Noninvasive diagnostics by sequencing 5-hydroxymethylated cell-free dna

Abstract

Provided herein is a method of sequencing hydroxymethyated cell-free DNA. In some embodiments, the method comprises adding an affinity tag to only hydroxymethyated DNA molecules in a sample of cfDNA, enriching for the DNA molecules that are tagged with the affinity tag; and sequencing the enriched DNA molecules.

What is claimed is: 
     
         1 . A method for identifying more highly expressed genes in a cell-free nucleic acid sample comprising cell-free DNA, wherein the method comprises:
 (a) determining hydroxymethylation profiles for the cell-free DNA in the sample;   (b) comparing the hydroxymethylation profiles to identify locations with 5hmC enrichment; and   (c) identifying the more highly expressed genes in the sample as those with gene bodies around which 5hmC is enriched.