DETECTION OF LUNG NEOPLASIA BY ANALYSIS OF METHYLATED DNA

• US 20190330702A1
• Filed: 07/02/2019
• Published: 10/31/2019
• Est. Priority Date: 05/05/2016
• Status: Active Grant

• Current Assignee: Exact Sciences Corporation
• Original Assignee: Exact Sciences Development Company LLC (Exact Sciences Corporation), Mayo Foundation For Medical Education And Research (Mayo Clinic)
• Inventors: Allawi, Hatim, Lidgard, Graham P., Giakoumopoulos, Maria, Ahlquist, David A., Taylor, William R., Mahoney, Douglas
• Granted Patent: US 11,028,447 B2
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.

Claims

1. A method of processing a sample, the method comprising:

a) assaying a sample from a subject for an amount of at least one methylation marker selected from the group consisting of BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNF132, MAX chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, EMX1, HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12A8, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, S1PR4, SKI, SUCLG2, TBX15, ZDHHC1 and ZNF329;

b) assaying said sample for an amount of a reference marker;

c) comparing the amount of said at least one methylation marker to the amount of reference marker in said sample to determine a methylation state for said at least one methylation marker in said sample; and

optionally

d) generating a record reporting the methylation state for said at least one methylation marker in said sample.

2. The method of claim 1, wherein said assaying comprises obtaining a sample comprising DNA from a subject and treating DNA obtained from the sample with a reagent that selectively modifies unmethylated cytosine residues in the obtained DNA to produce modified residues.

3. The method of claim 1 or claim 2, wherein said at least one methylation marker comprises a methylation marker selected from the group consisting of SLC12A8, KLHDC7B, PARP15, OPLAH, BCL2L11, MAX.chr12.526, HOXB2, EMX1, CYP26C1, SOBP, SUCLG2, SHOX2, ZDHHC1, NFIX, FLJ45983, HOXA9, B3GALT6, ZNF781, SP9, BARX1, and SKI.

4. The method of any one claims 1 to 3, wherein said at least one methylation marker comprises at least two of said methylation markers, preferably 2 to 21 markers, preferably 2 to 8 markers, preferably 4 to 6 markers.

5. The method of claim any one of claims 1 to 4, wherein said at least one methylation marker comprises a group of methylation markers selected from:

the group consisting of ZNF781, BARX1, and EMX1;

the group consisting of SHOX2, SOBP, ZNF781, CYP26C1, SUCLG2, and SKI;

the group consisting of SLC12A8, KLHDC7B, PARP15, OPLAH, BCL2L11, MAX.chr12.526, HOXB2, and EMX1;

the group consisting of SHOX2, SOBP, ZNF781, BTACT, CYP26C1, and DLX4; and

the group consisting of SHOX2, SOBP, ZNF781, CYP26C1, SUCLG2, and SKI.

6. The method of claim 5, wherein said at least one methylation marker comprises the group consisting of ZNF781, BARX1, and MIXT, and further comprises SOBP and/or HOXA9.

7. The method of claim 2, wherein said reagent comprises a bisulfite reagent.

8. The method of any one of claims 1 to 7, wherein assaying the methylation state of the methylation marker in the sample comprises determining the methylation state of one base.

9. The method of any one of claims 1 to 7, wherein assaying the methylation state of a methylation marker in the sample comprises determining the extent of methylation at a plurality of bases.

10. The method of any one of claims 1 to 9, wherein the methylation state of the methylation marker comprises increased or decreased methylation of the methylation marker relative to a methylation state of the same methylation marker in one or more normal samples, and/or wherein the methylation state of the methylation marker comprises a different pattern of methylation relative to a pattern of methylation of the same methylation marker in one or more normal samples.

11. The method of any one of claims 1 to 10, wherein said reference marker is a methylated reference marker.

12. The method of any one of claims 1 to 11, wherein the sample is a tissue sample, a blood sample, a serum sample, or a sputum sample.

13. The method of claim 12, wherein said tissue sample comprises lung tissue.

14. The method of any one of claims 1 to 12, wherein said sample is a plasma sample.

15. The method of any one of claims 1 to 12, wherein said sample is DNA isolated from plasma.

16. The method of any one of claims 1 to 15, wherein said subject has or is suspected of having a lung neoplasm.

19. The method of any one of claims 1 to 18, wherein the assaying comprises using polymerase chain reaction, nucleic acid sequencing, mass spectrometry, methylation specific nuclease, mass-based separation, or target capture.

20. The method of claim 19, wherein the assaying comprises using a flap endonuclease assay.

21. The method of any one of claims 1 to 20, wherein the assaying comprises bisulfite converting said marker DNA and said reference nucleic acid.

22. The method of claim 21, wherein determining the methylation level of one or more methylation markers is achieved by a technique selected from the group consisting of methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, flap endonuclease assay, and bisulfite genomic sequencing PCR.

