ArticleProceedings of the National Academy of Sciences of the United States of America2023
Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 37 citations in OpenAlex.
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- Clinician perspectives on the clinical utility of Belay Summit™ 2.0 cerebrospinal fluid test - A mixed methods study.The journal of liquid biopsy · 2026Article
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- Variant Allelic Frequency to Track Therapy Response and Evaluate Leptomeningeal Disease in Metastatic Central Nervous System Cancers.Diagnostics (Basel, Switzerland) · 2026Article
- Article
- Clinical utility impact of DNA-based cytology using droplet digital methylation-specific PCR in gastric cancer.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- The Clinical Utility of Cell-Free DNA in Brain Tumor Management: A Comprehensive Review.Journal of molecular neuroscience : MN · 2025Review
- Improved circulating tumor DNA profiling by simultaneous extraction of DNA methylation and copy number information from methylated DNA sequencing data.NPJ precision oncology · 2025Article
- Molecular Evidence of Multiorgan Damage in Patients with Immune-Related Adverse Events.The New England journal of medicine · 2025Article
- Methylation-specific qPCR for the EBV C promoter to quantify EBV methylation.Infectious agents and cancer · 2025Article
- Detection of Human Brain Cancers using Genomic and Immune Cell Characterization of Cerebrospinal Fluid through CSF-BAM.Cancer discovery · 2025Article
- De novo rates of aProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Next-Generation Sequencing of Intraoperatively Acquired Cerebrospinal Fluid and Matched Tumor Tissue in Patients Undergoing Surgical Resection for Glioblastoma.JCO precision oncology · 2025Article
- Demonstrating the clinical utility of genomic profiling using cerebrospinal fluid to inform management of central nervous system tumors - a meta analysis of the literature.The journal of liquid biopsy · 2025Review
- A DNA alteration and methylation co-detection method for clinical purpose.EMBO molecular medicine · 2025Article
- Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities.Molecular oncology · 2025Review
- Analytical Validation and Clinical Sensitivity of the Belay Summit Assay for the Detection of DNA Variants in Cerebrospinal Fluid of Primary and Metastatic Central Nervous System Cancer.The Journal of molecular diagnostics : JMD · 2025Article
- Analytical validation of the Belay Vantage™ assay for evaluation of MGMT promoter methylation using enzymatically converted tumorDNA from cerebrospinal fluid.Cancer genetics · 2025Article
- Methyl-CODEC enables simultaneous methylation and duplex sequencing.Nucleic acids research · 2025Article
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Authors and funding
21 authors at 4 institutions in 5 countries.
Funding
Abstract
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.