Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients

Study ID Alternative Stable ID Type
EGAS00001006198 Other

Study Description

Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive ... (Show More)

Study Datasets 2 datasets.

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Dataset ID Description Technology Samples
Heatrich-BS was performed on 14 patients monitored across 5-8 timepoints each. The predicted tumor fraction trend was compared with CEA values and tumor measurements from CT scans.
Illumina MiSeq,Illumina NovaSeq 6000 79
Heatrich-BS was performed on 5 healthy volunteers and 15 CRC patient cell-free DNA. The Heatrich-BS predicted tumor fractions were compared with tumor burden values obtained by genomic methods such as targeted amplicon sequencing and low pass sequencing.
Illumina HiSeq 2000,Illumina MiSeq 20

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