Non-invasive blood based monitoring of genomic alterations in cancer

A method to monitor cell free DNA comprising:

• (i) obtaining a body fluid sample from a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer;
• (ii) isolating cell free nucleic acids from the body fluid sample obtained from the subject;
• (iii) measuring the amount of a housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample, wherein the amount of the housekeeping gene and/or total DNA in the sample correlates to the amount of Line 1 and the amount of Line 1 is within a range of 3,000-700,000 pg/μL;
• (iv) measuring the amount of a first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the body fluid sample;
• and
• (v) measuring the apparent amount of the first of the pair of mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first of the pair of mutually exclusive mutations in the cell free nucleic acids isolated from the body fluid sample from the subject;
• and
• (vi) indicating in a report that the subject has the first of the pair of mutually exclusive mutations when (a) the amount of the housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample correlates to the amount of Line 1 and the amount of Line 1 is within the range of 3,000-700,000 pg/μL and (b) the amount of the first of the pair of mutually exclusive mutations is increased as compared to the apparent amount of the first of the pair of mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from control subjects.

A method to treat cancer comprising:

• (i) obtaining a body fluid sample from a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer;
• (ii) isolating cell free nucleic acids from the body fluid sample obtained from the subject;
• (iii) measuring the amount of a housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample, wherein the amount of housekeeping gene and/or total DNA in the sample correlates to the amount of Line 1 and the amount of Line 1 is within a range of 3,000-700,000 pg/μL;
• (iv) measuring the amount of a first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the body fluid sample;
• (v) measuring the apparent amount of the first of the mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first of the mutually exclusive mutations in the cell free nucleic acids isolated from the body fluid sample from the subject;
• and
• (vi) treating the subject with an anti-cancer therapy when (a) the amount of the housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample is within the range of 3,000-700,000 pg/μL and (b) the amount of the first of the pair of mutually exclusive mutations is increased as compared to the apparent amount of the first of the pair of mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from control subjects.

A method comprising:

• (i) administering an anti-cancer therapy to a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer;
• (ii) obtaining a body fluid sample from the subject;
• (iii) isolating cell free nucleic acids from the body fluid sample obtained from the subject;
• (iv) measuring the amount of a housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample to confirm that the amount of the housekeeping gene and/or total DNA in the sample correlates to the amount of Line and the amount of Line 1 is within a range of 3,000-700,000 pg/μL;
• (v) measuring the amount of a first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the body fluid sample;
• and
• (vi) measuring the apparent amount of the first of the pair of mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first of the pair of mutually exclusive mutations in the cell free nucleic acids isolated from the body fluid sample from the subject.

A method to monitor cell free DNA comprising:

• (i) obtaining a body fluid sample from a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer;
• (ii) isolating cell free nucleic acids from the body fluid sample obtained from the subject;
• (iii) measuring the amount of a housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the body fluid sample, wherein the amount of a housekeeping gene and/or total DNA in the sample correlates to the amount of Line and the amount of Line 1 is within a range of 3,000-700,000 pg/μL of body fluid;
• (iv) measuring the amount of the first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the body fluid sample;
• and
• (v) measuring the apparent amounts of the first of the pair of mutually exclusive mutations in control cell free nucleic acids isolated from body fluid samples obtained from a plurality of control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first of the pair of mutually exclusive mutations in the cell free nucleic acids isolated from the body fluid sample from the subject;
• and
• (vi) indicating a result in a report wherein:
• the amount measured in (iv) is greater than the highest amount measured in (v) and indicating in a report that the body fluid sample from the subject has the first of the pair of mutually exclusive mutations;
• or the amount measured in (iv) is less than the highest amount measured in (v) and indicating a report that the body fluid sample from the subject does not have the first of the pair of mutually exclusive mutations.