Disclosed are method for predicting naltrexone response in subjects with AUD. In some embodiments, the methods include performing or having performed one or more methylation assays on a genomic DNA sample isolated from the subject to determine the methylation status of one or more regions of the isolated genomic DNA, wherein the one or more regions are subsequences of a gene selected from a mu opioid receptor (OPRM1) gene, a catechol-O-methyltransferase (COMT) gene, and a dopamine transporter (SLC6A3) gene, wherein the methylation status of the one or more regions of the isolated genomic DNA determined is predictive of naltrexone response in the subject. Also provided are method for treating patients diagnosed with AUD with the medication naltrexone based on a methylation status of a combination of specific methylation sites located associated with an OPRM1 gene, a COMT gene, and/or an SLC6A3 gene in obtained from each AUD patient.

The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.

The present invention provides methods of detecting, screening, monitoring, staging, classification, selecting treatment for, ascertaining whether treatment is working in, and/or prognostication of prostate cancer comprising determining the average methylation ratio at 10 or more genomic regions as set out in the application, and associated methods of selecting a treatment or ascertaining whether a treatment is effective. The present invention also provides a method for determining a solid cancer circulating free DNA (cfDNA) methylome signature for use in the detecting, screening, monitoring, staging, classification, selecting treatment for, ascertaining whether treatment is working in, and/or prognostication of the solid cancer in a sample obtained from a subject comprising determining the average methylation ratio at 10 or more genomic regions as set out in the application.

Temporal variations in one or more characteristics measured from a cell-free DNA sample are used to estimate a gestational age of a fetus. Example characteristics include the methylation level measured from the cell-free DNA sample, size of DNA fragments measured from the cell-free DNA sample (e.g., proportion of fetal-derived DNA fragments longer than a specified size), and ending patterns of the DNA fragments align to a reference genome.

The invention is directed to a method for the early detection of gastric cancer, by detecting the increase in DNA methylation of the promoter region of the microRNA-335-5p in samples obtained non-invasively, preferably in plasma. Thus, it is a contribution for the early detection of gastric cancer, without invasive procedures, with rapid collection of the sample and of the delivery of the results, and of lower cost than the technologies that employ invasive diagnostic techniques to the human and animal body in general.

The present invention relates to a method to determine bisulfite conversion of unmethylated cytosine to uracil in genomic DNA, comprising the steps of providing a first set of amplification primers for amplifying bisulfite converted copies of a repetitive DNA element by qPCR and a second set of amplification primers for amplifying unconverted copies of said repetitive DNA element by qPCR, performing a multiplex qPCR with said first and second set of amplification primers to generate amplicons, and determining the bisulfite conversion efficiency by comparing the amounts of said first and second amplicon.

The current disclosure provides, inter alia, method of determining benign nodules from thyroid cancer in a subject that is found to have a thyroid nodule, method of treating thyroid cancer in a subject detected to have thyroid cancer by the method of the current disclosure, compositions for determining benign nodules from thyroid cancer in a subject, and kits including reagents and composition for determining benign nodules from thyroid cancer in a subject.

Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.

A computer-implemented method of establishing an epigenetic clock for an avian species including: (a) identifying and determining methylation levels of specific CpG sites within a genomic DNA obtained from a plurality of different biological sample materials deriving from the avian species and representing specific time points within a chronological lifespan of the avian species, (b) excluding all CpG sites associated with single nucleotide polymorphisms (SNPs) from the CpG sites identified in (a), (c) excluding all CpG sites located on sex chromosomes from the CpG sites obtained in (b), (d) performing a tissue-specific normalization for the CpG sites obtained in (c), and (e) correlating the CpG methylation levels of the CpG sites obtained in (d) with chronological age with a penalized regression model.

Provided herein are epigenetic modifications that are associated with prior exposure to chemotherapy agents. In particular, differential DNA methylation regions (DMRs) that are characteristic of, and can thus be used to identify and/or treat, a male subject who has undergone chemotherapy are provided. The DMRs are used to screen for pregnancy complications, infertility, and passage of heritable mutations to an infant.