Patent ID: 11959142
Assignee: THE JOHNS HOPKINS UNIVERSITY
Field: Computer technology (Electrical engineering)
Classification: CPC C  G | IPC C  G

Claim 7:
8. A method for identifying the presence of circulating tumor DNA in a subject, and treating said subject comprising:
detecting one or more genetic alterations in cell-free DNA in a biological sample isolated from the subject, wherein the step of detecting is performed when the subject is not known to harbor a cancer cell; and wherein the step of detecting one or more genetic alterations in cell-free DNA includes using a method comprising steps of:
i) extracting cell-free DNA from blood;
ii) ligating a low complexity pool of dual index barcode adapters to the cell-free DNA to generate a plurality of barcode adapter-ligated cell-free DNA segments;
iii) capturing the plurality of barcode adapter-ligated cell-free DNA segments;
iv) sequencing the plurality of captured barcode adapter-ligated cell-free DNA segments, wherein the captured DNA segments are sequenced at least three times with a distribution of start positions as compared to a reference genome;
v) aligning the sequenced plurality of captured barcode adapter-ligated cell-free DNA segments to a reference genome;
vi) identifying sequence alterations using aligned sequences of multiple distinct molecules containing identical redundant changes;
vii) identifying the presence of circulating tumor DNA when at least one of the detected genetic alterations in the cell-free DNA is a cancer cell mutation; and
administering a therapeutic agent to the subject.