HYDROXYMETHYLATION ANALYSIS OF CELL-FREE NUCLEIC ACID SAMPLES FOR ASSIGNING TISSUE OF ORIGIN, AND RELATED METHODS OF USE
A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.
1 . A method for probabilistically assigning a tissue of origin to a nucleic acid in a cell-free fluid sample obtained from a human subject, comprising:
(a) generating a hydroxymethylation profile of the nucleic acid;
(b) comparing the hydroxymethylation profile of the nucleic acid with each of a plurality of reference hydroxymethylation profiles in a reference data set, each reference hydroxymethylation profile corresponding to a reference locus contained within a genomic region associated with a tissue-specific gene;
(c) identifying at least one reference locus having a reference hydroxymethylation profile that is substantially similar to the detected hydroxymethylation profile in (a); and
(d) assigning at least one tissue of origin to the nucleic acid based on the at least one reference locus identified in (c) and the corresponding tissue-specific gene.