Abstract: Methods for mitigation of methylation bias during preparation of sequencing libraries are described. The methods may comprise, e.g., extracting DNA fragments from a sample; performing at least one of: (i) a first end repair reaction, where the first end repair reaction comprises the use of a non-strand-displacing DNA polymerase; or (ii) a second end repair reaction, where the second end repair reaction comprises the use of a chain termination mechanism; performing at least one of: (iii) a tailing reaction to add an overhanging polynucleotide strand to the end-repaired DNA fragments, where the tailing reaction comprises the use of a single deoxynucleotide triphosphate (dNTP); or (iv) a nick/gap repair reaction using a DNA ligase to fill in single-stranded nicks or gaps in the end-repaired DNA fragments, to generate a plurality of modified DNA fragments; and performing methylation analysis of nucleic acid molecules derived from the plurality of modified DNA fragments.

Abstract: Methods for generating and evaluation methylation meta scores and their use for the detection of disease and prediction of tumor tissue of origin are described. The methods may comprise, e.g., generating annotated genomic interval data comprising at least one of: (i) genomic coordinates, and (ii) associated genomic annotation data; providing annotated patient sample data comprising at least one of: (i) methylation sequencing data, and (ii) associated clinical annotation data; generating an aggregated methylation meta score matrix comprising candidate methylation meta scores; inputting (i) the aggregated methylation meta score matrix, and (ii) the associated clinical annotation data for at least a subset of patient samples as training data for training a machine learning model; and training the model using the training data to identify an optimal methylation meta score for disease detection and/or prediction of disease tissue of origin (TOO) for at least one disease type based on methylation sequencing data.

Abstract: Techniques for predicting expression of cancer cells based on the methylation status of a region of DNA are described. An example method includes identifying data indicative of cell free DNA (cfDNA) from a sample derived from a subject. A methylation status of one or more regions of circulating tumor DNA (ctDNA) among the cfDNA is identified by analyzing the data. The example method further includes inputting input data including the methylation status of the one or more regions into at least one model configured to generate a probability that cancer cells of the subject express a predetermined sequence. In addition, the example method includes generating a report based on the probability that the cancer cells of the subject express the predetermined sequence.

Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may use a single flow cell to perform unbiased and/or biased sequencing to generate libraries of nucleic acid molecules. An aspect of the present disclosure provides a method for increasing complexity of a sample for sequencing, the method comprising: providing a first nucleic acid sample having a first degree of complexity that differs from a desired degree of complexity; providing a second nucleic acid sample having a second degree of complexity that differs from the first degree of complexity and that differs from the desired degree of complexity; pooling at least a portion of the first nucleic acid sample and at least a portion of the second nucleic acid sample, thereby generating a pooled nucleic acid sample having the desired degree of complexity; and sequencing at least a portion of the pooled nucleic acid sample.

Abstract: Provided herein are methods related to detecting DNA methylation (e.g., level of methylation at CpG dinucleotide cluster(s)), as well as methods of treatment, uses, systems, and computer readable storage media related thereto. These methods allow for detection of aberrant DNA methylation patterns with low background and increased signal-to-background ratio, which can be useful, inter alia, in the early detection or monitoring of cancer.

Abstract: The present disclosure provides methods of assessing tumor status (e.g., progression, regression, recurrence, etc.) in a subject. In an aspect, a method for assessing tumor status (e.g., progression, regression, recurrence, etc.) of a subject may comprise: based on first and second WGS data of cfDNA molecules of a subject at different time points, determing (i) a first and second plurality of CNAs and (ii) a first and a second plurality of fragment lengths; processing the first and second plurality of CNAs to determine a CNA profile change; comparing the first and second plurality of fragment lengths to determine a fragment length profile change; determining a first or second tumor fraction of the subject at the first or second timepoint, based at least in part on the CNA profile change and the fragment length profile change; and detecting a tumor status of the subject based at least in part on the first or second tumor fraction.

Abstract: The invention disclosed herein generally relates to methods of assessing microsatellite instability in a subject. In an aspect, the present disclosure provides a computer-implemented method of assessing microsatellite instability of a subject, comprising: obtaining a quantitative measure of a plurality of microsatellite repeat elements from a blood sample of a subject; processing the plurality of quantitative measures to obtain a statistical measure of deviation of the plurality of quantitative measures; and detecting a presence of the microsatellite instability (MSI) of the subject when the statistical measure of deviation of the plurality of quantitative measures satisfies a predetermined criterion, or detecting an absence of the microsatellite instability (MSI) of the subject when the statistical measure of deviation of the plurality of quantitative measures does not satisfy the predetermined criterion.

Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may use a single flow cell to perform unbiased and/or biased sequencing to generate libraries of nucleic acid molecules. An aspect of the present disclosure provides a method for increasing complexity of a sample for sequencing, the method comprising: providing a first nucleic acid sample having a first degree of complexity that differs from a desired degree of complexity; providing a second nucleic acid sample having a second degree of complexity that differs from the first degree of complexity and that differs from the desired degree of complexity; pooling at least a portion of the first nucleic acid sample and at least a portion of the second nucleic acid sample, thereby generating a pooled nucleic acid sample having the desired degree of complexity; and sequencing at least a portion of the pooled nucleic acid sample.

Abstract: The present disclosure provides methods for fingerprinting of biological samples of a subject.

Abstract: Disclosed are insulated nanoelectrode associated with nanopores, useful in macromolecular analysis devices. Also disclosed are related methods of fabrication and use.

Abstract: Disclosed are insulated nanoelectrode associated with nanopores, useful in macromolecular analysis devices. Also disclosed are related methods of fabrication and use.