Abstract: Described herein are methods, systems, compositions, and macromolecule complexes, for detecting, analyzing, evaluating, screening for, prognosing, diagnosing, and/or monitoring, of donor DNA in a transplant recipient for possible transplant rejection in the transplant recipient.

Abstract: Methods for differentially quantifying nucleic acids in a biological sample using differentially methylated loci include forming a digested biological sample in a solution of a methylation-sensitive restriction enzyme to cleave an unmethylated group of nucleic acids, forming a reaction mixture, amplifying the reaction mixture to generate a first signal from the a group of detection probes and a second signal from a second group of detection probes, determining a ratio comprising a first value derived from the first signal to a second value derived from the second signal, and identifying the proportion of nucleic acid in the biological sample originating from the first plurality of nucleic acids.

Abstract: Disclosed are methods for identifying the presence or absence of a target nucleic acid from one or more organisms in a biological sample, said method comprising: (a) spinning the sample at a rotational velocity sufficient to pellet cellular debris and fluorescence inhibitors present within the sample and reduce fluorescence interference or quenching in the sample; and (b) directly amplifying and detecting the target nucleic acid in the sample.

Abstract: Disclosed are methods for identifying the presence or absence of a target nucleic acid from one or more organisms in a biological sample, said method comprising: (a) spinning the sample at a rotational velocity sufficient to pellet cellular debris and fluorescence inhibitors present within the sample and reduce fluorescence interference or quenching in the sample; and (b) directly amplifying and detecting the target nucleic acid in the sample.