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US 11,959,142 B2Granted
Detection of cancer
AssigneeThe Johns Hopkins University
InventorsVictor Velculescu, Jillian A. Phallen
Life of this patent
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Abstract
Provided herein are methods of detecting circulating tumor DNA, cancer cell mutations, and/or cancer cells harboring one or more cancer cell mutations. In some embodiments, methods provided herein include detecting one or more genetic alterations in cell-free DNA. In some embodiments, methods provided herein for detecting one or more genetic alterations in cell-free DNA can be performed when the subject is not known to harbor a cancer cell and/or a cancer cell mutation (e.g., when the subject is not known to harbor a cancer cell having the cancer cell mutation).
Claims8
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, wherein the barcodes each consist of 6 or 8 base pairs;
- 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;
- and,
- 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 mutations;
- and thereafter
- administering a therapeutic agent to the subject.
9 more elements
A method for identifying the presence of a lung cancer cell in a subject and treating the 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 lung 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, wherein the barcodes each consist of 6 or 8 base pairs;
- 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;
- and
- vii) identifying the presence of circulating tumor DNA when at least one of the detected genetic alterations in the cell-free DNA is a lung cancer cell mutation;
- and
- viii) identifying the presence of the lung cancer cell when the presence of circulating tumor DNA is identified;
- and thereafter
- administering a therapeutic agent to the subject.
11 more elements
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.
8 more elements
Dependencies are inferred from the claim text.