Hydroxymethylation analysis of cell-free nucleic acid samples for assigning tissue of origin, and related methods of use

Abstract

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.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority under 35 U.S.C. § 119(e)(1) to provisional U.S. Applications Ser. No. 62 / 688,975, filed Jun. 22, 2018, and Ser. No. 62 / 746,237, filed Oct. 16, 2018. The disclosures of the foregoing applications are incorporated by reference in their entireties.TECHNICAL FIELD[0002]The present invention relates generally to biotechnology, and more particularly relates to applications of the epigenetic analysis of cell-free DNA. The invention finds utility in the fields of genomics, medicine, diagnostics, and epigenetic research.BACKGROUND[0003]In many fields related to medicine, such as diagnostics, theranostics, and patient monitoring, there is an ongoing need for more precise methods of analyzing biological samples and extracting useful information from those analyses, with the often competing goals of accuracy and efficiency. Analytical methods should lend themselves to high speed processing and automation, yield the ne...

AI Technical Summary

Benefits of technology

The patent describes a method for detecting the tissue of origin of a nucleic acid in a human sample. This is important for forensic and medical applications. The method involves comparing the hydroxymethylation profile of the nucleic acid with a reference data set containing profiles of reference hydroxymethylation loci associated with tissue-specific genes. The method is efficient and selective, with high sensitivity and specificity. The invention is predicated on the use of 5-hydroxymethylation profiles to probabilistically assign a tissue of origin to a nucleic acid in a sample.

Problems solved by technology

However, analysis of cell-free DNA also presents unique challenges, particularly since cell-free DNA samples are very small and typically contain only a few nanograms of DNA per mL of plasma.

The problem is compounded when cell-free DNA is used in conjunction with epigenetic analyses, in which relatively rare DNA modifications, such as 5-methylcytosine and the even rarer 5-hydroxymethylcytosine, require detection.

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