RNA is treated so as to differentiate RNA sequences from DNA sequences derived from the same sample. In some embodiments, the RNA and DNA are cell-free polynucleotides.

Abstract: A system and method described in this disclosure seeks to create new ways of defining and mapping relationships between content items in order to create more relevant content recommendations. Semiotic analysis, unlike semantic analysis, looks at how words mean rather than what words mean. Semiotics can define an emotional context for content items, which may be leveraged into content recommendations to users, creating more personalized and meaningful recommendations. The system and method analyze the semiotic context by analyzing the semiotic nature of the content itself through analysis of the writing style or genre of the content item, and the tone in which the content item is written; by analyzing the semiotic nature of the entities extracted from content items; and by analyzing the semiotic nature of the publisher or author who created the content item.