17. A method of analyzing a plasma sample obtained from a subject suspected of having a lung neoplasm, the method comprising:

a) combining the plasma sample with;

i) protease; and

ii) a first lysis reagent, said first lysis reagent comprising

guanidine thiocyanate; and

non-ionic detergent;

to form a mixture wherein proteins are digested by said protease;

b) to the mixture of step a) adding

iii) silica particles, and

iv) a second lysis reagent, said second lysis reagent comprising;

guanidine thiocyanate;

non-ionic detergent; and

isopropyl alcohol;

under conditions wherein DNA is bound to said silica particles;

c) separating silica particles with bound DNA from the mixture of b);

d) to the separated silica particles with bound DNA adding a first wash solution, said first wash solution comprising A) guanidine hydrochloride or guanidine thiocyanate, and B) ethyl alcohol;

e) separating the silica particles with bound DNA from said first wash solution;

f) to the separated silica particles with bound DNA adding a second wash solution, said second wash solution comprising a buffer and ethyl alcohol;

g) separating washed silica particles with bound DNA from said second wash solution; and

h) eluting DNA from the washed silica particles with bound DNA separated in step g);

i) assaying eluted DNA for an amount of at least one methylated methylation marker and for an amount of reference marker in said eluted DNA;

j) comparing the amount of said at least one methylated methylation marker to the amount of reference marker in said DNA to determine a methylation state for said at least one methylation marker in said plasma sample; and

optionally

d) generating a record reporting the methylation state for said at least one methylation marker in said plasma sample.

18. The method of claim 17, wherein said at least one methylation marker is selected from the group consisting of BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNF132, MAX chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, EMX1, HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12A8, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, S1PR4, SKI, SUCLG2, TBX15, ZDHHC, and ZNF329.

23. The method of any one of claims 17 to 22, wherein said assaying comprises analyzing multiple DNA methylation markers using a PCR pre-amplification and a PCR-flap assay by a process comprising:

a) providing bisulfite-treated DNA comprising a plurality of different DNA methylation marker target regions in a first reaction mixture comprising PCR amplification reagents, wherein said PCR amplification reagents comprise;

i) a plurality of different primer pairs for amplifying said plurality of different target regions, if present in said sample, from said bisulfite-treated DNA;

ii) thermostable DNA polymerase;

iii) dNTPs; and

iv) a buffer comprising Mg⁺⁺

b) exposing said first reaction mixture to thermal cycling conditions wherein a plurality of different DNA methylation marker target regions, if present in the sample, are amplified to produce a pre-amplified mixture, and wherein said thermal cycling conditions are limited to a number of thermal cycles that maintain amplification in an exponential range, preferably fewer than 20, more preferably fewer than 15, more preferably 10 or fewer thermal cycles;

c) partitioning said pre-amplified mixture into a plurality of PCR-flap assay reaction mixtures, wherein each PCR-flap assay reaction mixture comprises;

i) an additional amount of a primer pair selected from said plurality of different primer pairs of step a) i);

ii) thermostable DNA polymerase;

iii) dNTPs;

iv) said buffer comprising Mg⁺⁺

v) a flap endonuclease;

vi) a flap oligonucleotide, and

vi) a hairpin oligonucleotide comprising a region that is complimentary to a portion of said flap oligonucleotide;

and

d) detecting amplification of one or more different DNA methylation marker target regions from said bisulfate-treated DNA during PCR-flap assay reactions.

24. The method of claim 23, wherein said bisulfate-treated DNA is prepared from a plasma sample of at least one mL, preferably at least 5 mL, more preferably at least 10 mL, and wherein the volume of said bisulfate-treated DNA comprising a plurality of different DNA methylation marker target regions in the amplification reaction of step b is at least 20 to 50% of the total volume of the amplification reaction.

25. A kit, comprising:

a) at least one oligonucleotide, wherein at least a portion of said oligonucleotide specifically hybridizes to a methylation marker selected from the group consisting of BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNF132, MAX_chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, EMX1, HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12A8, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, S1PR4, SKI, SUCLG2, TBX15, ZDHHC1, and ZNF329, and

b) at least one additional oligonucleotide, wherein at least a portion of said additional oligonucleotide specifically hybridizes to a reference nucleic acid.

26. The kit of claim 25, wherein said portion of said oligonucleotide specifically hybridizes to a bisulfate-treated DNA comprising said methylation marker.

27. The kit of claim 25 or claim 26, wherein said kit comprises at least two additional oligonucleotides.

28. The kit of claim 25 or claim 26, wherein said kit further comprises bisulfate.

29. The kit of any one of claims 25 to 28, wherein at least a portion of said oligonucleotide specifically hybridizes to a methylation marker selected from the group consisting of SLC12A8, KLHDC7B, PARP15, OPLAH, BCL2L11, MAX.chr12.526, HOXB2, EMX1, CYP26C1, SOBP, SUCLG2, SHOX2, ZDHHC1, NFIX, FLJ45983, HOXA9, B3GALT6, ZNF781, SP9, BARX1, and SKI.

