Sampling device and analysis of methylated dna

A method of obtaining a cell sample from a subject, comprising:

• a) orally administering an abrasive sponge housed within a dissolvable capsule of a ingestible cell sampling device of to the subject, wherein the ingestible cell sampling device comprises:
• i) an abrasive sponge housed within a dissolvable capsule, the dissolvable capsule comprising an exterior surface exposed to an external environment, wherein the abrasive sponge is retained in a compressed state by the dissolvable capsule.;
• ii) a molded cap comprising a cap interior surface and a cap exterior surface;
• and
• iii) a string having a first end attached to the molded cap, wherein the string passes through a portion of the abrasive sponge, and
• b) withdrawing from the subject the abrasive sponge, wherein the abrasive sponge collects a cell sample from the subject during the withdrawing.

A method of characterizing an esophageal cell sample from a subject, comprising:

• a) preparing DNA from the esophageal cell sample from the subject;
• b) treating the DNA with bisulfite to produce bisulfite-treated DNA;
• and
• c) amplifying the bisulfite-treated DNA to determine an amount of at least one methylated biomarker gene selected from the group of methylation biomarker genes consisting of ANKRD13B, BMP3, CD1D, CDKN2A , CHST2, CNNM1, DIO3, DOCK2, DTX1, ELMO1, FER1L4, FERMT3, FLI1, GRIN2D, HUNK, JAM3, LRRC4, NDRG4, OPLAH, PDGFD, PKIA, PPP2R5C, QKI, SEP9, SFMBT2, SLC12A8, TBX15, TSPYL5, VAV3, ZNF304, ZNF568, ZNF671, and ZNF682;
• d) assaying the bisulfite-treated DNA from the esophageal cell sample for an amount of a reference DNA;
• and
• e) comparing the amount of the at least one methylated biomarker gene to the amount of the reference DNA to determine a methylation state for the at least one methylation biomarker gene in the esophageal cell sample.