| CPC C12Q 1/705 (2013.01) [C12Q 1/6858 (2013.01); C12Q 1/6886 (2013.01); C12Q 1/6893 (2013.01); G16B 30/00 (2019.02); G16B 30/10 (2019.02); Y02A 50/30 (2018.01)] | 12 Claims |
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1. A method of determining the presence or absence of one or more foreign elements in a subject, the method comprising:
obtaining a biological sample of the subject, the biological sample comprising polynucleotides, wherein the polynucleotides comprise a genome of the subject;
removing host polynucleotides from the biological sample, wherein the host polynucleotides are bound with a methyl-CpG binding domain (MBD), and wherein the removal of the host polynucleotides comprises binding the methyl-CpG binding domain with protein A magnetic beads;
labeling the polynucleotides in a sequence-specific manner to provide a pattern of sequence-specific labels on the polynucleotides, wherein the labeling comprises non-cutting labeling of the polynucleotides, and wherein labeling the polynucleotides in the sequence-specific manner to provide the pattern of sequence-specific labels on the polynucleotides comprises labeling the polynucleotides with labeling probes or enzymes having a lower label density for the genome of the subject than for the foreign elements;
linearizing the polynucleotides in nanochannels following labeling, whereby the nanochannels comprise labeled single molecule polynucleotides;
obtaining images of labeled single-molecule polynucleotides linearized in the nanochannels;
processing the images into digital representations of relative label locations in the polynucleotides;
aligning the relative label locations on the polynucleotides in silico against a foreign reference map comprising relative locations of labels on foreign elements, thereby determining a quantity of the polynucleotides that align to relative locations of label locations of foreign elements, wherein the foreign reference map comprising relative locations of labels on foreign elements comprises a label density of about 5 labels to about 20 labels per 100 kb; and
determining the presence of foreign elements in the subject when the quantity exceeds a limit of detection, wherein the one or more foreign elements comprise a viral sequence and/or a transposable element sequence.
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