30. The kit of any one of claims 25 to 29, wherein said at least one methylation marker comprises at least two of said methylation markers, preferably 2 to 21 markers, preferably 2 to 8 markers, preferably 4 to 6 markers.

31. The kit of any one of claims 25 to 30, wherein said at one methylation markers comprises a group of methylation markers selected from:

the group consisting of ZNF781, BARX1, and EMX1;

group consisting of SHOX2, SOBP, ZNF781, CYP26C1, SUCLG2, and SKI;

the group consisting of SLC12A8, KLHDC7B, PARP15, OPLAH, BCL2L11, MAX.chr12.526, HOXB2, and EMX1;

the group consisting of SHOX2, SOBP, ZNF781, BTACT, CYP26C1, and DLX4; and

the group consisting of SHOX2, SOBP, ZNF781, CYP26C1, SUCLG2, and SKI.

32. The kit of claim 31, wherein said at least one methylation marker comprises the group consisting of ZNF781, BARX1, and EMX1, and further comprises SOBP and/or HOXA9.

33. The kit of any one of claims 25 to 32, wherein said oligonucleotide is selected from one or more of a capture oligonucleotide, a pair of nucleic acid primers, a nucleic acid probe, and an invasive oligonucleotide.

34. The kit of any one of claims 25 to 33, wherein said kit further comprises a solid support.

35. The kit of claim 34, wherein said solid support is a magnetic bead.

36. The kit of claim 35, wherein said solid support comprises one or more capture reagents.

37. The kit of claim 36, wherein said capture reagents are oligonucleotides complementary said one or more methylation markers.

38. A composition comprising a reaction mixture comprising a complex of a target nucleic acid selected from the group consisting of BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNF132, MAX_chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, MIXT HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12a, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, S1PR4, SKI, SUCLG2, TBX15, ZDHHC1, and ZNF329, and an oligonucleotide that specifically hybridizes to said target nucleic acid.

39. The composition of claim 38, wherein said target nucleic acid is bisulfite-converted target nucleic acid.

40. The composition of claim 38 or claim 39, wherein said reaction mixture comprises a complex of a target nucleic acid selected from the group consisting of SLC12A8, KLHDC7B, PARP15, OPLAH, BCL2L11, MAX.chr12.526, HOXB2, EMX1, CYP26C1, SOBP, SUCLG2, SHOX2, ZDHHC1, NFIX, FLJ45983, HOXA9, B3GALT6, ZNF781, SP9, BARX1, and SKI, and an oligonucleotide that specifically hybridizes to said target nucleic acid.

41. The composition of any one of claims 38 to 40, wherein said oligonucleotide is selected from one or more of a capture oligonucleotide, a pair of nucleic acid primers, a hybridization probe, a hydrolysis probe, a flap assay probe, and an invasive oligonucleotide.

42. The composition of any one of claim 38, 40 or 41, wherein said target nucleic acid comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOS:

1, 6, 11, 16, 21, 28, 33, 38, 43, 48, 53, 58, 63, 68, 73, 78, 86, 91, 96, 101, 106, 111, 116, 121, 126, 131, 136, 141, 146, 151, 156, 161, 166, 171, 176, 181, 186, 191, 196, 201, 214, 219, 224, 229, 234, 239, 247, 252, 257, 262, 267, 272, 277, 282, 287, 292, 298, 303, 308, 313, 319, 327, 336, 341, 346, 351, 356, 361, 366, 371, 384, and 403.

43. The composition of any one of claim 39, 40 or 41, wherein said bisulfate-converted target nucleic acid comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOS:

2, 7, 12, 17, 22, 29, 34, 39, 44, 49, 54, 59, 64, 69, 74, 79, 87, 92, 97, 102, 107, 112, 117, 122, 127, 132, 137, 142, 147, 152, 157, 162, 167, 172, 177, 182, 187, 192, 197, 202, 210, 215, 220, 225, 230, 235, 240, 248, 253, 258, 263, 268, 273, 278, 283, 288, 293, 299, 304, 309, 314, 320, 328, 337, 342, 347, 352, 357, 362, 367, 372, 385, and 404.

44. The composition of any one of claims 38 to 43, wherein said oligonucleotide comprises a reporter molecule.

45. The composition of claim 44, where said reporter molecule comprises a fluorophore.

46. The composition of claim any one of claims 38 to 45, wherein said oligonucleotide comprises a flap sequence.

47. The composition of any one of claims 38 to 46, further comprising one or more of a FRET cassette;

a FEN-1 endonuclease and a thermostable DNA polymerase.