ENRICHMENT OF MUTATED CELL FREE NUCLEIC ACIDS FOR CANCER DETECTION

1 - 40 . (canceled)

41 . A method for analyzing the genome of a cancer patient, comprising:

providing an endonuclease system that comprises a plurality of crRNAs, or derivatives thereof, and a plurality of Cas proteins, or variants thereof;

wherein each crRNA comprises a targeting sequence; and

wherein each Cas protein is capable of binding to a PAM site on a target nucleic acid;

contacting a patient sample, obtained from the cancer patient and comprising a plurality of target nucleic acids, with the endonuclease system to obtain a pool of target nucleic acid fragments associated with the patient sample,

wherein each target nucleic acid fragment of the pool of target nucleic acid fragments is a DNA fragment of cell-free DNA (cfDNA);

sequencing the pool of target nucleic acid fragments to obtain first sequencing data from the cancer patient; and

comparing the first sequencing data from the cancer patient with second sequencing data from a reference genome fragmented by the endonuclease system to detect structural rearrangements and mutations in the genome of the cancer patient.

42 . The method of claim 41 , wherein comparing the sequencing data comprises:

comparing a first fragmentation pattern of the pool of target nucleic acids fragments associated with the patient sample with a second fragmentation pattern of a pool of target nucleic acids fragments from the reference genome.

43 . The method of claim 42 , further comprising:

contacting a control sample, obtained from a control subject and comprising a plurality of target nucleic acids, with the endonuclease system to obtain the pool of target nucleic acid fragments from the reference genome and associated with the control sample; and

sequencing the pool of target nucleic acid fragments associated with the control sample to obtain the second sequencing data from the reference genome.

44 . The method of claim 43 , wherein the endonuclease system cleaves target nucleic acids in the control sample at a predetermined interval.

45 . The method of claim 44 , wherein the predetermined interval is about 300 bp.

46 . The method of claim 41 , wherein the plurality of Cas proteins comprises Cas9, or a variant thereof, a Cas9 ortholog, or a variant thereof, or Cpf1, or a variant thereof.

47 . The method of claim 46 , wherein the Cas9, or variant thereof, is derived from Streptococcus pyogenes, and wherein the Cpf1, or variant thereof, is derived from Francisell novicida U112.

48 . The method of claim 41 , wherein the patient sample comprises a blood sample, a serum sample, a plasma sample, a urine sample, or a cerebrospinal fluid sample.

49 . The method of claim 41 , wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a mutant allele sequence selected from a group consisting of: AKT1, BRAF, EGFR, KRAS, MAP2K1, NRAS, PI3KCA and PTEN.

50 . The method of claim 41 , wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a point mutation of at least one base pair.

51 . The method of claim 41 , wherein the cfDNA comprises circulating tumor DNA (ctDNA) that includes a mutation selected from a group consisting of: a single nucleotide mutation, an insertion, and a deletion.

52 . The method of claim 41 , wherein a target nucleic acid fragment of the pool of target nucleic acid fragments has either a blunt end or a staggered end.

53 . The method of claim 41 , wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a mutant allele sequence selected from a group consisting of: AKT1-E17K, BRAF-V600E, BRAF-L597V, BRAF-G469A, BRAF-G466V, EGFR-E709 T710delins, EGFR-G719S, EGFR-G719C, EGFR-G719A, EGFR-Exon19del, EGFR-T790M, EGFR-L858R, EGFR-L861Q, KRAS-Q61H, KRAS-Q61L, KRAS-Q61R, KRAS-Q61K, KRAS-G13A, KRAS-G13D, KRAS-G13C, KRAS-G13R, KRAS-G13D, KRAS-G13C, KRAS-G13R, KRAS-G13S, KRAS-G12V, KRAS-G12A, KRAS-G12D, KRAS-G12D, KRAS-G12C, KRAS-G12R, KRAS-G12S, MAP2K1-Q56P, NRAS-Q61H, NRAS-Q61L, NRAS-Q61R, NRAS-Q61K, NRAS-G12A, NRAS-G12D, NRAS-G12C, NRAS-G12R, NRAS-G12S, PI3KCA-E542K, PI3KCA-E545Q, PI3KCA-E545K, PI3KCA-H1047R, PI3KCA-H1047L, and PTEN-R233*.

54 . The method of claim 41 , wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a mutation identified in FIG. 7 .