Personalized tumor biomarkers

A method of assessing or detecting tumor in a patient, comprising:

• amplifying a DNA fragment using a template from the patient's tissues or body fluids and primers that span a patient-specific, tumor-specific rearrangement breakpoint, wherein the rearrangement breakpoint is between genes or gene loci involved in rearrangements in <1% of tumors of patients with the same type of tumor;
• determining the amount or proportion of amplified DNA fragment in the patient's tissue or body fluid.

A method of identifying a personalized tumor marker for a cancer patient, comprising:

• determining sequence of two ends of each of a plurality of fragments of DNA from the cancer patient;
• determining regions of copy number differences among regions in the tumor DNA of the patient;
• identifying fragments of the plurality of fragments which map within a region of copy number difference or spanning a boundary of copy number difference as potential markers of a tumor-specific DNA rearrangement in the cancer patient.

A method of identifying a personalized tumor marker for a cancer patient, comprising:

• testing a plurality of mate paired tags of a library of mate paired tags by comparing to non-tumor DNA or to sequence of non-tumor DNA, wherein each of said mate paired tags comprises two genomic tags that are co-linear but not contiguous in a segment of tumor DNA of the cancer patient;
• and
• identifying a tumor-specific DNA rearrangement if the two genomic tags of a mate paired tag are at different locations or in a different orientation within a chromosome or on different chromosomes of non-tumor DNA compared to tumor DNA.

A method of identifying a personalized tumor marker for a cancer patient, comprising:

• testing two ends of a plurality of fragments of tumor DNA of the cancer patient by comparing to non-tumor DNA or to sequence of non-tumor DNA;
• and
• identifying a tumor-specific DNA rearrangement if the ends of a fragment are at different locations or in a different orientation within a chromosome or on different chromosomes of non-tumor DNA compared to tumor DNA.

A method of screening for a cancer in a human, comprising:

• testing a plurality of mate paired tags of a library of mate paired tags by comparing to normal DNA or to sequence of normal DNA, wherein each of said mate paired tags comprises two genomic tags that are co-linear but not contiguous in a segment of DNA in the blood of the human;
• and
• identifying DNA rearrangement if the two genomic tags of a mate paired tag are at different locations or in a different orientation within a chromosome or on different chromosomes of normal DNA compared to blood DNA, wherein the presence of a DNA rearrangement suggests the presence of a cancer in the human.

A method of screening for a cancer in a human, comprising:

• testing two ends of a fragment of blood DNA of the human by comparing to normal DNA or to sequence of normal DNA;
• and
• identifying a DNA rearrangement if the ends are at different locations or in a different orientation within a chromosome or on different chromosomes of normal DNA compared to blood DNA, wherein the presence of a DNA rearrangement suggests the presence of a cancer in the human.

A kit for monitoring presence or amount of a breakpoint in a somatic DNA rearrangement in tumor DNA of a patient, comprising:

• one or more pairs of amplification primers, wherein each pair is complementary to priming sites on opposite sides of a breakpoint, wherein the priming sites are separated by less than 200 basepairs in the tumor DNA, and wherein the DNA rearrangement occurs in <1% of tumors of patients with the same type of tumor.