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Nucleic Acids Res. 2015 Dec 15;43(22):e154. doi: 10.1093/nar/gkv795. Epub 2015 Aug 24.

DREAMing: a simple and ultrasensitive method for assessing intratumor epigenetic heterogeneity directly from liquid biopsies.

Author information

1
Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA.
2
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
3
Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.
4
Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
5
Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA hermanj3@upmc.edu.
6
Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA thwang@jhu.edu.

Abstract

Many cancers comprise heterogeneous populations of cells at primary and metastatic sites throughout the body. The presence or emergence of distinct subclones with drug-resistant genetic and epigenetic phenotypes within these populations can greatly complicate therapeutic intervention. Liquid biopsies of peripheral blood from cancer patients have been suggested as an ideal means of sampling intratumor genetic and epigenetic heterogeneity for diagnostics, monitoring and therapeutic guidance. However, current molecular diagnostic and sequencing methods are not well suited to the routine assessment of epigenetic heterogeneity in difficult samples such as liquid biopsies that contain intrinsically low fractional concentrations of circulating tumor DNA (ctDNA) and rare epigenetic subclonal populations. Here we report an alternative approach, deemed DREAMing (Discrimination of Rare EpiAlleles by Melt), which uses semi-limiting dilution and precise melt curve analysis to distinguish and enumerate individual copies of epiallelic species at single-CpG-site resolution in fractions as low as 0.005%, providing facile and inexpensive ultrasensitive assessment of locus-specific epigenetic heterogeneity directly from liquid biopsies. The technique is demonstrated here for the evaluation of epigenetic heterogeneity at p14(ARF) and BRCA1 gene-promoter loci in liquid biopsies obtained from patients in association with non-small cell lung cancer (NSCLC) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN), respectively.

PMID:
26304549
PMCID:
PMC4678844
DOI:
10.1093/nar/gkv795
[Indexed for MEDLINE]
Free PMC Article

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