Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules

Yuxuan Wang, Christopher Douville, Joshua D. Cohen, Austin Mattox, Sam Curtis, Natalie Silliman, Maria Popoli, Janine Ptak, Lisa Dobbyn, Nadine Nehme, Jonathan C. Dudley, Mahmoud Summers, Ming Zhang, Lan T. Ho-Pham, Bich N.H. Tran, Thach S. Tran, Tuan V. Nguyen, Chetan Bettegowda, Nickolas Papadopoulos, Kenneth W. KinzlerBert Vogelstein

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article numbere2220704120
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number15
StatePublished - Apr 11 2023


  • biomarker
  • cfDNA
  • copy number alteration
  • methylation
  • mutation

ASJC Scopus subject areas

  • General


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