The Board of Trustees of the Leland Stanford Junior University

Systems and methods for trapping and detecting a polynucleotide strand in a channel. Methods may include labeling at least one subsequence within a polynucleotide strand to obtain a labeled polynucleotide strand having at least one label. Methods may additionally include providing a polymer to a surface of a channel and physically interacting the polymer with the surface of the channel. Methods may also include providing a sample including the labeled polynucleotide strand to the channel, applying an electric field to the labeled polynucleotide strand to promote a physical interaction between the labeled polynucleotide strand and the polymer at the surface of the channel to trap the labeled polynucleotide strand at the surface of the channel, and detecting the at least one label within the labeled polynucleotide strand.

Systems and methods for trapping a polynucleotide strand at a surface of a channel. Methods may include providing a polymer to the surface of the channel and physically interacting the polymer with the surface of the channel. Methods may also include providing a sample including the polynucleotide strand to the polymer interacting with the surface of the channel and applying an electric field to the polynucleotide strand to promote a physical interaction between the polynucleotide strand and the polymer to trap the polynucleotide strand at the surface of the channel.

Systems and methods for trapping a polynucleotide strand at a defined surface of a channel. Methods may include providing a device including a channel and providing to a defined surface of the channel a polymer capable of modifying an electroosmotic flow in the channel and a sample including a polynucleotide strand. Methods may also include physically interacting the polymer with the defined surface of the channel and applying an electric field to the defined surface of the channel to promote a physical interaction between the polynucleotide strand and the polymer to trap the polynucleotide strand at the defined surface of the channel.

Processes and materials to detect cancer, transplant rejection, or fetal genetic abnormalities from a biopsy are described. In some cases, nucleic acid molecules, such as cell-free nucleic acids, can be sequenced, and the sequencing result can be utilized to detect sequences indicative of a neoplasm, transplant rejection, or fetal genetic abnormality. Detection of somatic variants occurring in phase and/or insertions and deletions (indels) can indicate the presence of cancer, transplant rejection, or fetal genetic abnormalities in a diagnostic scan, and a clinical intervention can be performed.

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