Methods of preparing a DNA fraction enriched with circulating tumor DNA

A method for preparing a deoxyribonucleic acid (DNA) fraction enriched with circulating tumor DNA (ctDNA) from a cancer patient, comprising:

• (a) obtaining a fluid sample taken from the cancer patient while the cancer patient is in remission, wherein the fluid sample comprises blood plasma or blood serum;
• (b) extracting cell-free DNA (cfDNA) from the fluid sample;
• (c) enriching a fraction of ctDNA by contacting the cfDNA with a plurality of oligonucleotides, wherein the plurality of oligonucleotides comprises at least 10 distinct oligonucleotides and each of the at least 10 distinct oligonucleotides comprises a nucleic acid sequence that is capable of hybridizing to a DNA fragment comprising a corresponding tumor-specific somatic mutation sequence selected from a predetermined set of tumor-specific somatic mutation sequences, wherein the predetermined set of tumor-specific somatic mutation sequences is was prepared by:
• (i) obtaining a tumor sample and a non-tumor sample from the cancer patient;
• (ii) sequencing genomic DNA from the tumor sample and sequencing genomic DNA from the non-tumor sample, thereby obtaining sequences of genomic DNA from the tumor sample and sequences of genomic DNA from the non-tumor sample;
• (iii) aligning the sequences of genomic DNA from the tumor sample to a reference human genome that is not from the patient thereby obtaining a set of tumor-specific mutations and further obtaining from the set of tumor-specific mutations a set of tumor-specific somatic mutation sequences that are present in the sequences of genomic DNA from the tumor sample but not present in the sequences of genomic DNA from the non-tumor sample.

A method for preparing a deoxyribonucleic acid (DNA) fraction enriched with circulating tumor DNA (ctDNA) from a cancer patient, comprising:

• (a) obtaining a fluid sample taken from the cancer patient at a time coinciding with or prior to surgery;
• following, during, or prior to administration of chemotherapy;
• or following, during, or prior to radiation therapy;
• wherein the fluid sample comprises blood plasma or blood serum;
• (b) extracting cell-free DNA (cfDNA) from the fluid sample;
• (c) enriching a fraction of ctDNA by contacting the cfDNA with a plurality of oligonucleotides, wherein the plurality of oligonucleotides comprises at least 10 distinct oligonucleotides and each of the at least 10 distinct oligonucleotides comprises a nucleic acid sequence that is capable of hybridizing to a DNA fragment comprising a corresponding tumor-specific somatic mutation sequence selected from a predetermined set of tumor-specific somatic mutation sequences, wherein the predetermined set of tumor-specific somatic mutation sequences is was prepared by:
• (i) obtaining a tumor sample and a non-tumor sample from the cancer patient;
• (ii) sequencing genomic DNA from the tumor sample and sequencing genomic DNA from the non-tumor sample, thereby obtaining sequences of genomic DNA from the tumor sample and sequences of genomic DNA from the non-tumor sample;
• (iii) aligning the sequences of genomic DNA from the tumor sample to a reference human genome that is not from the patient thereby obtaining a set of tumor-specific mutations and further obtaining from the set of tumor-specific mutations a set of tumor-specific somatic mutation sequences that are present in the sequences of genomic DNA from the tumor sample but not present in the sequences of genomic DNA from the non-tumor sample.