Cell-free DNA hydroxymethylation profiles in the evaluation of pancreatic lesions

A method for monitoring the effectiveness of treatment in a patient with a pancreatic lesion identified on an imaging scan, the method comprising:

• (a) obtaining an initial cell-free DNA sample that comprises genes relevant to PDAC and its variants from a patient who is being treated for a pancreatic lesion;
• (b) enriching for hydroxymethylated DNA in the sample;
• (c) quantifying the hydroxymethylated DNA in the enriched initial sample that map to each of a plurality of selected loci in a reference hydroxymethylation profile, wherein the selected loci comprise hydroxymethylation biomarkers related to the presence, absence, or risk of pancreatic PDAC and its variants comprising ADARB2-AS1, ANKRD36B, ASAH2B, ATG4B, ATP8B1, BOLA1, C11orf88, C17orf97, C1orf170, C3orf36, C8orf74, CAMSAP2, CCDC54, CCDC59, CKAP2, CLK2P, CRTC1, CSRP2, CYB5D1, DNAJC27, DYNAP, FAM166A, FAM188B, FAM196A, FAM86JP, FAT4, FBXO5, FGF2, FUT2, GAS2L2, GAS6, GGACT, GLRX5, GPX1, GPX5, HBD, HLA-A, HTR1F, IL36G, KANSL1, KCNH6, KCTD15, KLHL38, KLK2, KRT6B, LAMC1, LGALS14, LGALS8-AS1, LIFR, LINC00266-1, LINC00310, LOC100130452, LOC100130557, LOC100130894, LOC100288778, LOC100505633, LOC100505648, LOC100505738, LOC100652909, LOC389033, LOC90784, LRRC37A2, MED11, MRPL23-AS1, NAT8L, NEUROD1, NEUROG2, NME5, NOMO3, NPRL2, NXN, ODF3L1, ODF3L2, OSCP1, PARD6G, PGAM1, PLA2G2E, PLSCR4, PPAP2A, PPP1R15A, PPP1R3E, RASL10B, REXO1L1, RIMBP3, RNF126P1, RNU6-76, RPP25, RPS27, SH3PXD2B, SHISA4, SLC25A38, SLC4A1, SLCO5A1, SPDEF, SRSF6, STRA6, SYNM, TBCB, TDRD6, TEX26, TMEM253, TNFSF13B, TTC14, TUBA4A, UBB, VAMP8, VGLL2, WASH2P, WNT9B, XBP1, and ZNF789;
• (d) comparing, at each selected locus, the hydroxymethylation level of the enriched cell-free DNA in the initial sample with the hydroxymethylation level in the reference profile, to ascertain differences in hydroxymethylation levels between the sample and the reference profile for each biomarker;
• (e) generating an initial hydroxymethylation profile for the patient comprising the hydroxymethylation level of the enriched cell-free DNA in the initial sample, at each selected locus;
• (f) repeating steps (a) through (c) at a later time with a subsequent cell-free DNA sample obtained from the patient;
• (g) generating a subsequent hydroxymethylation profile for the patient comprising the hydroxymethylation level of the enriched cell-free DNA in the subsequent sample, at each selected locus;
• (h) comparing, at each selected locus, the hydroxymethylation level of the enriched cell-free DNA in the subsequent hydroxymethylation profile to the hydroxymethylation level of the enriched cell-free DNA in the initial hydroxymethylation profile, to ascertain a change in the pancreatic lesion;
• and
• (i) identifying a change in the patient's hydroxymethylation profile that correlate with a progression toward cancer;
• and
• (j) commencing the adminstration of treatment for PDAC and its variants after a change has been identified in step (i).