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Docket #: S23-034

Improved cfDNA methylation profiling through correction of misrepaired jagged-ends

Stanford researchers have developed an in silico method, JEEPERS, that corrects DNA methylation errors at jagged-ends, improving cfDNA methylation profiling for early cancer detection and tissue-of-origin classification.

Cell free DNA (cfDNA) methylation profiling allows early cancer detection and tissue-of-origin classification. However, end repair process during library preparation for cfDNA sequencing may introduce changes in methylation patterns. To address this issue, Stanford researchers have developed JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences), a novel in silico method for correcting errors in methylation data resulting from the end repair process in double-stranded library preparation. It detects and corrects errors at jagged-ends (JEs) in silico, leveraging support from complementary strands and sibling reads.

Stage of Development
Proof of Concept


  • Early cancer detection


  • Superior cfDNA genotyping
  • Identification of allele-specific methylation, hemi-methylation, and gene expression
  • Compatible with other methylation datasets
  • Low cost

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