Abstract: Methods and systems are described herein that include using sequence reads of linear DNA molecules naturally present in a biological sample to classify a set of the linear DNA molecules that are eccDNA remnants, i.e., linear DNA molecules resulting from in vivo opening of eccDNA molecules. In various embodiments, characteristics of the classified eccDNA remnants can be analyzed to determine a property of the biological sample or of the subject from whom the biological sample was obtained. Examples of properties that can be determined include a classification of a pathology, e.g., a level of a cancer, or an inferred age of the subject.

Abstract: Techniques are provided for analyzing circular DNA in a biological sample (e.g., including cell-free DNA, such as plasma). For example, to measure circular DNA, cleaving can be performed to linearize the circular DNA so that they may be sequenced. Example cleaving techniques include restriction enzymes and transposases. Then, one or more criteria can be used to identify linearized DNA molecules, e.g., so as to differentiate from linear DNA molecules. An example criterion is mapping a pair of reversed end sequences to a reference genome. Another example criterion is identification of a cutting tag, e.g., associated with a restriction enzyme or an adapter sequence added by a transposase. Once circular DNA molecules (e.g., eccDNA and circular mitochondrial DNA) are identified, they may be analyzed (e.g., to determine a count, size profile, and/or methylation) to measure a property of the biological sample, including genetic properties and level of a disease.

Abstract: Techniques are provided for analyzing circular DNA in a biological sample (e.g., including cell-free DNA, such as plasma). For example, to measure circular DNA, cleaving can be performed to linearize the circular DNA so that they may be sequenced. Example cleaving techniques include restriction enzymes and transposases. Then, one or more criteria can be used to identify linearized DNA molecules, e.g., so as to differentiate from linear DNA molecules. An example criterion is mapping a pair of reversed end sequences to a reference genome. Another example criterion is identification of a cutting tag, e.g., associated with a restriction enzyme or an adapter sequence added by a transposase. Once circular DNA molecules (e.g., eccDNA and circular mitochondrial DNA) are identified, they may be analyzed (e.g., to determine a count, size profile, and/or methylation) to measure a property of the biological sample, including genetic properties and level of a disease.

Abstract: Systems and methods for determining base modifications using electrical signals and other data is described herein. Embodiments can make use of features derived from electrical signals related to sequencing, such as those acquired from using a nanopore, that are affected by the various base modifications, as well as an identity of nucleotides in a window around a target position whose methylation status is determined. Other features may include a vector of statistical values of a segment of the electrical signal corresponding to the nucleotide and a statistical value of the electrical signal in a window in a region of the nucleic acid molecule. The detected base modifications can be used for additional analysis of a biological sample.

Abstract: Techniques are provided for analyzing circular DNA in a biological sample (e.g., including cell-free DNA, such as plasma). For example, to measure circular DNA, cleaving can be performed to linearize the circular DNA so that they may be sequenced. Example cleaving techniques include restriction enzymes and transposases. Then, one or more criteria can be used to identify linearized DNA molecules, e.g., so as to differentiate from linear DNA molecules. An example criterion is mapping a pair of reversed end sequences to a reference genome. Another example criterion is identification of a cutting tag, e.g., associated with a restriction enzyme or an adapter sequence added by a transposase. Once circular DNA molecules (e.g., eccDNA and circular mitochondrial DNA) are identified, they may be analyzed (e.g., to determine a count, size profile, and/or methylation) to measure a property of the biological sample, including genetic properties and level of a disease.